Purification to homogeneity and characterization of a novel Pseudomonas putida chromate reductase

Simultaneous high molecular weight PAHs degradation and chromate and arsenite detoxification by Altererythrobacter sp. H2

The cooccurrence of high molecular weight PAHs and heavy metals Cr and As is frequently observed in soil and water and challenges public health and environmental management. Yet the limited microbial resources were reported to simultaneously detoxify PAHs, Cr(VI) and As(III), which restricts the bioremediation of co-contaminated soil by PAHs, Cr and As. Here, we isolated Altererythrobacter sp. H2 and found it could degrade various PAHs, including phenanthrene, fluoranthene, pyrene, benzo[a]anthracene, and benzo[a]pyrene, and tolerate and detoxify high concentrations of Cr(VI) and As(III). Genomic, transcriptomic, and biochemical assays reveal strain H2 degrades PAHs, reduces Cr(VI), and oxidize As(III) via a horizontally transferred RHO gene cluster, a chromate reductase ChrR, and a arsenite resistance gene cluster arsRBC. The horizontally transferred PAHs-degrading gene cluster encodes the Rieske dioxygenase three-component system and other enzymes required for PAHs degradation, which suggested those heavy metal-detoxifying bacteria could be excellent PAHs-degrading and heavy metal-detoxifying agents after accommodating a PAHs degradation gene cluster like strain H2 did. To our knowledge, strain H2 is the only reported Altererythrobacter member that uses a classical Rieske dioxygenase three-component system to initial PAHs degradation and the only one could simultaneously detoxify PAHs, Cr(VI), and As(III). Our study provides insights into the PAHs degradation mechanism of Altererythrobacter members and demonstrates the excellent potential of H2 in the bioremediation of both PAHs and heavy metal pollutants.

Sphingobium sp. SJ10-10 encodes a not-yet-reported chromate reductase and the classical Rieske dioxygenases to simultaneously degrade PAH and reduce chromate

Both polycyclic aromatic hydrocarbons (PAHs) and heavy metals persist in the environment and are toxic to organisms. Their co-occurrence makes any of them difficult to remove during bioremediation and poses challenges to environmental management and public health. Microorganisms capable of effectively degrading PAHs and detoxifying heavy metals concurrently are required to improve the bioremediation process. In this study, we isolated a new strain, Sphingobium sp. SJ10-10, from an abandoned coking plant and demonstrated its capability to simultaneously degrade 92.6 % of 75 mg/L phenanthrene and reduce 90 % of 3.5 mg/L hexavalent chromium [Cr(VI)] within 1.5 days. Strain SJ10-10 encodes Rieske non-heme iron ring-hydroxylating oxygenases (RHOs) to initiate PAH degradation. Additionally, a not-yet-reported protein referred to as Sphingobium chromate reductase (SchR), with low sequence identity to known chromate reductases, was identified to reduce Cr(VI). SchR is distributed across different genera and can be classified into two classes: one from Sphingobium members and the other from non-Sphingobium species. The widespread presence of SchR in those RHO-containing Sphingobium members suggests that they are excellent candidates for bioremediation. In summary, our study demonstrates the simultaneous removal of PAHs and Cr(VI) by strain SJ10-10 and provides valuable insights into microbial strategies for managing complex pollutant mixtures.

A PadR family transcriptional repressor regulates the transcription of chromate efflux transporter in Enterobacter sp. Z1

Chromium is a prevalent toxic heavy metal, and chromate [Cr(VI)] exhibits high mutagenicity and carcinogenicity. The presence of the Cr(VI) efflux protein ChrA has been identified in strains exhibiting resistance to Cr(VI). Nevertheless, certain strains of bacteria that are resistant to Cr(VI) lack the presence of ChrB, a known regulatory factor. Here, a PadR family transcriptional repressor, ChrN, has been identified as a regulator in the response of Enterobacter sp. Z1(CCTCC NO: M 2019147) to Cr(VI). The chrN gene is cotranscribed with the chrA gene, and the transcriptional expression of this operon is induced by Cr(VI). The binding capacity of the ChrN protein to Cr(VI) was demonstrated by both the tryptophan fluorescence assay and Ni-NTA purification assay. The interaction between ChrN and the chrAN operon promoter was validated by reporter gene assay and electrophoretic mobility shift assay. Mutation of the conserved histidine residues His14 and His50 resulted in loss of ChrN binding with the promoter of the chrAN operon. This observation implies that these residues are crucial for establishing a DNA-binding site. These findings demonstrate that ChrN functions as a transcriptional repressor, modulating the cellular response of strain Z1 to Cr(VI) exposure.

