Multimetal Tolerance Mechanisms in Bacteria the Resistance Strategies

Aquatic Toxicology 212 (2019) 1–10

Contents lists available at ScienceDirect

Aquatic Toxicology

journal homepage: www.elsevier.com/locate/aqtox

Multimetal tolerance mechanisms in bacteria: The resistance strategies acquired by bacteria that can be exploited to ‘clean-up’ heavy metal T contaminants from water ⁎ ⁎ Manisha Nandaa, , Vinod Kumarb, , D.K. Sharmac a Department of Biotechnology, Dolphin (PG) Institute of Biomedical and Natural Sciences, Dehradun, 248007, India b Department of Chemistry, Uttaranchal University, Dehradun, 248007, India c Department of Zoology and Biotechnology, H.N.B. Garhwal Central University, SRT Campus, Badshahi Thaul, Tehri, Uttarakhand, India

ARTICLE INFO ABSTRACT

Keywords: Heavy metal pollution is one of the major environmental concerns worldwide. Toxic heavy metals when un- Effluent treated get accumulated in environment and can pose severe threats to living organisms. It is well known that Heavy metal metals play a major role either directly or indirectly in different metabolic processes of bacteria. This allows Pollution bacterial cells to grow even in the presence of some toxic heavy metals. Microbial biotechnology has thus Bacteria emerged as an effective and eco friendly solution in recent years for bioremediation of heavy metals. Therefore, Mechanism this review is focused on summarising bacterial adaptation mechanisms for various heavy metals. It also shares some applications of have metal tolerant bacteria in bioremediation. Bacteria have evolved a number of processes for heavy metal tolerance viz., transportation across cell membrane, accumulation on cell wall, intra as well as extracellular entrapment, formation of complexes and redox reactions which form the basis of different bioremediation strategies. The genetic determinants for most of these resistances are located on plasmids however some may be chromosomal as well. Bacterial cells can uptake heavy by both ATP dependent and ATP independent processes. Bacterial cell wall also plays a very important role in accumulating heavy metals by bacterial cells. Gram-positive bacteria accumulate much higher concentrations of heavy metals on their cell walls than that of metals gram -ve bacteria. The role of bacterial metallothioneins (MTs) in heavy metal has also been reported. Thus, heavy metal tolerant bacteria are important for bioremediation of heavy metal pollutants from areas containing high concentrations of particular heavy metals.

1. Introduction bioremediation as a potential alternative for environmental restoration. It involves the use of bacteria, fungi, plants, algae etc. to reduce, de- The discharge of industrial effluent containing toxic heavy metals grade/detoxify different environmental pollutants (Dua et al., 2002). (e.g. Cd, As, Hg) and their simultaneous accumulation in the environ- Bacteria being ubiquitous in nature are involved in almost all bio- ment can be a severe threat to life of plants, animals as well as humans logical processes of life. It is well known that metals play a major role (Zhang et al., 2014; Nouha et al., 2016; Cao et al., 2019; Dumont et al., either directly or indirectly in different metabolic processes of bacteria. 2019; Sandhu et al., 2019). Heavy metals with no cellular (Cd, As) roles This allows bacterial cells to grow even in the presence of some toxic are toxic in nature (Shi et al., 2002; Pan et al., 2018; Shen et al., 2019) heavy metals. However, higher concentrations of heavy metals are toxic while others (Co, Zn, Ni) may be essential at low (nM) concentrations to microorganisms as it results conformational alterations in nucleic (Badar et al., 2000). These may also become toxic at μM or mM c on- acids as well as polypeptides. They also disturb oxidative phosphor- centrations (Nies, 1992). Thus, it is necessary to control the increasing ylation and osmotic balance (Poole and Gadd, 1989). concentrations of these heavy metal contaminants in the environment. Heavy metal tolerant bacterial species can be employed for the The traditional different types of chemical and biological methods are bioremediation of heavy metal. Microbial biotechnology has thus used in treating the heavy metals in industrial effluent and soils emerged as an effective and eco friendly solution in recent years for (Ahluwalia and Goyal, 2007; Kuan et al., 2009; Mouedhen et al., 2009). bioremediation of heavy metals. The site from where a particular bac- The advancements in environmental biotechnology have focused terial species has been isolated can very well help us predict the

⁎ Corresponding authors. E-mail addresses: [email protected] (M. Nanda), [email protected] (V. Kumar). https://doi.org/10.1016/j.aquatox.2019.04.011 Received 15 January 2019; Received in revised form 10 April 2019; Accepted 15 April 2019 Available online 16 April 2019 0166-445X/ © 2019 Elsevier B.V. All rights reserved. M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10 behavior of those bacteria. Thus, bacteria isolated from heavy metal et al., 2007). contaminated sites pose to be the most suitable candidates for heavy Apart from the bacterial cell wall extracellular polysaccharides have metal bioremediation (Malik, 2004). Unlike other environmental pol- also been reported to accumulate heavy metals but it varies from one lutants heavy metals cannot be biologically degraded in order to reduce bacterial species to the other (Yee and Fein, 2001). Several bacterial their toxic behaviour. They can only be transformed by bacteria to a species have been reported to bioaccumulate metal cations extra- lesser toxic form or oxidation state which makes it less bioavailable cellularly e.g., Klebsiella aerogenes, Pseudomonas putida, and Arthrobacter (Knox et al., 2000; Garbisu et al., 2017). viscosus (Ayangbenro and Babalola, 2017; Ilyas et al., 2017). Bacteria have evolved a number of processes for heavy metal tolerance viz., transportation across cell membrane, accumulation on cell 4. Bacterial resistance mechanisms to different heavy metals wall, intra as well as extracellular entrapment, formation of complexes and redox reactions which form the basis of different bioremediation Bacteria can grow almost everywhere on earth. The discharge of strategies (Veglio et al.,1997; Ahemad, 2012). The genetic determinants heavy metals into different microbial habitats has led to the develop- for most of these resistances are located on plasmids however some may ment of different heavy metal resistances in them. The genetic de- be chromosomal also (Jasmine et al., 2012). terminants for these heavy metal resistances can be either chromosomal Biosorption is actually the passive removal of heavy metals by their or on plasmids and the resistance determinants also varies from species adsorption on non-living biomass. It is metabolism-independent. to species (Hall, 2002; Nies, 1999). However, the chromosomal and Whereas, bioaccumulation is the metabolism-dependent accumulation plasmid mediated resistance systems are quite different. Chromosomal of heavy metals in living bacterial cells. Gram-positive bacteria accu- encoded resistance mechanisms are more complex. Plasmids generally mulate much higher concentrations of heavy metals on their cell walls encode ion efflux systems and hence are transferable to other organisms than that of metals Gram-negative bacteria (Rani and Goel, 2009). (Silver and Walderhaug, 1992). Bacterial plasmids harbor various genes The present review offers a critical summary of bacterial tolerance that confer resistance to different toxic heavy metals e.g., Sb3+ Zn2+ to various heavy metals along with their underlying mechanisms which etc. (Cavicchioli and Thomas, 2002). is very important to understand especially in the context of environ- There is no mechanism of resistance that can be generalized to mental protection. The study therefore also attempts to review the different metals (Nies, 1999). The various possible mechanisms for findings of previous researchers that can be applied efficiently in the heavy metal tolerance reported by different researchers include: ex- bioremediation of heavy metal contaminants. tracellular efflux by pumps, formation of complexes with other components, redox reactions, intra and extra-cellular sequestration (Malik, 2. Uptake of heavy metals by bacteria cell 2004; Veglio et al., 1997; Liu et al., 2004). Some metal ions may also utilize as terminal electron acceptors during anaerobic respiration Two different mechanisms are present in bacteria through which the (Gadd, 1990). heavy metal can enter a bacterial cell. The first one is a nonspecific Since heavy metals cannot be degraded or detoxified like many mechanism that works on secondary active transport (ATP in- other environmental pollutants, bacteria have developed efflux me- dependent) and utilizes the chemiosmotic gradient across the cell chanisms that actively pumps these toxic elements out of the bacterial membrane for heavy metal uptake. This mechanism allows fast trans- cells. This reduces the accumulation and increase in concentration of a port of heavy metal into the cells. The other is an ATP dependent me- particular heavy metal in a bacterial cell (Nies and Silver, 1995). Some chanism for heavy metal uptake by bacterial cells. It is comparatively cations have also been studied and reported getting segregated as slower and highly substrate-specific as compared to the ATP in- complex compounds with thiol containing molecules in the cell. Enzy- dependent mechanism (Ahemad, 2012; Spain and Alm, 2003). matic reduction is another strategy adopted by bacterial cells through which they transform them to less toxic oxidation states. The reduced 3. The role of bacterial cell wall in heavy metal tolerance form of the metal should be exported out of the cell before it gets re- oxidized (Nies, 1999). In order to protect essential components of their cell from toxic The CorA Mg2+ transport system studied by Nies (1999) is a metal heavy metals microorganisms alter the composition of their cell wall transport system that non specifically accumulates divalent heavy metal and/or cell membrane which restricts metal permeability e.g., E.coli is ions within bacterial cells. Other inducible transport systems that are capable of excluding Cu(II) by altering the production of porin, a highly specific also exist, but they work only during starvation (Nies, membrane channel protein as a defense mechanism against copper 1999). toxicity (Rouch et al., 1995). The role of bacterial metallothioneins (MTs) in heavy metal has also The first component of the bacterial cell that is encountered with been reported. Metallothioneins are small, cysteine rich proteins that metals ions is the cell wall. The heavy metals then get accumulated on can bind metal ions (Blindauer, 2011). They are found in all eukaryotes different chemical groups available on the cell wall. Peptidoglycan and various bacteria. The first known bacterial MT was the cadmium layer containing different groups in gram + ve bacteria and gram -ve induced SmtA in marine cyanobacterium Synechococcus sp. RRIMP N1 bacteria determines the metal-binding capability. Out of these carboxyl (Olafson et al., 1979) and the gamma proteobacterium Pseudomonas groups being abundant and negatively charged most actively bind putida (Higham et al.,1984). Homologues for SmtA are also reported in metal cations (Doyle et al., 1980). Gram-positive bacteria accumulate cyanobacteria, pseudomonas, alphaproteobacteria, gammaproteobacteria, much higher concentrations of heavy metals on their cell walls than and firmicutes. Another bacterial metallothionein, the MymT (4.9 kDa) that of metals gram -ve bacteria (Rani and Goel, 2009). Golab and protein was found in Mycobacterium tuberculosis, the expression of Breitenbach (1995) have reported the binding of copper by carboxyl MymT that conferred resistance to Cu and Cd (Gold et al., 2008). groups of peptidoglycan in Streptomyces pilosus. Amine groups have been reported to chelate and adsorb anionic metal species through 4.1. Resistance to arsenic and antimony electrostatic interaction or H- bonding by Kang et al. (2007). Different methods can be used for studying and determining the Due to very similar chemical properties arsenic and antimony also mechanisms of biosorption by bacterial cell wall components e.g., X-ray have similar the transport and tolerance genetic determinants in bac- diffraction, potentiometric titrations, Transmission Electron teria (Silver and Phung, 1996). A number of studies (Rosenstein et al., Microscopy (TEM), Scanning Electron Microscope (SEM) and Fourier- 1992; Nies and Silver, 1995) have also reported detoxification of anti- transform Infrared (FTIR) spectroscopy (Texier et al., 2000; Lopez et al., mony by arsenite efflux systems. Bacterial cells reduce As (V) to As (III) 2000; Kazy et al., 2006; Vannela and Verma, 2006; Vijayaraghavan which is further exported out of the cell by a metal efflux system e.g.,

