Polypeptides for heavy-metal biosorption: capacity and specificity of two heterogeneous MerP proteins

Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.

Molecular Identification, Characterization and Improvement of A Chitinase Producing Bacillus strain Showing Significant Control against Some Dermatophytic Fungi

Bacillus bacteria are advantageous antagonistic organisms that can be used as bio-control agents. This study is aimed at screening the antagonistic activity of different strains of isolated Bacillus bacteria and molecular identification of the superior chitinase producer strain against dermatophytes fungi. Soil samples were collected from different places of Kotoor city, Gharbia Governorate, Egypt and Al Madina Al Munawwarah, Kingdom of Saudi Arabia. A collection of Bacillus isolated from soil was tested in vitro against the dermatophytes: Microsporum sp. and Trichophyton sp. The bacterial strains Kh-B1 and Kh-B2 showed the highest antagonistic activity against dermatophytes pathogenic fungi. The highest amount of chitinase productivity (13.6 units/ml) was obtained from the original Bacillus strain (Kh-B1) at 3 days of incubation. BLAST analysis of the amplified 16S ribosomal RNA gene sequence identified the Bacillus strain (Kh-B1) as Paenibacillus macerans. Upon the mutation induction by UV light, the highest chitinase-producing mutant was Kh-UVB-4 as it showed 305.88 percent production higher than the wild-type strain. While, upon the mutation induction by EMS, the highest amount of chitinase produced was 54.8 units/ml by mutant Kh-ESB-20, and it has produced 402.94% more than the original untreated strain. The application of RAPD-PCR protocol using three 15-mer random primers was used to determine the genetic effects of mutagenic treatments on the wild type strain (Kh-B1) as well as to demonstrate the genetic variability between the five most chitinase producing mutants and the wild type (Paenibacillus macerans).

Enhanced removal of trivalent chromium from leather wastewater using engineered bacteria immobilized on magnetic pellets

Leather wastewater contains various toxic contaminants, with trivalent chromium (Cr(III)) having high concentration and adversely affecting wastewater treatment. In this study, a Cr(III) adsorption protein (MerP) was displayed on the cell surface of Escherichia coli and then coupled with a magnetic pellet system to facilitate Cr(III) adsorption. The results showed the engineered strain M-BL21 achieved an in vitro Cr(III) adsorption capacity of 2.38 mmol/g. Next, the magnetic pellets were prepared as component ratios of sodium alginate (2.5%), polyvinyl alcohol (8%), Fe₃O₄ nanoparticles (3.5%), and M-BL21 at 3 g/L. The optimized system was capable of Cr(III) adsorption at an efficiency of 91.29%, which was substantially higher than that of the magnetic carrier alone (67%). Results of scanning electron microscopy with energy-dispersive X-ray analysis proved that Cr(III) was absorbed on the magnetic pellet. The recyclable performance of magnetic property (13.34185 emu/g) and high Cr(III) adsorption efficiency (68.75%) remained after five cycles of Cr(III) absorption. In the medium-scale experiment, 25 L of leather wastewater were treated with magnetic pellet and the Cr(III) removal efficiency reached 88.2%. Thus, our results present an advanced, fully operational, and eco-friendly method for in situ removal of Cr(III) from contaminated wastewater.

MerP/MerT-mediated mechanism: A different approach to mercury resistance and bioaccumulation by marine bacteria

Currently, mechanism underlying mercury resistance and bioaccumulation of marine bacteria remains little understood. A marine bacterium Pseudomonas pseudoalcaligenes S1 is resistant to 120 mg/L Hg²⁺ with bioaccumulation capacity of 133.33 mg/g. Accordingly, Hg²⁺ resistance and bioaccumulation mechanism of S1 was investigated at molecular and cellular level. Annotation of S1 transcriptome reveals 772 differentially expressed genes, including Hg²⁺-relevant genes merT, merP and merA. Both merT and merP gene have three complete copies in S1 genome, while merA gene has only one. In order to evaluate the function of these Hg²⁺-relevant genes, three recombinant strains were constructed to express MerA (named as A), MerT/MerP (TP) and MerT/MerP/MerA (TPA), respectively. The results show that Hg²⁺ resistance of strain TP, TPA, and A are improved with minimum inhibition concentration (MIC) being 60 mg/L, 40 mg/L, and 20 mg/L, respectively compared to 2 mg/L of host strain. Strain TP and TPA exhibit enhanced Hg²⁺ bioaccumulation capacity, while strain A does not differ from the control. Their equilibrium Hg²⁺ bioaccumulation capacities are 110.48 mg/g, 94.49 mg/g, 83.76 mg/g and 82.29 mg/g, respectively. Summarily, different from most microorganisms that exhibit Hg²⁺ resistance by MerA-mediated mechanism, marine bacterium S1 achieves Hg²⁺ resistance and bioaccumulation capability via MerT/MerP-mediated strategy.