Simultaneous conversion of chromium and malachite green coexists in halophilic bacterium Halomonas xianhensis SUR308 isolated from a solar saltern

Many industries are known to use heavy metals like chromium (Cr) to fix dyes in the fabrication processes and malachite green (MG) as colorant. Alkalinity, elevated temperature, or salinity of the industrial effluents makes conventional physicochemical removal of MG and hexavalent chromium [Cr(VI)] more difficult to apply and demands to perceive potential cost-effective and environment-friendly treatment methods to eliminate or convert them into less toxic compounds. Here, we report simultaneous removal and bioconversion of MG and Cr(VI) by a halophilic biofilm-forming bacterium Halomonas xianhensis SUR308. It can efficiently produce exopolysaccharides as extracellular polymeric substances (EPS) and form biofilm under oxygen limiting condition. The reduction of hexavalent chromium [Cr(VI)] to trivalent chromium [Cr(III)] is about 100%, and 95% after 84 h of growth in shaken and stagnant culture, respectively. The strain completely decolorizes MG after 48 h of growth in shaken culture. Furthermore, we found that strain SUR308 can efficiently detoxify chromium by reduction and degrades MG via producing various intermediate products simultaneously. Most interestingly, such conversions can also take place in alkaline environment and in environment where substantial amount of salt is present. These unique features of strain SUR308 make it suitable for the simultaneous remediation of toxic heavy metals and hazardous dye even from the environment having higher pH and salinity. The detail molecular mechanism of the bioconversion with its application in open environment would be the future research focus for bioprospecting strain SUR308.

Structural-functional analysis and molecular characterization of arsenate reductase from Enterobacter cloacae RSC3 for arsenic biotransformation

Enterobacter cloacae RSC3 isolated from an industrial pesticide site transformed arsenate into arsenite. The arsenate is transported by membrane-bound phosphate transporter and transformed to arsenite by arsenate reductase (arsC). E. cloacae RSC3 produced an arsenate reductase enzyme with a maximum activity of 354 U after 72 h of incubation. Arsenate reductase was found to be active and stable at a wide range of temperatures (20 and 45 °C) and pH (5-10), with maximum activity at 35 °C and pH 7.0. The arsenate reductase protein was further characterised molecularly using different bioinformatics tools. The 3D structure of ArsC protein was predicted by homology modelling and validated by the Ramachandran plot with 91.9% residues in the most favoured region. ArsC protein of E. cloacae RSC3 revealed structural homology with ArsC from PDB ID: 1S3C. The gene ontology results also showed that the ArsC protein had a molecular functionality of the arsenate reductase (glutaredoxin) activity and the biological function of cellular response to DNA damage stimulus. Molecular docking analysis of 3D structures using AutoDock vina-1.5.7 server predicted four ligand binding active site residues at Gln70, Asp68, Leu68, and Leu63. Strong ArsC-arsenate ion interaction was observed with binding energy -1.03 kcal/mol, indicating significant arsenate reductase activity and specificity of ArsC protein. On the basis of molecular dynamics simulation analysis, the RMSD and RMSF values revealed the stability of ArsC protein from E. cloacae RSC3.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03730-9.

Influencing factors and mechanism of Cr(VI) reduction by facultative anaerobic Exiguobacterium sp. PY14