2 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

Fig. 1. Overview of arsRDABC operon for bacterial resistance to Arsenic, When As (III) is not present the repressor protein (ArsR) occupies the operator and restricts its own expression as well as the other genes of the ars operon. Entry of As (V) into bacterial cell is mediated by phosphate transporters (Pit and the Pst pumps) whereas As (III) enters via GlpF. Reduction of As(v) to As (III) is catalysed by ArsC (arsenate reductase). As (III) exported out of the cell by a metal eﬄux system, arsenite ATPase formed of ArsA (catalytic subunit) and ArsB (membrane subunit) proteins. ArsD transfers As (III) to ArsA ATPase.

arsenite ATPase of Gram-negative bacteria (Nies, 1999; Ji and Silver, called the Ncc (Schmidt and Schlegel, 1994). Mts proteins (smt) have 1995; Wu and Rosen, 1993). The genetic determinants of the arsenite been reported in cyanobacteria to determine tolerance to cadmium efflux system are found on the chromosome in gram -ve bacteria (Olafson et al., 1979). The smt operon consists of the SmtA gene (Mt whereas these reside on the plasmids in gram + ve bacteria (Nies, protein), the SmtB gene that controls the expression of smtA gene and 1999). the operator-promoter region between the two genes (Fig. 2)(Huckle Resistance to both antimony and arsenic is regulated by the ars et al., 1993). operon (Fig. 1)inE. coli as well as S. Aureus (Rosen, 2002; Bhattacharjee et al., 2000). As (III) and Sb (III) enters the bacterial cells 4.3. Resistance to mercury through the G1pF transporter protein (Sanders et al., 1997; Rosen, 2002). Entry of As(V) into bacterial cells is mediated by transporters The mer operon located on bacterial plasmids (Pseudomonas, that usually carry other compounds e.g., phosphate transporters (Pit Escherichia coli and Staphylococcus aureus) imparts resistance to mercury and the Pst pumps) in Escherichia coli. However, the Pit system is pre- in both gram -ve and gram + ve bacteria (Nies, 1999; Wagner-Döbler fi ferred system for arsenate uptake. It is less speci c and accumulates et al., 2000). The inducible, intracellular enzyme, mercuric reductase arsenate into bacterial cells during abundance of phosphate. The Pst encoded by the merA gene converts Hg2+ into volatile metallic mercury fi being highly speci c transports phosphate only during phosphate by an NADPH-dependent process (Summers, 1986). Resistance to in- starvation with the help of two proteins viz., the PstS (binds phosphate) organic mercury is governed by the narrow spectrum mer resistance and the PstABC ATPase complex (Rosen, 2002). system whereas resistances to both inorganic Hg and methylmercury The ars operon in E. coli plasmid bears three structural genes viz., and phenylmercury is governed by the broad-spectrum mer resistance arsA, arsB and arsC. Two more regulatory proteins, ArsR (repressor) system (Silver and Phung, 1996; Bogdanova et al., 1998). and ArsD (co-regulator) also control the ars RDABC operon (Wu and The mer operon comprises regulatory proteins (merR, merD), pro- Rosen, 1993). The change of As(v) to As(III) is mainly catalysed by ArsC teins for transport (merT, mer P) and proteins catalysing mercury re- ffl (arsenate reductase). Further the reduced product is e uxed by an duction i.e., merA. The merR protein control both positive and negative ATPase formed of ArsA (catalytic subunit) and ArsB (membrane sub- regulation of the other genes. It also negatively controls self expression. unit) proteins. ArsD transfers As (III) to ArsA ATPase (Lin et al., 2006). merD is secondary regulatory gene and it down-regulates the mer op- When As (III) is not present the repressor protein (ArsR) occupies the eron (Fig. 3)(Nucifora et al., 1990; Mukhopadhyay et al., 1991). The operator and restricts its own expression as well as the other genes of proteins encoded by structural genes (merT and merP) located down- the ars operon (Rosen, 2002). stream of the operator-promoter aid in mercuric ion transport Glutathione serves as the source of reducing potential in E. coli (Summers, 1986). whereas in Staphylococcus aureus the reducing potential is aided by Many bacterial species have been reported to carry merB genes thioredoxin (Nies and Silver, 1995). The optional substrate for ArsB (encoding organomercurial lyase) that imparts tolerance to different protein is Antimonite therefore the ars determinants also govern re- forms of mercury viz., organomercurials, methylmercury and phe- sistance to Sb (Nies and Silver, 1995). nylmercury. The enzyme cleaves the C-Hg bond, and then reduces Hg2+ into volatile metallic which moves out of the cell. The additional merB 4.2. Resistance to cadmium genes are present downstream of the merA gene (Osborn et al., 1997). However, in case of Pseudomonas stutzeri, the merB gene lies between The CadA system (Fig. 2) governs the resistance to Cadmium in merR and merT (Reniero et al., 1995). merB is rarely found in case of gram positive bacteria in response to accumulation of cadmium inside gram negative bacteria cells (Bogdanova et al., 1998). Other genes bacterial cells. MIT, the metal ion transporter allows entry of cadmium imparting organomercury resistance have also been reported viz., merG into bacterial cells. CadA is a plasmid borne resistance system that and merE (Huang et al., 1999). actively pumps cadmium out of bacterial cells (Nies and Silver, 1995; Nies, 1999; Bruins et al., 2000; Haferburg and Kothe, 2007). A reg- 4.4. Resistance to cobalt and nickel ulatory protein called the Cad C protein controls the expression of other genes of the resistance system. Another protein which is Cad A gene Cobalt [Co(II)] is a necessary trace element for living organisms. Ni product (P-type ATPase) actively pumps cadmium out of the cells (Oden (II) functions to be a cofactor for few enzymes only (Nies, 2004). et al., 1994; Nies and Silver, 1995). However very high concentrations of both Co and Ni can be toxic to The gram-negative bacteria cells manage resistance to cadmium by bacterial cells and therefore they are detoxified by cation efflux (Nies, the RND-driven (resistance, nodulation, cell division) zinc exporter viz., 2004). The specific uptake of these metals is mediated either by either the Czc system (Nies and Silver, 1995; Nies, 1999) and a nickel exporter secondary transport systems or by ATCases (ATP binding cassette)