Chromosomal expression of CadR on Pseudomonas aeruginosa for the removal of Cd(II) from aqueous solutions

Genetically engineered bacteria for pollution control of heavy metal have been widely studied, however, using Pseudomonas aeruginosa (P. aeruginosa) that can adapt to various circumstances to remediate heavy metal pollution is rarely reported. In this study, we employed CadR, a cadmium (Cd)-specific binding protein, displaying on the surface of P. aeruginosa with chromosomal expression. The genetically engineered (GE) P. aeruginosa still flourished in the 30th generation in the LB broth which contained 100 μM Cd(II), exhibiting an excellent genetic stability. Chromosomally expressed P. aeruginosa showed an adsorption capacity of up to 131.9 μmol/g of Cd(II). In addition, the low concentration of the coexisting two valence ions has no significant effect on adsorption capacity of Cd(II). This study provides a direction for application of P. aeruginosa in environment remediation.

Efficient Cadmium Bioaccumulation by Displayed Hybrid CS3 Pili: Effect of Heavy Metal Binding Motif Insertion Site on Adsorption Capacity and Selectivity

The objective of this study was to evaluate the influence of insertion site of the metal binding motif on the bioaccumulation capacity of the hybrid CS3 pili displayed on the surface of Escherichia coli using both computational and experimental methods. Two metal binding motifs (cadmium binding motif (cbm) and cadmium binding beta motif (cbβm)), identified by searching against the PROSITE database, were inserted into five putative permissive sites of CstH protein (CS3 pili subunit) by using SOEing PCR technique. The expression and surface display of the hybrid pili were evaluated using dot and Western blotting methods and also immunofluorescence microscopy. The cadmium binding affinity and selectivity of the recombinant bacteria displaying various hybrid pili were evaluated using atomic absorption procedure. The results showed that the cadmium binding motifs enabled the cells to sequester cadmium 8- to 16-fold higher than the E.coli expressing native pili. The location of the metal binding motifs in the pili subunit had also a significant effect on the metal-binding properties of the hybrid pili. The insertion at positions 107-108 and 92-93 of the mature CstH showed the highest adsorption in comparison to other positions.

Competition of zinc(II) with cadmium(II) or mercury(II) in binding to a 12-mer peptide

Speciation of the complexes of zinc(II) with a dodecapeptide (Ac-SCPGDQGSDCSI-NH2), inspired by the metal binding domain of MerR metalloregulatory proteins, have been studied by pH-potentiometric titrations, UV, SRCD (synchrotron radiation circular dichroism) and (1)H NMR experiments. (MerR is a family of transcriptional regulators the archetype of which is the Hg(2+)-responsive transcriptional repressor-activator MerR protein.) The aim of the ligand-design was to retain the advantageous metal binding features of MerR proteins in a model peptide for the efficient capture of toxic metal ions. The peptide binds zinc(II) via two deprotonated Cys-thiol groups and one of the Asp-carboxylates in the ZnL parent complex, possessing a remarkably high stability (logK=9.93). In spite of the relatively long peptide loop, bis-complexes are also formed with the metal ion under basic conditions. In a competition with cadmium(II) or mercury(II), zinc(II) cannot prevent the binding of toxic metal ions by the thiolate donor groups of the ligand. Around neutral pH one equivalent of mercury(II) was shown to fully replace zinc(II) from the ZnL species. Partial replacement of zinc(II) from the peptide by one equivalent of cadmium(II), relative to zinc(II) and the ligand, is also presumable, nevertheless, spectroscopic data may suggest the formation of mixed metal ion complexes, as well. Based on the obtained results the investigated dodecapeptide can be a promising candidate for capturing toxic metal ions in practical applications.