Microbial reduction is an effective way to deal with hexavalent chromium [Cr(VI)] contamination in the environment, which can significantly mitigate the biotoxicity and migration of this pollutant. The present study investigated the influence of environmental factors on aqueous Cr(VI) removal by a newly isolated facultative anaerobic bacterium, Exiguobacterium sp. PY14, and revealed the reduction mechanism. This strain with a minimum inhibitory concentration of 400 mg/L showed the strongest Cr(VI) removal capacity at pH 8.0 because of its basophilic nature, which was obviously depressed by increasing the Cr(VI) initial concentration under both aerobic and anaerobic conditions. In contrast, the removal rate constant for 50 mg/L of Cr(VI) under anaerobic conditions (1.82 × 10-2 h-1) was 3.3 times that under aerobic conditions. The co-existence of Fe(III) and Cu(II) significantly promoted the removal of Cr(VI), while Ag(I), Pb(II), Zn(II), and Cd(II) inhibited it. Electron-shuttling organics such as riboflavin, humic acid, and anthraquinone-2,6-disulfonate promoted the Cr(VI) removal to varying degrees, and the enhancement was more significant under anaerobic conditions. The removal of aqueous Cr(VI) by strain PY14 was demonstrated to be due to cytoplasmic rather than extracellular reduction by analyzing the contributions of different cell components, and the end products existed in the aqueous solution in the form of organo-Cr(III) complexes. Several possible genes involved in Cr(VI) metabolism, including chrR and chrA that encode well-known Chr family proteins responsible for chromate reduction and transport, respectively, were identified in the genome of PY14, which further clarified the Cr(VI) reduction pathway of this strain. The research progress in the influence of crucial environmental factors and biological reduction mechanisms will help promote the potential application of Exiguobacterium sp. PY14 with high adaptability to environmental stress in Cr(VI) removal in the actual environment.

Cr(VI)-bioremediation mechanism of a novel strain Bacillus paramycoides Cr6 with the powerful ability to remove Cr(VI) from contaminated water

This research provided an excellent novel hexavalent chromium (Cr(VI))-removal bacterium, Bacillus paramycoides Cr6, and investigated its removal mechanism from the perspective of molecular biology. Cr6 could resist up to 2500 mg/L Cr(VI), and the removal rate of 2000 mg/L Cr(VI) reached 67.3% under the optimal culture conditions of 220 r/min, pH 8 and 31 ℃. When the initial concentration of Cr(VI) was 200 mg/L, Cr6 had a removal rate of 100% within 18 h. The differential transcriptome analysis identified two key structural genes named bcr005 and bcb765 of Cr6, which were upregulated by Cr(VI). Their functions were predicted and further confirmed by bioinformatic analyses and in vitro experiments. bcr005 encodes Cr(VI)-reductase BCR005, and bcb765 encodes Cr(VI)-binding protein BCB765. Real-time fluorescent quantitative PCRs were performed, and the data illustrated a parallel pathway (one is Cr(VI) reduction, and the other is Cr(VI) immobilisation) of Cr6 to remove Cr(VI), which relies on the synergistic expression of the genes bcr005 and bcb765 induced by different concentrations of Cr(VI). In summary, a deeper molecular mechanism of Cr(VI) microorganism removal was elaborated; Bacillus paramycoides Cr6 was an exceptional novel Cr(VI)-removed bacterial resource, while BCR005 and BCB765 were two new-found efficient enzymes that have potential practical applications for sustainable microbial remediation of Cr-contaminated water.

Hexavalent chromate bioreduction by a magnetotactic bacterium Magnetospirillum gryphiswaldense MSR-1 and the effect of magnetosome synthesis

Magnetotactic bacteria (MTB) are receiving attention for heavy metal biotreatment due to their potential for biosorption with heavy metals and the capability of the magnetic recovery. In this study, we investigated the characteristics of Cr(VI) bioreduction and biosorption by an MTB isolate, Magnetospirillum gryphiswaldense MSR-1, which has a higher growth rate and wider reflexivity in culture conditions. Our results demonstrated that the MSR-1 strain could remove Cr(VI) up to the concentration of 40 mg L^-1 and with an optimal activity at neutral pH conditions. The magnetosome synthesis existed regulatory mechanisms between Cr(VI) reduction and cell division. The addition of 10 mg L^-1 Cr(VI) significantly inhibited cell growth, but the magnetosome-deficient strain, B17316, showed an average specific growth rate of 0.062 h^-1 at the same dosage. Cr(VI) reduction examined by the heat-inactivated and resting cells demonstrated that the main mechanism for MSR-1 strain to reduce Cr(VI) was chromate reductase and adsorption, and magnetosome synthesis would enhance the chromate reductase activity. Finally, our results elucidated that the chromate reductase distributes diversely in multiple subcellular components of the MSR-1 cells, including extracellular, membrane-associated, and intracellular cytoplasmic activity; and expression of the membrane-associated chromate reductase was increased after the cells were pre-exposed by Cr(VI).