3 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

Fig. 2. Overview of bacterial resistance to Cadmium, (i) Binding of Cd2+ on bacterial cell surface. (ii) MIT metal ion transporter.(iii) Intracellular sequestration by bacterial Metallothionein (MT), SmtA protein. (iv) Efflux of Cd2+ by CadA transporter (P-type ATPase). systems (Rodionov et al., 2006). Plasmid encoded nickel and/or cobalt resistance determinants include cation antiporter CzcCBA (cobalt-zinc- cadmium), the cobalt-nickel resistance (CnrCBA) and the nickel-cobalt- cadmium resistance i.e., NccCBA efflux systems (Nies, 1995; Schmidt and Schlegel, 1994). The RND-driven efflux systems impart a very strong resistance to cobalt in bacterial cells (Nies, 2003). In E. coli chromosomal located yohM (rcnA) gene expressing a transmembrane protein determines Ni and Co tolerance. The RcnA/ YohM protein belongs to the NiCoT transporter family (Eitinger et al., 2005). Nickel resistance in bacteria have also been reported by cnr/ncc- and cnr/ncc/nreB-like tolerance systems (Stoppel and Schlegel, 1995). The cnr and ncc genes carry a protein which is Resistance Nodulation Cell Division (RND). The CnrCBA protein complex exports nickel outside the cell (Nies, 2003). cnrCBA efflux system is expressed by the cnrYHXCBAT gene system (Fig. 4). It consists of three structural genes cnrC, cnrB, cnrA whose protein products complex together to form the efflux system that pumps nickel out of bacterial cells. As nickel enters ffl the periplasmic space the regulatory genes cnrY and cnrC initiate the Fig. 4. Overview of the cnrCBA e ux system for bacterial resistance to Nickel, The CnrCBA protein complex exports nickel outside the cell. The cnrCBA efflux transcription at the promoter region. The proteins encoded by the system is expressed by the cnrYHXCBAT gene system. It consists of three cnrYXH genes regulate the expression of all other genes. cnrH con- structural genes cnrC, cnrB, cnrA whose protein products complex together to stitutively activates cnrCBA expression (Fig. 4)(Tseng et al., 1999). form the efflux system that pumps Nickel out of bacterial cells. As nickel enters NreB belongs to the MFS protein superfamily that exports Ni(II) the periplasmic space the regulatory genes cnrY and cnrC initiate the tran- across the cytoplasmic membrane (Saier, 2000). The nickel resistance scription at the promoter region. The proteins encoded by the cnrYXH genes determinants in K. oxytoca have been described to contain four genes regulate the expression of all other genes. cnrH constitutively activates cnrCBA viz., nirABCD (Stoppel et al., 1995). expression.

Fig. 3. Overview of bacterial resistance to Mercury, The mer operon comprises of regulatory proteins (merR, merD), proteins for transport (merT, mer P) and proteins catalysing mercury reduction (merA). (i)The protein encoded by merT structural gen aid in mercuric ion transport. (ii) The merR protein control both positive and negative regulation of the other genes. It also negatively controls self expression. merD is secondary regulatory gene and it down-regulates the mer operon. (iii) merB genes (encoding organomercurial lyase) imparts tolerance to diﬀerent forms of mercury viz., organomercurials, methylmercury and phenylmercury. (iv) The enzyme mercuric reductase encoded by the merA gene converts Hg2+ into volatile metallic mercury that moves out of the cell.

4 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

4.5. Resistance to copper 4.6. Resistance to zinc

Bacteria are exposed to extremely high concentrations of copper in Zinc is an essential trace element is an integral part of many cellular soil and water as Cu is extensively used during mining, industry pro- enzymes and complexes e.g. zinc fingers in DNA (Nies, 1999). Zinc cesses, and agricultural practices which is discharged into the en- enters into bacterial cells by an unspecific but fast mechanism which is vironment along with their effluent. Low concentrations of copper al- also coupled to magnesium uptake mechanisms in bacteria (Nies and lows biosynthesis of several metabolic enzymes e.g., cytochrome c Silver, 1995). However high concentrations of zinc can inhibit many oxidase in bacterial cells. Copper acts as a cofactor for many enzymes cellular enzymes.g., ETC and thus inhibit many crucial functions including oxidase and hydroxylase. However, higher concentrations of (Chvapil, 1973; Beard et al., 1995). copper are highly toxic to bacterial cells thus bacteria have developed Two efflux systems have been reported to regulate zinc resistance in different mechanisms to defend against copper induced biotoxicity bacteria. First is a chromosomal regulated P-type ATPase (encoded by (Issazadeh et al., 2013; Lu et al., 1999). the zntA gene) that allows the efflux of zinc ions across plasma mem- The genetic determinants for regulation of copper are frequently brane by an ATP driven active transport (Fig. 6)(Beard et al., 1995). found on chromosomes in most living organisms (Liu et al., 2002). Second is a proton gradient driven RND transporter found commonly in However, in case of bacteria they are generally found in plasmids case of gram-negative bacteria (Nies, 1999). (Cooksey, 1993). Various researchers (Fong et al., 1995; Rogers et al., Another well known zinc tolerance system is the Czc system of the 1991) have also a reported a co-ordination of both the plasmid and gram negative soil bacterium Ralstonia. This plasmid borne operon chromosomal genes to regulate copper in bacteria. system also imparts resistance to cadmium and cobalt and functions as Resistance to Cu is mainly regulated by P-type ATPases that pump cation/proton antiporter that effluxes cations from the cells. The czc copper out of bacterial cells (Odermatt et al., 1993; Rensing et al., operon is constituted by three structural genes, czcC, czcB and czcA that 2000). In E. coli the CusCBA multi protein complex controls Cu efflux together form the cation efflux system (Nies, 1992, 1995; Nies et al., (Outten et al., 2001; Franke et al., 2003). CusA is an RND protein, 1989). driven by the proton motive force, that transport Cu out of bacterial CzcB displays homology to membrane fusion proteins, calphotin cells with the help of CusB and CusC gene products (Seeger et al., (calcium-mobilizing protein) found in sponges (Ji and Silver, 1995). 2006). The third component of Cu homeostasis in E. coli is Multi Copper CzcB brings the outer membrane near to the CzcA (cation/H + Oxidase (MCO) that concerts Cu(I) to Cu(II) and protects the peri- antiporter) antiporter that resembles the RND superfamily (Goldberg plasmic proteins (Singh et al.,2004). et al., 1999; Rensing et al., 1997). The copper inducible cop operon (Fig. 5) located on plasmids in A resistance system for both Cd and Zn is reported in P. aeruginosa Pseudomonas sp. imparts resistance to Cu. It consists of four proteins CMG103 called the Czr system. It consists of czrCBA genes that is very CopA, CopB, CopC and CopD. These accumulate copper and simulta- similar to the Czc system of R. eutrophus CH34 (Hassan et al., 1999). neous compartmentalization in the cell’s periplasm and the outer membrane which imparts protection against copper. The extracellular Cu2+ enters the bacterial cell through the porous outer membrane. 4.6.1. Post-efflux control and zinc-binding proteins CopA (periplasmic protein) binds Cu2+ and further transports them to Presence of a post efflux mechanisms that restricts the re-entry of CopD (inner membrane Cu2+ transporter protein) through CopC pro- e ffluxed zinc ions has also been reported by several researchers tein. CopD transports Cu2+ inside bacterial cell (inner membrane pro- (Choudhury and Srivastava, 2001a,b; Diels et al., 1995; Saxena and tein) senses raised Cu2+ concentrations in the periplasmic space and Srivastava, 1998). This involves either precipitation, attachment to a CopS transmits the same to CopR which induces the expression of co- protein or forming a complex with some cellular component e.g., pABCD genes (Cooksey, 1993; Nies, 1999). periplasmic storage of effluxed Zn 2+ in P. syringae and E. coli (Brown Copper homeostasis in E. hirae is maintained by the copYZAB op- et al., 1995; Cervantes and Silver, 1996). In Ralstonia sp. the metal is eron. Resistance to Cu is mainly regulated by. CopA proteins mediates finally precipitated in the form of bicarbonates and hydroxides as a Cu uptake under Cu-limiting conditions. CopB is a P-type ATPases that post-efflux management (Choudhury and Srivastava, 2001a,b). The pumps excess of copper out of bacterial cells. CopY (transcription re- ZnuABC (Fig. 6) is a well known periplasmic binding protein dependent pressor) and CopZ (a Cu chaperon) proteins regulate the expression of zinc transport system in E. coli (Patzer and Hantke, 1998). This is an the cop operon (Solioz and Stoyanov, 2003). effective approach where efflux immediately controls metal toxicity whereas binding and storage impart long term tolerance. The effluxed Zn is then reserved that can be later used for some other cellular

Fig. 5. Overview of bacterial resistance to Copper, The copper inducible copABCD operon located on plasmids in Pseudomonas sp. imparts resistance to Cu. The extracellular Cu2+ enters the bacterial cell through the porous outer membrane. CopA (periplasmic protein) binds Cu2+ and further transports them to CopD (inner membrane Cu transporter protein) through CopC protein. CopD transports Cu2+ inside bacterial cell. CopS (inner membrane protein) senses raised Cu2+ concentrations in the periplasmic space and transmits the same to CopR which induces the expression of copABCD genes.