Synthetic phytochelatin surface display in Cupriavidus metallidurans CH34 for enhanced metals bioremediation

This work describes the effects of the cell surface display of a synthetic phytochelatin in the highly metal tolerant bacterium Cupriavidus metallidurans CH34. The EC20sp synthetic phytochelatin gene was fused between the coding sequences of the signal peptide (SS) and of the autotransporter β-domain of the Neisseria gonorrhoeae IgA protease precursor (IgAβ), which successfully targeted the hybrid protein toward the C. metallidurans outer membrane. The expression of the SS-EC20sp-IgAβ gene fusion was driven by a modified version of the Bacillus subtilis mrgA promoter showing high level basal gene expression that is further enhanced by metal presence in C. metallidurans. The recombinant strain showed increased ability to immobilize Pb(2+), Zn(2+), Cu(2+), Cd(2+), Mn(2+), and Ni(2+) ions from the external medium when compared to the control strain. To ensure plasmid stability and biological containment, the MOB region of the plasmid was replaced by the E. coli hok/sok coding sequence.

Biosorption: a new rise for elemental solid phase extraction methods

Biosorption is a term that usually describes the removal of heavy metals from an aqueous solution through their passive binding to a biomass. Bacteria, yeast, algae and fungi are microorganisms that have been immobilized and employed as sorbents in biosorption processes. The binding characteristics of microorganisms are attributed to functional groups on the surface providing some features to the biosorption process like selectivity, specificity and easy release. These characteristics turn the biosorption into an ideal process to be introduced in solid phase extraction systems for analytical approaches. This review encompasses the research carried out since 2000, focused on the employment of biosorption processes as an analytical tool to improve instrumental analysis. Since aminoacids and peptides as synthetic analogues of natural metallothioneins, proteins present in the cell wall of microorganisms, have been also immobilized on solid supports (controlled pore glass, carbon nanotubes, silica gel polyurethane foam, etc.) and introduced into solid phase extraction systems; a survey attending this issue will be developed as well in this review.

Equilibrium, thermodynamic and kinetic studies for the biosorption of aqueous lead(II) ions onto the seed husk of Calophyllum inophyllum

Biosorption of lead(II) ions from aqueous solution onto the seed husk of Calophyllum inophyllum was investigated in a batch system. Equilibrium, thermodynamics and kinetic studies were conducted by considering the effects of pH, initial metal ion concentration, contact time, and temperature. The results showed that the uptake of the metal ions increased with increase in initial metal ion concentration. The pH for optimum adsorption was 4 for the Pb(II) ions (q=4.86 mg/g and 97.2% adsorption). Langmuir isotherm described the biosorption of Pb(II) ions onto the biomass (R(2)=0.9531) better than the Freundlich model (R(2)=0.7984), and the Temkin model (R(2)=0.8761). Biosorption kinetics data obtained for the metal ions sorption were fitted using pseudo-first-order and pseudo-second-order. It was found that the kinetics data fitted well into the pseudo-second-order kinetics. Thermodynamic parameters such as Gibbs free energy (DeltaG), standard enthalpy (DeltaH) and standard entropy (DeltaS) were evaluated. The result showed that biosorption of the metal ion onto C. inophyllum biomass was spontaneous and endothermic in nature. The results of FTIR (Fourier-transform infrared spectroscopy) revealed that carboxyl, amine, and hydroxyl groups on the biomass surface were involved in the adsorption of Pb(II) ions.

Effects of heavy metal contamination upon soil microbes: lead-induced changes in general and denitrifying microbial communities as evidenced by molecular markers

Lead (Pb) is a common environmental contaminant found in soils. Unlike other metals, Pb has no biological role, and is potentially toxic to microorganisms. Effects of low (1 ppm) and high (500–2000) levels of lead (Pb) upon the soil microbial community was investigated by the PCR/DGGE analysis of the 16S and nirK gene markers, indicative of general microbial community and denitrifying community, respectively. Community analysis by use of those markers had shown that Pb has detectable effects upon the community diversity even at the lowest concentration tested. Analysis of sample diversity and similarity between the samples suggested that there are several thresholds crossed as metal concentration increase, each causing a substantial change in microbial diversity. Preliminary data obtained in this study suggest that the denitrifying microbial community adapts to elevated levels of Pb by selecting for metal-resistant forms of nitrite reductases.