Chromium Toxicity in Plants: Signaling, Mitigation, and Future Perspectives

Plants are very often confronted by different heavy metal (HM) stressors that adversely impair their growth and productivity. Among HMs, chromium (Cr) is one of the most prevalent toxic trace metals found in agricultural soils because of anthropogenic activities, lack of efficient treatment, and unregulated disposal. It has a huge detrimental impact on the physiological, biochemical, and molecular traits of crops, in addition to being carcinogenic to humans. In soil, Cr exists in different forms, including Cr (III) "trivalent" and Cr (VI) "hexavalent", but the most pervasive and severely hazardous form to the biota is Cr (VI). Despite extensive research on the effects of Cr stress, the exact molecular mechanisms of Cr sensing, uptake, translocation, phytotoxicity, transcript processing, translation, post-translational protein modifications, as well as plant defensive responses are still largely unknown. Even though plants lack a Cr transporter system, it is efficiently accumulated and transported by other essential ion transporters, hence posing a serious challenge to the development of Cr-tolerant cultivars. In this review, we discuss Cr toxicity in plants, signaling perception, and transduction. Further, we highlight various mitigation processes for Cr toxicity in plants, such as microbial, chemical, and nano-based priming. We also discuss the biotechnological advancements in mitigating Cr toxicity in plants using plant and microbiome engineering approaches. Additionally, we also highlight the role of molecular breeding in mitigating Cr toxicity in sustainable agriculture. Finally, some conclusions are drawn along with potential directions for future research in order to better comprehend Cr signaling pathways and its mitigation in sustainable agriculture.

Resistance mechanisms and remediation potential of hexavalent chromium in Pseudomonas sp. strain AN-B15

The understanding of bacterial resistance to hexavalent chromium [Cr(VI)] are crucial for the enhancement of Cr(VI)-polluted soil bioremediation. However, the mechanisms related to plant-associated bacteria remain largely unclear. In this study, we investigate the resistance mechanisms and remediation potential of Cr(VI) in a plant-associated strain, AN-B15. The results manifested that AN-B15 efficiently reduced Cr(VI) to soluble organo-Cr(III). Specifically, 84.3 % and 56.5 % of Cr(VI) was removed after 48 h in strain-inoculated solutions supplemented with 10 and 20 mg/L Cr(VI) concentrations, respectively. Transcriptome analyses revealed that multiple metabolic systems are responsible for Cr(VI) resistance at the transcriptional level. In response to Cr(VI) exposure, strain AN-B15 up-regulated the genes involved in central metabolism, providing the reducing power by which enzymes (ChrR and azoR) transformed Cr(VI) to Cr(III) in the cytoplasm. Genes involved in the alleviation of oxidative stress and DNA repair were significantly up-regulated to neutralize Cr(VI)-induced toxicity. Additionally, genes involved in organosulfur metabolism and certain ion transporters were up-regulated to counteract the starvation of sulfur, molybdate, iron, and manganese induced by Cr(VI) stress. Furthermore, a hydroponic culture experiment showed that toxicity and uptake of Cr(VI) by plants under Cr(VI) stress were reduced by strain AN-B15. Specifically, strain AN-B15 inoculation increased the fresh weights of the wheat root and shoot by 55.5 % and 18.8 %, respectively, under Cr(VI) stress (5 mg/L). The elucidation of bacterial resistance to Cr(VI) has an important implication for exploiting microorganism for the effective remediation of Cr(VI)-polluted soils.