5 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

Fig. 6. Zn tolerance systems in bacterial cells, ZntA is a P-type ATPase that allows the eﬄux of zinc ions across plasma membrane by an ATP driven active transport. The ZnuABC is a periplasmic binding protein dependent zinc transport system. Czc system is a plasmid borne operon system that in addition to zinc also imparts resistance to cadmium and cobalt in and functions as cation/proton antiporter that eﬄuxes cations from the cells.

function (Nies, 1999). 5.2. Bioattenuation

The removal of heavy metals contaminants naturally by the resident 5. Potential applications of bacteria in heavy metal bacterial population is involved in bioattenuation also called as natural bioremediation attenuation. It is a slow but inexpensive process that sometimes has to accelerated by either biostimulation or bioaugmentation (Mulligan and Heavy metal tolerance in bacteria has been extensively studied Yong, 2004; Li et al., 2010). worldwide. A number of bacterial species have been reported for heavy Jasmine et al. (2012) isolated heavy metal resistant bacteria from metal resistance (Table 1). Most of the bacterial species that pose to be sewage water collected in and around Trichy district, South India. Their potential candidates for bioremediation of heavy metals belong to the results showed Pseudomonas sp. to be highly resistant to Cu, Ag and Zn. genus Bacillus, Pseudomonas, Streptomyces, and Pseudomonas (Uslu and Therefore, such bacteria could be utilized for detoxification and re- Tanyol, 2006. Bioremediation of heavy metals can be achieved through moval of heavy metals from polluted environment. Dinu et al. (2011) different methods like bioaugmentation, biostimulation, and bioatte- have also reported the resistance of Pseudomonas sp. against Cd, Pb, Zn nuation. and Ni. Hakeem and Bhatnagar (2010) isolated three indigenous strains of Streptococcus sp., Staphylococcus sp. and Pseudomonas sp from effluent of 5.1. Bioaugmentation a pulp and paper industry to be used in bioremediation of heavy metals. They also tested the heavy metal removal capabilities of the isolated Bioaugmentation is an approach used for bioremoval of different bacteria and found Pseudomonas sp. to effectively remove cadmium, metal contaminated sites by the introduction of specific bacteria or manganese and mercury. Whereas Streptococcus sp. and Staphylococcus genetically engineered bacteria that are capable of fighting against that sp. were able to remove Cu more efficiently. particular heavy metal contaminant. This is a highly efficient approach fi with greater substrate speci city and sustainability (Mrozik and 5.3. Biostimulation Piotrowska-Seget, 2010). It is an in situ approach and thus is affected by ff di erent abiotic and biotic factors. Emenike et al. (2018) suggested Biostimulation is an approach where the indigenous bacteria are bioaugmentation and biostimulation as the most acceptable methods provided with conditions suitable to stimulate their metal resistant for bioremediation of metal polluted environments. They have also potential and thus enhance bioremediation (Atagana, 2008). This in- ff proposed the use of a consortium of di erent strains over a single strain. volves addition of nutrients (phosphorus, nitrogen, oxygen, carbon) fi Further, genetically modi ed bacteria strains with upgraded catabolic that enhances the growth of resident bacterial species for biodegrada- ffi abilities are considered to be more e cient for bioaugmentation than tion (Al-Sulaimani et al., 2010; Bundy et al., 2012). Biostimulation has the wild ones (Mrozik and Piotrowska-Seget, 2010; Mrozik et al., 2011). been studied by a number of researchers for bioremediation of different Apart from this bioaugmentation where the genetic determinants heavy metals viz., Fe, Cu, Cd, Fe and Cr (Fulekar et al., 2012; Kanmani are located on plasmids can give more promising outputs as it can be et al., 2012). easily transferred to the indigenous bacterial population of the con- In a study conducted by Anderson and Cook (2004) highly arsenic taminated site. But for the approach to be successful it requires a very resistant bacteria have been reported in Bacillus and Pseudomonas. deep understanding of the donor as well as the recipient bacterial po- Several other studies have also reported high arsenic resistance in pulation (Garbisu et al., 2017). species of Bacillus, Methylobacterium, Pseudomonas Arthrobacter, Sta- Emenike et al. (2017) applied bioaugmentation for removing of phylococcus (Zolgharnein et al., 2007; Suresh et al., 2004; Cervantes metal contaminants from leachate polluted soil. They used a blend of et al., 1994; Ahmed and Rehman, 2009). bacterial strains belonging to Bacillus sp., Lysinibacillus sp. and Rhodo- Grewal and Tiwari (1990) isolated heavy metal resistant strains of coccus sp. and obtained a reduction of, Al (72%), Cu (88%), Cd (41%), E. coli from foodstuffs. Most of the isolates (94.9%) was resistant to Cd, Mn (65%) and Pb(71%). followed by As (76.9%), Hg (71.8%) and Hg (61.5%). The authors also Fauziah et al. (2017) also studied metal (Al, Cd, Cr, Fe, Ni, Pb and found most of the strains displayed multiple heavy metal resistances Zn) reduction potential of bacteria in leachate contaminated soil with B. viz., three metals (35.9%), four metals (38.5%) metals two metals thuringiensis, L. sphaericus and R. wratislaviensis. They were able to attain (18%) and one metal (7.7%). the best results with Ni (> 50%). Sevgi et al. (2010) reported resistance to heavy metals in industrial

6 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

Table 1 Table 1 (continued) − Heavy metal removal using bacteria (mg g 1 or %). Bacteria Heavy Removal of References Bacteria Heavy Removal of References metal heavy metal − metal heavy metal (mg g 1 or %) − (mg g 1 or %) Ziagova et al. Bacillus sp. Pb 92.3 Tunali et al. (2007) Cu 16.3 (2006) Staphylococcus Cr(VI) 24.1% Jencarova and Cu 69.34% Hussein et al. saprophyticus Pb 100% Luptakova (2012) (2004) Cu 14.5% Cu 84.0% Azzam and Tawfik Micrococcus sp. Pb 84.27% Hussein et al. Pb 99.5% (2015) (2004) Cd 72.9% Cr(VI) 92% Sulaymon et al. Hg 45% Nanda et al. Ni 90% (2012) Cu 62% (2011) E. coli Cd 63.39% Huang et al. Bacillus firmus Zn 418 Salehizadeh and Pb 68.51% (2001) Shojaosadati Cr 60.26 % (2003) Bacterial Mixtures Pb 98.3% Kang et al. (2016) Bacillus cereus Cu 50.32 Babak et al. (Viridibacillus arenosi B-21, Cd 85.4% Pb 36.71 (2012) Sporosarcina soli B-22, Cu 5.6% Bacillus licheniformis Cr 95% Karakagh et al. Enterobacter cloacae KJ- Fe 52% (2012) 46, and E. cloacae KJ-47) Cu 32% Bacillus subtilis Cd 69.90% Huang et al. Pb 67.36% (2001) Cr 54.56 % soil isolates of Pseudomonas spp. and Bacillus spp. Most of the bacteria Cu 20.8 Nakajima et al. (73.9%) displayed resistance to Chromium. 26% were found resistant to (2001) Ni. Whereas lower resistances i.e., 18.4%, 11.5%, 9.2% and 7.3% were Thiobacillus ferrooxidans Zn 172.4 Liu et al. (2004) recorded for Zinc, Cadmium, Cobalt and Copper respectively. Thiobacillus thiooxidans Zn 95.24 Nagashetti et al. Samanta et al. (2012) isolated a Gram positive Bacillus sp. from a Cu 39.84 (2013) ff Geobacillus Cu 57 Samarth et al. heavy metal contaminated soil. The isolated strain showed di erent thermodenitrificans Zn 18 (2012) levels of tolerance to the metals under investigation and as indicated by Pb 53 different MTC values. It was found that among four experimental heavy Geobacillus Cu 65 Samarth et al. metals, the strain showed high resistance to cadmium showing the themocatenulatus Zn 12.3 (2012) growth of microorganisms up to 1.0 mg/ml (i.e.1000 μg/ml) and less Pb 54 Enterobacter sp. Pb 50.9 Lu et al. (2006) resistance to cobalt showing growth of microorganism up to 0.4 mg/ml Cu 32. 5 (i.e.400 μg/ml). The pattern of metal tolerance were in the order Cd 46.2 Cd2+ >Cr6+ >Ni2+ >Co2+. Enterobacter cloacae Pb 67.9% Rani et al. (2010) In another study conducted by Bisht et al. (2012) heavy metal tol- Cu 78.9% ffi Cr 55.8% erance e ciency of Staphylococcus aureus, Staphylococcus epidermidis Hg 43.23% and Staphylococcus saprophyticus was studied. Staphylococcus saprophy- Cd 58.9% ticus was found more resistant to Cu than the other bacterial species. In Pseudomonas sp. Cd 278.0 Ziagova et al. case of zinc Staphylococcus aureus and Staphylococcus epidermidis dis- 90.41% (2007) played better resistance. 500 Hussein et al. (2004) Gaballa et al. (2003) have also isolated and reported the resistance Liu et al. (2004) of Staphylococcus sp. for Cd and Ni. Sri Kumaran et al. (2011) isolated a Cu 70.4% Azzam and Tawfik heavy metal tolerant Pseudomonas sp. that was capable of effectively Pb 97.8% (2015) removing 41%, 62.8%, 87.9%,53% and 49.8% of Cadmium, Iron, Lead, Cd 93.5% Cr 8.9-238 Liu et al., 2004 Nickel and Zinc respectively. Cu 8.9-238 Lin and Harichund (2011) studied the removal of heavy metals from Ni 556 chemical industry effluent and found that Bacillus sp. was able to re- Cd 56% Nanda et al. move 20.3% As and 16.7% Hg effectively from the effluent. Pena- As 34% (2011) Montenegro et al., 2015 in 2015 have also reported bioremediation of Co 53% Pseudomonas Cr(VI) 1.07 Babak et al. heavy metals (cobalt, copper, chromium and lead) using bacteria. In aeruginosa Cu 0.67 (2012) 2014 Jain and Bhatt, 2014 isolated the two cadmium resistant strains Zn 1.33 viz., Pseudomonas putida SB32 and Pseudomonas monteilii SB35. The Pb 79.5 Chang et al. genetic determinants for the resistance the plasmid encoded czc system, Cu 23.1 (1997) ffl Cd 42.4 which is responsible for the e ux of metal ions. Pseudomonas putida Zn 17.7 Chen et al. (2005) Nanda et al. (2011a,b) have reported different bacteria to be effi- Cu 15.8 cient in removing heavy present from pharmaceutical industrial ef- Pb 270. 4 Uslu and Tanyol fluent samples. Bacillus sp was able to remove Hg (45%) and Cu (62%). Cu 96.9 (2006) Pseudomonas sp. was able to remove 56% Cd, 34% As and 53% of Co. A Cd 8.0 Pardo et al. (2003) Cu 6.6 reduction of 44% Cd and 34% Cu reduction was recorded by Staphy- Streptomyces rimosus Pb 135.0 Selatnia et al. lococcus sp. (2004) Kang et al. (2016) suggested the use of consortium of bacteria in- Zn 80.0 Mameri et al. stead of single bacterial species for efficient bioremediation of heavy (1999) Staphylococcus Sp. Cd 44% Nanda et al. metals from water. They worked on removal of a number of metal Cu 34% (2011) contaminants using bacterial consortium and have reported a reduction Staphylococcus xylosus Cd 250.0 of 98.3%, 85.4% and 5.6% for lead, Cadmium and Copper respectively.