Expressing a bacterial mercuric ion binding protein in plant for phytoremediation of heavy metals

A specific mercuric ion binding protein (MerP) originating from transposon TnMERI1 of Bacillus megaterium strain MB1 isolated from Minamata Bay displayed good adsorption capability for a variety of heavy metals. In this study, the Gram-positive MerP protein was expressed in transgenic Arabidopsis to create a model system for phytoremediation of heavy metals. Under control of an actin promoter, the transgenic Arabidpsis showed higher tolerance and accumulation capacity for mercury, cadium and lead when compared with the control plant. Results from confocal microscopy analysis also indicate that MerP was localized at the cell membrane and vesicles of plant cells. The developed transgenic plants possessing excellent metal-accumulative ability could have potential applications in decontamination of heavy metals.

Biosorption of nickel, chromium and zinc by MerP-expressing recombinant Escherichia coli

Escherichia coli hosts able to over-express metal-binding proteins (MerP) originating from Gram-positive (Bacillus cereus RC607) and Gram-negative (Pseudomonas sp. K-62) bacterial strains were used to adsorb Ni(2+), Zn(2+) and Cr(3+) in aqueous solutions. The initial adsorption rate and adsorption capacity were determined to evaluate the performance of the biosorbents. With the expression of MerP protein, the metal adsorption capacity of the recombinant strains for Ni(2+), Zn(2+) and Cr(3+) significantly improved. The cells carrying Gram-positive merP gene (GB) adsorbed Zn(2+) and Cr(3+) at a capacity of 22.3 and 0.98 mmol/g biomass, which is 121% and 72% higher, respectively, over that of the MerP-free host cells. Adsorption capacity of the cells carrying Gram-negative merP gene (GP) also increased 144% and 126% for Zn(2+) and Cr(3+), respectively. Both recombinant strains also exhibited 24% and 5% enhancement in adsorption of Ni(2+) for GB and GP, respectively. The initial adsorption rate of the recombinant biosorbents was also higher than that of the MerP-free host, suggesting an increased metal-binding affinity with MerP expression. Severe cell damage on GB biosorbent was observed after Cr(3+) adsorption, probably due to the metal toxicity effect on the cells.

Exploring multi-metal biosorption by indigenous metal-hyperresistant Enterobacter sp. J1 using experimental design methodologies

A novel experimental design, combining mixture design and response surface methodology (RSM), was developed to investigate the competitive adsorption behavior of lead, copper and cadmium by an indigenous isolate Enterobacter sp. J1 able to tolerate high concentrations of a variety of heavy metals. Using the proposed combinative experimental design, two different experiment designs in a ternary metal biosorption system can be integrated to a succinct experiment and the number of experimental trials was markedly reduced from 38 to 26 by reusing the mutual experimental data. Triangular contour diagrams and triangular three-dimensional surface plots were generated to describe the ternary metal biosorption equilibrium data in mixture design systems. The results show that the preference of metal sorption of Enterobacter sp. J1 decreased in the order of Pb(2+)>Cu(2+)>Cd(2+). The presence of other metals resulted in a competitive effect. The influence of the other two metals in ternary metal biosorption system can be easily determined by comparing the stray distance from the single metal biosorption. The behavior of competitive biosorption was successfully described and predicted using a combined Langmuir-Freundlich model along with new three-dimensional contour-surface plots.

Localization effect on the metal biosorption capability of recombinant mammalian and fish metallothioneins in Escherichia coli

In this study, we examined the expression of mammalian and fish metallothioneins (MTs) in Escherichia coli as a strategy to enhance metal biosorption efficiency of bacterial biosorbents for lead (Pb), copper (Cu), cadmium (Cd), and zinc (Zn). In addition, MT proteins were expressed in either the cytoplasmic or periplasmic compartment of host cells to explore the localization effect on metal biosorption. The results showed that MT expression led to a significant increase (5-210%) in overall biosorption efficiency (eta(ads)), especially for biosorption of Cd. The MT-driven improvement in metal biosorption relied more on the increase in the biosorption rates (r(2), a kinetic property) than on the equilibrium biosorption capacities (q(max), a thermodynamic property), despite a 10-45% and 30-80% increase in q(max) of Cd and Zn, respectively. Periplasmic expression of MTs appeared to be more effective in facilitating the metal-binding ability than the cytoplasmlic MT expression. Notably, disparity of the impacts on biosorption ability was observed for the origin of MT proteins, as human MT (MT1A) was the most effective biosorption stimulator compared to MTs originating from mouse (MT1) and fish (OmMT). Moreover, the overall biosorption efficiency (eta(ads)) of the MT-expressing recombinant biosorbents was found to be adsorbate-dependent: the eta(ads) values decreased in the order of Cd > Cu > Zn > Pb.