Identification and Characterization of a Au(III) Reductase from Erwinia sp. IMH

Microorganisms contribute to the formation of secondary gold (Au) deposits through enzymatic reduction of Au(III) to Au(0). However, the enzyme that catalyzes the reduction of Au(III) remains enigmatic. Here, we identified and characterized a previously unknown Au reductase (GolR) in the cytoplasm of Erwinia sp. IMH. The expression of golR was strongly up-regulated in response to increasing Au(III) concentrations and exposure time. Mutant with in-frame deletion of golR was incapable of reducing Au(III), and the capability was rescued by reintroducing wild-type golR into the mutant strain. The Au(III) reduction was determined to occur in the cytoplasmic space by comparing the TEM images of the wild-type, mutant, and complemented strains. In vitro assays of the purified GolR protein confirmed its ability to reduce Au(III) to Au nanoparticles. Molecular dynamic simulations demonstrated that the hydrophobic cavity of GolR may selectively bind AuCl₂(OH)₂ ^-, the predominant auric chloride species at neutral pH. Density functional theory calculations revealed that AuCl₂(OH)₂ ^- may be coordinated at the Fe-containing active site of GolR and is probably reduced via three consecutive proton-coupled electron transfer processes. The new class of reductase, GolR, opens the chapter for the mechanistic understanding of Au(III) bioreduction.

NahAa can convert naphthalene and reduce chromate simultaneously and immobilized on functional multiwall carbon nanotubes for wastewater treatment

Pseudomonas brassicacearum LZ-4 is a facultative anaerobic bacterium, can efficiently degrade naphthalene and reduce chromate simultaneously. In this study, we showed that the naphthalene degradation enzyme NahAa from P. brassicacearum LZ-4 can reduce Cr(VI). Heterologous expression in E. coli S17-1 along with RNA interference of NahAa in strain LZ-4 showed the enzyme can reduce chromate in vivo. In vitro, purified NahAa was identified and can catalyze Cr(VI) reduction by 64.2%. Flavin adenine dinucleotide (FAD) was identified as a cofactor of NahAa, which Cr(VI) could obtain electrons from NADH through NahAa-associated FAD for reduction. Immobilized NahAa on functional multi walled carbon nanotubes via physical adsorption method to produce a stable, high efficient composite MWCNT-NahAa. The maximum efficiency of MWCNT-NahAa composite was obtained in enzyme concentrations of 6 mg/mL and 20 min immobilization time. The optical reaction conditions for MWCNT-NahAa were pH 7.0 and 30 °C, still retaining 50% of its initial activities after five consecutive cycles. Application of composites in wastewater can reduce 90.4% Cr(VI), higher than free NahAa that was 63.5%. To our best knowledge, this is the first report immobilized enzyme in polycyclic aromatic hydrocarbons-degradation pathway for Cr(VI) wastewater treatment, providing a new insights on combined pollution remediation.

Impact of Soil Inoculation with Bacillus amyloliquefaciens FZB42 on the Phytoaccumulation of Germanium, Rare Earth Elements, and Potentially Toxic Elements

Bioaugmentation promises benefits for agricultural production as well as for remediation and phytomining approaches. Thus, this study investigated the effect of soil inoculation with the commercially available product RhizoVital^®42, which contains Bacillus amyloliquefaciens FZB42, on nutrient uptake and plant biomass production as well as on the phytoaccumulation of potentially toxic elements, germanium, and rare earth elements (REEs). Zea mays and Fagopyrum esculentum were selected as model plants, and after harvest, the element uptake was compared between plants grown on inoculated versus reference soil. The results indicate an enrichment of B. amyloliquefaciens in inoculated soils as well as no significant impact on the inherent bacterial community composition. For F. esculentum, inoculation increased the accumulation of most nutrients and As, Cu, Pb, Co, and REEs (significant for Ca, Cu, and Co with 40%, 2042%, and 383%, respectively), while it slightly decreased the uptake of Ge, Cr, and Fe. For Z. mays, soil inoculation decreased the accumulation of Cr, Pb, Co, Ge, and REEs (significant for Co with 57%) but showed an insignificant increased uptake of Cu, As, and nutrient elements. Summarily, the results suggest that bioaugmentation with B. amyloliquefaciens is safe and has the potential to enhance/reduce the phytoaccumulation of some elements and the effects of inoculation are plant specific.