7 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

6. Conclusions Horizontal spread of mer operons among gram-positive bacteria in natural environments. Microbiology 144, 609–620. ff Brown, N.L., Barrett, S.R., Camakaris, J., Lee, B.T.O., Rouch, D.A., 1995. ) Molecular Microbial biotechnology is an e ective and eco friendly solution for genetics and transport analysis of the copper-resistance determinant (pco) from bioremediation of heavy metals. The site from where a particular bac- Escherichia coli plasmid pRJ1004. Mol. Microbiol. 17, 1153–1156. terial species has been isolated can very well help us predict the be- Bruins, M.R., Kapil, S., Oehme, F.W., 2000. Microbial resistance to metals in the environment. Ecotoxicol. Environ. Saf. 45, 198–207. haviour of that bacteria. Thus, bacteria isolated from heavy metal Bundy, J.G., Paton, G., Campbell, C.D., 2012. Microbial communities in different soils contaminated sites pose to be the most suitable candidates for heavy types do not converge after diesel contamination. J. Appl. Microbiol. 92, 276–288. metal bioremediation. Bacterial cells have evolved various mechanisms Cao, J., Wang, G., Wang, T., Chen, J., Wenjing, G., Wu, P., He, X., Xie, L., 2019. Copper fi for tolerating different heavy metals which also varies from one bac- caused reproductive endocrine disruption in zebra sh (Danio rerio). Aquat. Toxicol. 211, 124–136. terial population to another. The important heavy metal accumulating Cavicchioli, R., Thomas, T., 2002. Extremophiles. Encyclopedia of Microbiology, vol. 2. functional groups of the bacterial cell wall that play a very important Academic Press, San Diego, pp. 317–337. role in biosorption by either dead or inactive biomass are carboxyl, Cervantes, C., Silver, S., 1996. Metal resistance in Pseudomonas, genes and mechanisms. p. 398 In: Nakazawa, T., Furukawa, K., Haas, D., Silver, S. (Eds.), Molecular Biology phosphonate, amine and hydroxyl groups. Extracellular poly- of Pseudomonads. American Society for Microbiology, Washington, D.C. saccharides have also been reported to accumulate heavy metals in Cervantes, C., Ji, G., Ramirez, J.L., Silver, S., 1994. Resistance to arsenic compounds in – some bacteria. The bacterial metallothioneins (Mts), small cysteine rich microorganisms. FEMS Microbiol. 15, 355 367. ff Chang, J.S., Law, R., Chang, C.C., 1997. Biosorption of lead, copper and cadmium by proteins also impart heavy metal resistance to some bacteria. Di erent biomass of Pseudomonas aeruginosa PU21. Water Res. 31, 1651–1658. bacteria isolated from the same heavy metal contaminated environment Chen, X.C., Wang, Y.P., Lin, Q., Shi, J.Y., Wu, W.X., Chen, Y.X., 2005. Biosorption of show variation in their tolerance to the same heavy metals. Heavy copper (II) and zinc (II) from aqueous solution by Pseudomonas putida CZ1. Colloid Surf. B-Biointerfaces 46, 101–107. metal binding capability is more prominent in gram + ve than gram -ve Choudhury, R., Srivastava, S., 2001a. Mechanism of zinc resistance in Pseudomonas putida bacteria. The efficiency of a particular bacteria in removing different strain S4. World J. Microbiol. Biotechnol. 17, 149–153. heavy metals may vary. Also, the extent of removing a particular heavy Choudhury, R., Srivastava, S., 2001b. Zinc resistance mechanisms in bacteria. Curr. Sci. ff 81 (7), 768–775. metal from di erent sites/samples of the same bacteria also varies. The Chvapil, M., 1973. New aspects in the biological role of zinc, A stabilizer of macro- genes for resistance to heavy metals can be present on plasmids as well molecules and biological membranes. Life Sci. 13, 1041–1049. as on chromosomes. The current states about the application of bac- Cooksey, D.A., 1993. Copper uptake and resistance in bacteria. Mol. Microbiol. 7, 1–5. terial heavy metal bioremediation discussed here gives an insight of the Diels, L., Dong, Q., van der Lelie, D., Baeyens, W., Mergeay, M.J., 1995. The czc operon of Alcaligenes eutrophus CH34, from resistance mechanism to the removal of heavy potential of different bacteria towards heavy metal removal that can be metals. Ind. Microbiol. 14, 142–153. utilized for developing better techniques for environmental research. Dinu, L.A., Ahghel, L., Jurcoane, S., 2011. Isolation of heavy metal resistant bacterial strains from the battery manufactured polluted environment. Roman. Biotech. Lett. Keeping in view the limitations of bioremediation the future prospect – fi 16 (6), 102 106. looks promising in the direction of using genetically modi ed bacteria Doyle, R.J., Matthews, T.H., Streips, U.N., 1980. Chemical basis for selectivity of metal for bioremediation of heavy metals in the environment. Also, bacterial ions by the Bacillus subtilis cell wall. J. Bacteriol. 143, 471–480. biomass if combined with other biosorbents e.g. fungus can also give Dua, M., Singh, A., Sethunathan, N., Johri, A., 2002. Biotechnology and bioremediation, success and limitations. Appl. Microb. Biotechnol. 59 (2-3), 143–152. very promising results. Dumont, E.R., Larue, C., Lorber, S., Gryta, H., Billoir, E., Gross, E.M., Elger, A., 2019. Does intraspecific variability matter in ecological risk assessment? Investigation of geno- References typic variations in three macrophyte species exposed to copper. Aquat. Toxicol. https://doi.org/10.1016/j.aquatox.2019.03.012. Eitinger, T., Suhr, J., Moore, L., Smith, J.A.C., 2005. Secondary transporters for nickel and Ahemad, M., 2012. Implications of bacterial resistance against heavy metals in bior- cobalt ions, theme and variations. Biometals 18, 399–405. emediation, A Review. IIOABJ 3, 39–46. Emenike, C.U., Agamuthu, P., Fauziah, S., 2017. Sustainable remediation of heavy metal Ahluwalia, S.S., Goyal, D., 2007. Microbial and plant derived biomass for removal of polluted soil: a biotechnical interaction with selected bacteria species. J. Geochem. heavy metals from wastewater. Bioresour. Technol. 98, 2243–2257. Explor. 182, 275–278. Ahmed, A., Rehman, A., 2009. Isolation of Cr (VI) reducing bacteria from industrial ef- Emenike, C.U., Jayanthi, B., Agamuthu, P., Fauziah, S.H., 2018. Biotransformation and fluents and their potential use in bioremediation of chromium containing waste- removal of heavy metals: a review of phytoremediation and microbial remediation water. J. Environ. Sci. 21, 814–820. assessment on contaminated soil. Environ. Rev. 26 (2), 156–168. Al-Sulaimani, Y., Al-Wahaibi, S.N., Al-Bahry, Elshafie A., Al-Bemani, A.S., Joshi, J.S., Fauziah, S.H., Agamuthu, P., Hashim, R., Izyani, A.K., Emenike, C.U., 2017. Assessing the Zargari, S., 2010. Experimental investigation of biosurfactants produced by Bacillus bioaugmentation potentials of individual isolates from landfill on metal-polluted soil. species and their potential for MEOR in Omani oil field. Proceedings of the SPE EOR Environ. Earth Sci. 76, 401. Conference at Oil and Gas West Asia. pp. 378–386. Fong, S.T., Camakaris, J., Lee, B.T., 1995. Molecular genetics of a chromosomal locus Anderson, C.R., Cook, G.M., 2004. Isolation and characterization of arsenate-reducing involved in copper tolerance in Escherichia coli K12. Mol. Microbiol. 15, 1127–1137. bacteria from arsenic contaminated sites in New Zealand. Curr. Microbiol. 48, Franke, S., Grass, G., Rensing, C., Nies, D.H., 2003. Molecular analysis of the copper- 341–347. transporting efflux system CusCFBA of Escherichia coli. J. Bacteriol. 185, 3804–3812. Atagana, H.I., 2008. Compost bioremediation of hydrocarbon-contaminated soil in- Fulekar, M.H., Sharma, J., Tendulkar, A., 2012. Bioremediation of heavy metals using oculated with organic manure. Afr. J. Biotechnol. 7 (10), 1516–1525. biostimulation in laboratory bioreactor. Environ. Monit. Assess. 184 (12), Ayangbenro, A.S., Babalola, O.O., 2017. A new strategy for heavy metal polluted en- 7299–7307. vironments: a review of microbial biosorbents. Int. J. Environ. Res. Public Health Gaballa, A., Amer, R., Hussein, H., Moawad, H., Sabry, S., 2003. Heavy metals resistance 14, 94. pattern of moderately halophytic bacteria. Arab J. Biotech. 6 (2), 267–278. Azzam, A.M., Tawfik, A., 2015. Removal of heavy metals using bacterial bio-flocculants of Gadd, G.M., 1990. Microbiology of extreme environments. In: Ehrlich, H.L., Brierley, C.L. Bacillus Sp. and Pseudomonas Sp. J. Environ. Eng. Landsc. Manag. 23 (4), 288–294. (Eds.), Microbial Mineral Recovery. McGraw-Hill, New York, pp. 249–275. Babak, L., Šupinova, P., Zichova, M., Burdychova, R., Vitova, E., 2012. Biosorption of Cu, Garbisu, C., Garaiyurrebaso, O., Epelde, L., Grohmann, E., Alkorta, I., 2017. Plasmid- Zn and Pb by thermophilic bacteria–effect of biomass concentration on biosorption mediated bioaugmentation for the bioremediation of contaminated soils. Front. capacity. Acta Univ. Agric. Silvicult. Mend. Brunensis LX 5, 9–17. Microbiol. 8, 1–13. Badar, U., Ahmed, N., Beswick, A.J., Pattanapipitpaisal, P., Macaskie, L.E., 2000. Golab, Z., Breitenbach, M., 1995. Sites of copper binding in Streptomyces pilosus. Water Air Reduction of Chromate by microorganisms isolated from metal contaminated sites of Soil Pollut. 82, 713–721. Karachi, Pakistan. Biotechnol. Lett. 22, 829–836. Gold, B., Deng, H., Bryk, R., Vargas, D., Eliezer, D., Roberts, J., Jiang, Z., Nathan, C., Beard, S.J., Hughes, M.N., Poole, R.K., 1995. Inhibition of the cytochrome bd-terminated 2008. Identification of a copper-binding metallothionein in pathogenic mycobacteria. NADH oxidase system in Escherichia coli K-12 by divalent metal cations. FEMS Nat. Chem. Biol. 4 (10), 609–616. Microbiol. Lett. 131, 205–210. Goldberg, M., Pribyl, T., Juhake, S., Nies, D., 1999. Energetics and topology of CzcA, a Bhattacharjee, H., Zhou, T., Li, J., Gatti, D.L., Walmsley, D.R., Rosen, B.P., 2000. Cation/Proton antiporter of the resistance-nodulation-Cell division protein family. J. Structure-function relationships in an anion-translocating ATPase. Biochem. Soc. Biol. Chem. 274 (37), 26065–26070. Trans. 28, 520–526. Grewal, J.S., Tiwari, J.P., 1990. Resistance to metal ions and antibiotics in Escherichia coli Bisht, S.S., Praveen, B., Rukmini, M., Dhillon, H., 2012. Isolation and screening of heavy isolated from foodstuffs. J. Med. Microbiol. 32, 223–226. metal absorbing bacteria from the industry effluent sites of the river Nagavali. IJPSR Haferburg, G., Kothe, E., 2007. Microbes and metals, Interactions in the environment. J. 3 (5), 1448–1451. Basic Microbiol. 47, 453–467. Blindauer, C.A., 2011. Bacterial metallothioneins, past, present, and questions for the Hakeem, A.S., Bhatnagar, S., 2010. Heavy Metal Reduction of Pulp and Paper Mill future. J. Biol. Inorg. Chem. 16, 1011–1024. Effluent by Indigenous Microbes. Asian J. Exp. Biol. Sci. l (1), 201–203. Bogdanova, E.S., Bass, I.A., Minakhin, L.S., Petrova, M.A., Mindlin, S.Z., Volodin, A.A., Hall, J.L., 2002. Cellular mechanisms for heavy metal detoxification and tolerance. J. Kalyaeva, E.S., Tiedje, J.M., Hobman, J.L., Brown, N.L., Nikiforov, V.G., 1998. Exp. Bot. 53, 1–11.

8 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

Hassan, M.T., van Der Lelie, D., Springael, D., Romling, U., Ahmed, N., Mergeay, M., Technol. Expl. Eng. (IJITEE) 2 (6), 9–17. 1999. Identification of a gene cluster, czr, involved in cadmium and zinc resistance in Nakajima, A., Yasuda, M., Yokoyama, H., Ohya-Nishiguchi, H., Kamada, H., 2001. Copper Pseudomonas aeruginosa. Gene 239, 417–425. biosorption by chemically treated Micrococcus luteus cells. World J. Microbiol. Higham, D.P., Sadler, P.J., Scawen, M.D., 1984. Cadmium-resistant Pseudomonas putida Biotechnol. 17, 343–347. synthesizes novel cadmium proteins. Science 225, 1043–1046. Nanda, M., Sharma, D., Kumar, A., 2011a. Isolation and characterisation of Bacteria Huang, C.C., Narita, M., Yamagata, T., Endo, G., 1999. Identification of three merB genes Resistant to heavy metals cadmium (Cd), arsenic (As), mercury (Hg) from industrial and characterization of a broad-spectrum mercury resistance module encoded by a effluent. Glob. J. Appl. Environ. Sci. 2, 127–132. class II transposon of Bacillus megaterium strain MB1. Gene 239, 361–366. Nanda, M., Sharma, D., Kumar, A., 2011b. Removal of heavy metals from industrial ef- Huang, M., Pan, J., Zheng, L., 2001. Removal of heavy metals from aqueous solutions fluent using Bacteria. Int. J. Environ. Sci. 2, 781–787. using bacteria. J. Shanghai Univ. 5 (3), 253–259. Nies, D.H., 1992. Resistance to cadmium, cobalt, zinc, and nickel in microbes. Plasmid 27 Huckle, J.W., Morby, A.P., Turner, J.S., Robinson, N.J., 1993. Isolation of a prokaryotic (1), 17–28. metallothionein locus and analysis of transcriptional control by trace metal ions. Mol. Nies, D., 1995. The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes Microbiol. 177–187. eutrophus functions as a cation-proton antiporter in Escherichia coli. J. Bacteriol. 177, Hussein, H., Ibrahim, S.F., Kandeel, K., Moawad, H., 2004. Biosorption of heavy metals 2707–2712. from waste water using Pseudomonas sp. Electron. J. Biotechnol. 7 (1), 38–46. Nies, D.H., 1999. Microbial heavy-metal resistance. Appl. Microbiol. Biotechnol. 51, Ilyas, S., Kim, M.S., Lee, J.C., Jabeen, A., Bhatti, H.N., 2017. Bio-reclamation of strategic 730–750. and energy critical metals from secondary resources. Metals 7, 1–17. Nies, D., 2003. Efflux-mediated heavy metal resistance in prokaryotes. FEMS Microbiol. Issazadeh, K., Jahanpour, N., Pourghorbanali, F., Raeisi, G., Farkhondeh, J., 2013. Heavy 27, 313–339. metals resistance by bacterial strains. Ann. Biol. Res. 4 (2), 60–63. Nies, D.H., 2004. Essential and toxic effects of elements on microorganisms. In: Anke, K., Jain, S., Bhatt, A., 2014. Molecular and in situ characterization of cadmium-resistant di- Ihnat, M., Stoeppler, M. (Eds.), Metals and Their Compounds in the Environment. versified extremophilic strains of Pseudomonas for their bioremediation potential. Wiley-VCH, Weinheim (part II.1). Biotech 4, 297–304. Nies, D.H., Silver, S., 1995. Ion efflux systems involved in bacterial metal resistances. J. Jasmine, R., Venkadesan, B., Ragul, K., 2012. Identification and characterization of heavy Ind. Microbiol. 14, 186–199. metal-resistant Pseudomonas aeruginosa and its potential for bioremediation. Am. J. Nies, D.H., Nies, A., Chu, L., Silver, S., 1989. Expression and nucleotide sequence of a PharmTech Res. 2 (4), 783–787. plasmid determined divalent cation efflux system from Alcaligenes eutrophus. Proc. Jencarova, J., Luptakova, A., 2012. The elimination of heavy metal ions from waters by Natl. Acad. Sci. U.S.A. 86, 7351–7355. biogenic iron sulphides. Chem. Eng. Res. Des. 28, 205–210. Nouha, K., Kumar, R.S., Tyagi, D., 2016. Heavy metals removal from wastewater using Ji, G., Silver, S., 1995. Bacterial resistance mechanisms for heavy metals of environmental extracellular polymeric substances produced by Cloacibacterium normanense in was- concern. J. Ind. Microbiol. 14, 61–75. tewater sludge supplemented with crude glycerol and study of extracellular poly- Kang, S.Y., Lee, J.U., Kim, K.W., 2007. Biosorption of Cr (III) and Cr (VI) onto the cell meric substances extraction by different methods. Bioresour. Technol. 212, 120–129. surface of Pseudomonas aeruginosa. Biochem. Eng. J. 36, 54–58. Nucifora, G., Silver, S., Misra, T.K., 1990. Down regulation of the mercury resistance Kang, C.H., Kwon, Y.J., So, J.S., 2016. Bioremediation of heavy metals by using bacterial operon by the most promoter-distal gene merD. Mol. Gen. Genet. 220, 69–72. mixtures. Ecol. Eng. 89, 64–69. Oden, K.L., Gladysheva, T.B., Rosen, B.P., 1994. Arsenate reduction by the plasmid en- Kanmani, P., Aravind, J., Preston, D., 2012. Remediation of chromium contaminants coded ArsC protein is coupled to glutathione. Mol. Microbiol. 12, 301–306. using bacteria. Int. J. Environ. Sci. Technol. (Tehran) 9, 183–193. Odermatt, A., Suter, H., Krapf, R., Solioz, M., 1993. Primary structure of two P-type Karakagh, R.M., Chorom, M., Motamedi, H., Yuse Kalkhajeh, Y.K., Oustan, S., 2012. ATPases involved in copper homeostasis in Enterococcus hirae. J. Biol. Chem. 268, Biosorption of Cd and Ni by inactivated bacteria isolated from agricultural soil 12775–12779. treated with sewage sludge. Ecohydrol. Hydrobiol. 12 (3), 191–198 2012. Olafson, R.W., Abel, K., Sim, R.G., 1979. Prokaryotic metallothionein, preliminary Kazy, S.K., Das, S.K., Sar, P., 2006. Lanthanum biosorption by a Pseudomonas sp., equi- characterization of a blue-green alga heavy metal-binding protein. Biochem. Biophys. librium studies and chemical characterization. J. Ind. Microbiol. Biotech. 33, Res. Commun. 89 (1), 36–43. 773–783. Osborn, A.M., Bruce, K.D., Strike, P., Ritchie, D.A., 1997. Distribution, diversity and Knox, A.S., Seamans, J.C., Mench, M.J., Vangronsveld, J., 2000. Remediation of metals evolution of the bacterial mercury resistance (mer) operon. FEMS Microbiol. 19, and radionuclides. Contaminated Soil Using in Situ Stabilization Techniques. 239–262. Macmillan Publishers, New York, pp. 21–26. Outten, W., Huffman, D.L., Hale, J.A., O’Halloran, T.V., 2001. The independent cue and Kuan, W.H., Hu, C.Y., Chiang, M.C., 2009. Treatment of As (V) and As (III) by electro- cus systems confer copper tolerance during aerobic and anaerobic growth in coagulation using Al and Fe electrode. Water Sci. Technol. 60 (5), 1341–1346. Escherichia coli. J. Biol. Chem. 276, 30670–30677. Li, C.H., Wong, Y.S., Tam, N.F., 2010. Anaerobic biodegradation of polycyclic aromatic Pan, L., Wang, Y., Ma, J., Hu, Y., Su, B., Fang, G., Wang, L., Xiang, B., 2018. A review of hydrocarbons with amendment of iron (III) in mangrove sediment slurry. Bioresour. heavy metal pollution levels and health risk assessment of urban soils in Chinese Technol. 101, 8083–8092. cities. Environ. Sci. Pollut. Res. Int. 25 (2), 1055–1069. Lin, J., Harichund, C., 2011. Industrial effluent treatments using heavy-metal removing Pardo, R., Herguedas, M., Barrado, E., Vega, M., 2003. Biosorption of cadmium, copper, bacterial bioflocculants. Water SA 37 (2), 265–270. lead and zinc by inactive biomass of Pseudomonas putida. Anal. Bioanal. Chem. 376, Lin, Y.F., Walmsley, A.R., Rosen, B.P., 2006. An arsenic metallochaperone for an arsenic 26–32. detoxification pump. Proc. Natl. Acad. Sci. U.S.A. 103, 15617–15622. Patzer, S.I., Hantke, K., 1998. The ZnuABC high-affinity zinc uptake system and its reg- Liu, C.Q., Charoenchai, P., Khunajakr, N., Deng, Y., Widodo, N., Dunn, W., 2002. Genetic ulator Zur in Escherichia coli. Mol. Microbiol. 28, 1199–1210. and transcriptional analysis of a novel plasmid encoded copper resistance operon Pena-Montenegro, T.D., Lozano, L., Dussán, J., 2015. Genome sequence and description from Lactococcus lactis. Gene 297, 241–247. of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5. Liu, H.L., Chen, B.Y., Lan, Y.W., Chen, Y.C., 2004. Biosorption of Zn (II) and Cu (II) by the Stand. Genomic Sci. 10 (2). indigenous Thiobacillus thiooxidans. Chem. Eng. J. 97, 195–201. Poole, R.K., Gadd, G.M., 1989. Metals, Microbe Interactions. IRL Press, Oxford, pp. 1–37. Lopez, A., Lázaro, N., Priego, J.M., Marquès, A.M., 2000. Effect of pH on the biosorption Rani, A., Goel, R., 2009. Strategies for crop improvement in contaminated soils using of nickel and other heavy metals by Pseudomonas fluorescens 4F39. J. Ind. Microbiol. metal-tolerant bioinoculants. In: Khan, M.S., Zaidi, A., Musarrat, J. (Eds.), Microbial Biotech. 24, 146–151. Strategies for Crop Improvement. Springer, Berlin, pp. 105–132. Lu, Z.H., Copbine, P., Dameron, C.T., Solioz, M., 1999. How cells handle copper, a view Rani, M.J., Hemambika, B., Hemapriya, J., Rajesh Kannan, V., 2010. Comparative as- from microbes. J. Trace Elem. Exp. Med. 12, 347–360. sessment of heavy metal removal by immobilized and dead bacterial cells, A bio- Lu, W.B., Shi, J.J., Wang, C.H., Chang, J.S., 2006. Biosorption of lead, copper and cad- sorption approach. Afr. J. Environ. Sci. Tech. 4 (2), 077–083. mium by an indigenous isolate Enterobacter sp. J1 possessing high heavy-metal re- Reniero, D., Galli, E., Barbieri, P., 1995. Cloning and comparison of mercury- and orga- sistance. J. Hazard. Mater. 134, 80–86. nomercurial-resistance determinants from a Pseudomonas stutzeri plasmid. Gene 166, Malik, A., 2004. Metal bioremediation through growing cells. Environ. Int. 30, 261–278. 77–82. Mameri, N., Boudries, N., Addour, L., Belhocine, D., Lounici, H., Grib, H., 1999. Batch Rensing, C., Mitra, B., Rosen, B.P., 1997. The zntA gene of Escherichia coli encodes a Zn zinc biosorption by a bacterial nonliving Streptomyces rimosus biomass. Water Res. 33, (II)-translocating P-type ATPase. Proc. Natl. Acad. Sci. U.S.A. 94, 14326–14331. 1347–1354. Rensing, C., Fan, B., Sharma, R., Mitra, B., Rosen, B.P., 2000. CopA, An Escherichia coli Cu Mouedhen, G., Feki, M., De Petris-Wery, M., Ayedi, H.F., 2009. Electrochemical removal (I)-translocating P-type ATPase. Proc. Natl. Acad. Sci. U.S.A. 97, 652–656. of Cr (VI) from aqueous media using iron and aluminum as electrode materials, to- Rodionov, D.A., Hebbeln, P., Gelfand, M.S., Eitinger, T., 2006. Comparative and func- wards a better understanding of the involved phenomena. J. Hazard. Mater. 168 (2- tional genomic analysis of prokaryotic nickel and cobalt uptake transporters, evi- 3), 983–991. dence for a novel group of ATP-binding cassette transporters. J. Bacteriol. 188, Mrozik, A., Piotrowska-Seget, Z., 2010. Bioaugmentation as a strategy for cleaning up of 317–327. soils contaminated with aromatic compounds. Microbiol. Res. 165, 363–375. Rogers, S.D., Bhave, M.R., Mercer, J.F., Camakaris, J., Lee, B.T., 1991. Cloning and Mrozik, A., Miga, S., Piotrowska-Seget, Z., 2011. Enhancement of phenol degradation by characterization of cutE, a gene involved in copper transport in Escherichia coli.J. soil bioaugmentation with Pseudomonas sp. JS150. J. Appl. Microbiol. 111, Bacteriol. 173, 6742–6748. 1357–1370. Rosen, B.P., 2002. Biochemistry of arsenic detoxification. FEBS Lett. 529 (1), 86–92. Mukhopadhyay, D.H., Yu, H., Nucifora, G., Misra, T.K., 1991. Purification and functional Rosenstein, R., Pechel, A., Wieland, B., Gotz, F., 1992. Expression and regulation of an- characterization of MerD, a coregulator of the mercury resistance operon in Gram- timonite, arsenite, and arsenate resistance operon of Staphylococcus xylosus plasmid negative bacteria. J. Biol. Chem. 266, 18538–18542. pSX267. J. Bacteriol. 174, 3676–3683. Mulligan, C.N., Yong, R.N., 2004. Natural attenuation of contaminated soils. Environment Rouch, D.A., Lee, B.T.D., Morby, A.P., 1995. Understanding cellular responses to toxic International 30 (4), 587–601. agents, A model for mechanism choice in bacterial metal resistance. J. Ind. Microbiol. Nagashetti, V., Mahadeva Raju, G.K., Muralidhar, T.S., Javed, A., Trivedi, D., Bhusal, K.P., 14, 132–141. 2013. Biosorption of heavy metals from soil by Pseudomonas aeruginosa. Int. J. Innov. Saier, M.H.J., 2000. A functional phylogenetic classification system for transmembrane

9 M. Nanda, et al. Aquatic Toxicology 212 (2019) 1–10

solute transporters. Microbiol. Mol. Biol. 64, 354–411. Stoppel, R.D., Meyer, M., Schlegel, H.G., 1995. The nickel resistance determinant cloned Salehizadeh, H., Shojaosadati, S.A., 2003. Removal of metal ions from aqueous solution from the enterobacterium Klebsiella oxytoca, conjugational transfer, expression, reg- by polysaccharide produced from Bacillus firmus. Water Res. 37, 4231–4235. ulation and DNA homologies to various nickel-resistant bacteria. Biometals 8, 70–79. Samanta, A., Bera, P., Khatun, M., Sinha, C., Pal, P., Lalee, A., Mandal, A., 2012. An Sulaymon, A.H., Mohammed, A.A., Al-Musawi, T.J., 2012. Competitive biosorption of investigation on heavy metal tolerance and antibiotic resistance properties of bac- lead, cadmium, copper, and arsenic ions using algae. Environ. Sci. Pollut. Res. - Int. terial strain Bacillus sp. isolated from municipal waste. J. Microbiol. Biotech. Res. 2 20, 3011–3023. (1), 178–189. Summers, A.O., 1986. Organization, expression and evolution of genes for mercury re- Samarth, D.P., Chandekar, C.J., Bhadekar, R.K., 2012. Biosorption of Heavy Metals from sistance. Annu. Rev. Microbiol. 40, 607–634. Aqueous Solution using Bacillus Licheniformis. Int. J. Pure Appl. Sci. Technol. 10 (2), Suresh, K., Reddy, G.S.N., Sengupta, S., Shivaji, S., 2004. Deinococcus indicus sp. nov., an 12–19. arsenic-resistant bacterium from an aquifer in West Bengal, India. Int. J. Syst. Evol. Sanders, O., Rensing, I., Kuroda, M., Mitra, B., Rosen, B.P., 1997. Antimonite is accu- Microbiol. 54, 457–461. mulated by glycerol facilitator GIpF in Escherichia coli. J. Bacteriol. 179, 3365–3367. Texier, A.C., Andre`s, Y., Illemassene, M., Le Cloirec, P., 2000. Characterization of lan- Sandhu, N., Liang, L., McGeer, J., Dores, R.M., Vijayan, M.M., 2019. Cadmium disrupts thanide ions binding sites in the cell wall of Pseudomonas aeruginosa. Environ. Sci. melanocortin 2 receptor signaling in rainbow trout. Aquat. Toxicol. 209, 26–33. Technol. 34, 610–615. Saxena, D., Srivastava, S., 1998. Carbon source-starvation-induced precipitation of copper Tseng, T.T., Gratwick, K.S., Kollman, J., Park, D., Nies, D.H., Goffeau, A., Jr, Saier M.H., by Pseudomonas putida strain S4. World J. Microbiol. Biotechnol. 14, 291–293. 1999. The RND permease superfamily, an ancient, ubiquitous and diverse family that Schmidt, T., Schlegel, H.G., 1994. Combined nickel-cobalt-cadmium resistance encoded includes human disease and development proteins. J. Mol. Microbiol. Biotechnol. 1, by the ncc locus of Alcaligenes xylosoxidans 31A. J. Bacteriol. 176, 7045–7054. 107–125. Seeger, M.A., Schiefner, A., Eicher, T., Verrey, F., Diederichs, K., Pos, K.M., 2006. Tunali, S., Cabuk, A., Akar, T., 2006. Removal of lead and copper ions from aqueous Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science solutions by bacterial strain isolated from soil. Chem. Eng. J. 115, 203–211. 313, 1295–1298. Uslu, G., Tanyol, M., 2006. Equilibrium and thermodynamic parameters of single and Selatnia, A., Boukazoula, A., Kechid, N., Bakhti, M.Z., Chergui, A., Kerchich, Y., 2004. binary mixture biosorption of lead (II) and copper (II) ions onto Pseudomonas putida, Biosorption of lead (II) from aqueous solution by a bacterial dead Streptomyces ri- effect of temperature. J. Hazard. Mater. 135, 87–93. mosus biomas. Biochem. Eng. J. 19, 127–135. Vannela, R., Verma, S.K., 2006. Cu2+ removal and recovery by SpiSORB, batch stirred Sevgi, E., Coral, G., Gizir, A.M., Sangün, M.K., 2010. Investigation of heavy metal re- and up-flow packed bed columnar reactor systems. Bioprocess Biosyst. Eng. 29, 7–17. sistance in some bacterial strains isolated from industrial soils. Turk. J. Biol. 34, Veglio, F., Beolchini, F., Gasbarro, A., 1997. Biosorption of toxic heavy metals, an equi- 423–431. librium study using free cells of Arthrobacter sp. Process Biochem. 32, 99–105. Shen, Z., Xu, D., Li, L., Wang, J., Shi, X., 2019. Ecological and health risks of heavy metal Vijayaraghavan, K., Han, M.H., Choi, S.B., Yun, Y.S., 2007. Biosorption of Reactive black on farmland soils of mining areas around Tongling City, Anhui, China. Environ. Sci. 5 by Corynebacterium glutamicum biomass immobilized in alginate and polysulfone Pollut. Res. https://doi.org/10.1007/s11356-019-04463-0. matrices. Chemosphere 68, 1838–1845. Shi, W., Becker, J., Bischoff, M., Turco, R.F., Konopka, A.E., 2002. Association of mi- Wagner-Döbler, I., Lünsdorf, H., Lübbehüsen, T., Von Canstein, H.F., Li, Y., 2000. crobial community composition and activity with lead, chromium and hydrocarbon Structure and species composition of mercury-reducing biofilms. Appl. Environ. contamination. Appl. Environ. Microbiol. 68 (8), 3859–3866. Microbiol. 66, 4559–4569. Silver, S., Phung, L.T., 1996. Bacterial heavy metal resistance, new surprises. Annu. Rev. Wu, J., Rosen, B.P., 1993. Metalloregulated expression of the ars operon. J. Biol. Chem. Microbiol. 50, 753–789. 268, 52–58. Silver, S., Walderhaug, M., 1992. Gene regulation and chromosome determined inorganic Yee, N., Fein, J.B., 2001. Cd adsorption onto bacterial surfaces, A universal adsorption ion transport in bacteria. Microbiol. Rev. 56, 195–228. edge? Geochim. Cosmochim. Acta 65, 2037–2042. Singh, S.K., Grass, G., Crensing, C., Montfort, W.R., 2004. Cuprous oxidase activity of Zhang, C., Zeng, G.M., Huang, D.L., Lai, C., Huang, C., Li, N.J., Xu, P., Cheng, M., Zhou, CueO from Escherichia coli. J. Bacteriol. 186, 7815–7817. Y., Tang, W.W., He, X.X., 2014. Combined removal of di(2-ethylhexyl)phthalate Solioz, M., Stoyanov, J.V., 2003. Copper homeostasis in Enterococcus hirae. FEMS (DEHP) and Pb(II) by using a cutinase loaded nanoporous gold-polyethyleneimine Microbiol. 27, 183–195. adsorbent. RSC Adv. 4, 55511–55518. Spain, A., Alm, E., 2003. ) implications of microbial heavy metal tolerance in the en- Ziagova, M., Dimitriadis, G., Aslanidou, D., Papaioannou, X., Tzannetaki, E.L., vironment. Rev. Undergrad. Res. 2, 1–6. Liakopoulou-Kyriakides, M., 2007. Comparative study of Cd(II) and Cr(VI) biosorp- Sri Kumaran, N., Sundara Manickam, A., Bragadeeswaran, S., 2011. Absorption studies on tion on Staphylococcus xylosus and Pseudomonas sp. In single and binary mixtures. heavy metals by isolated bacterial strain (Pseudomonas sp.) from uppanar estuarine Bioresour. Technol. 98, 2859–2865. water, Southeast Coast of India. J. Appl. Sci. Environ. Sanit. 6 (4), 471–476. Zolgharnein, H., Azmi, M.L.M., Saad, M.Z., Mutalib, A.R., Mohamed, C.A.R., 2007. Stoppel, R.D., Schlegel, H.G., 1995. Nickel-resistant bacteria from anthropogenically Detection of plasmids in heavy metal resistance bacteria isolated from the Persian nickel-polluted and naturally nickel-percolated ecosystems. Appl. Environ. Microbiol. Gulf and enclosed industrial areas. Iran. J. Biotechnol. 5 (4), 232–239. 61, 2276–2285.