Aging shapes Cr(VI) speciation in five different soils

To make sound decisions regarding management of heavy metal contamination in soils, it is necessary to understand contaminant transformations over extended periods. In this study, sequential extraction methods were applied to quantify the changes of Cr fractions [available Cr(VI), immobile Cr(VI) and immobile Cr(III)] in five contrasting soils spiked with Cr(VI) over a 240-day incubation. Results showed that available Cr(VI) in soils continually decreased during aging, with a sharp decline occurring in the first 30 days. The best fit of available Cr(VI) data was obtained using an Elovich model for Brunisol and Anthrosol-1, a fractional power model for Anthrosol-2, and a pseudo first-order kinetic model for Luvisol-1 and Luvisol-2. After aging for 240 days, immobile Cr(VI) increased by 4.5-31% and immobile Cr(III) increased by 68-95% of total spiked Cr(VI) in Brunisol, Anthrosol-1 and Anthrosol-2. The two Luvisol soils had relatively high reduction rates with no Cr(VI) immobilized. A multireaction model was developed in MATLAB Simulink toolbox to describe transformation flow rates among soluble Cr(VI), adsorbed Cr(VI), immobilized Cr(VI) and immobilized Cr(III) in soils with aging. We conclude that (i) Cr(VI) reduction and immobilization were occurring concurrently in soils and competing for available Cr(VI) species; (ii) Cr(VI) reduction is favored by low soil pH and high organic carbon, while Cr(VI) immobilization occurs with cations (such as Ca²⁺) and Fe oxides.

Biotic and Abiotic Biostimulation for the Reduction of Hexavalent Chromium in Contaminated Aquifers

Hexavalent chromium is a carcinogenic heavy metal that needs to be removed effectively from polluted aquifers in order to protect public health and the environment. This work aims to evaluate the reduction of Cr(VI) to Cr(III) in a contaminated aquifer through the stimulation of indigenous microbial communities with the addition of reductive agents. Soil-column experiments were conducted in the absence of oxygen and at hexavalent chromium (Cr(VI)) groundwater concentrations in the 1000–2000 μg/L range. Two carbon sources (molasses and EVO) and one iron electron donor (FeSO4·7H2O) were used as ways to stimulate the metabolism and proliferation of Cr(VI) reducing bacteria in-situ. The obtained results indicate that microbial anaerobic respiration and electron transfer can be fundamental to alleviate polluted groundwater from hazardous Cr(VI). The addition of organic electron donors increased significantly Cr(VI) reduction rates in comparison to natural soil attenuation rates. Furthermore, a combination of organic carbon and iron electron donors led to a longer life span of the remediation process and thus increased total Cr(VI) removal. This is the first study to investigate biotic and abiotic Cr(VI) removal by conducting experiments with natural soil and by applying biostimulation to modify the natural existing microbial communities.

The potential of Pseudomonas for bioremediation of oxyanions

Non-metal, metal and metalloid oxyanions occur naturally in minerals and rocks of the Earth's crust and are mostly found in low concentrations or confined in specific regions of the planet. However, anthropogenic activities including urban development, mining, agriculture, industrial activities and new technologies have increased the release of oxyanions to the environment, which threatens the sustainability of natural ecosystems, in turn affecting human development. For these reasons, the implementation of new methods that could allow not only the remediation of oxyanion contaminants but also the recovery of valuable elements from oxyanions of the environment is imperative. From this perspective, the use of microorganisms emerges as a strategy complementary to physical, mechanical and chemical methods. In this review, we discuss the opportunities that the Pseudomonas genus offers for the bioremediation of oxyanions, which is derived from its specialized central metabolism and the high number of oxidoreductases present in the genomes of these bacteria. Finally, we review the current knowledge on the transport and metabolism of specific oxyanions in Pseudomonas species. We consider that the Pseudomonas genus is an excellent starting point for the development of biotechnological approaches for the upcycling of oxyanions into added-value metal and metalloid byproducts.

Biotransformation of Chromium (VI) via a Reductant Activity from the Fungal Strain Purpureocillium lilacinum

Industrial effluents from chromium-based products lead to chromium pollution in the environment. Several technologies have been employed for the removal of chromium (Cr) from the environment, including adsorption, ion-exchange, bioremediation, etc. In this study, we isolated a Cr (VI)-resistant fungus, Purpureocillium lilacinum, from contaminated soil, which could reduce chromium. We also characterized a reductant activity of dichromate found in the cellular fraction of the fungus: optimal pH and temperature, effect of enzymatic inhibitors and enhancers, metal ions, use of electron donors, and initial Cr (VI) and protein concentration. This study also shows possible mechanisms that could be involved in the elimination of this metal. We observed an increase in the reduction of Cr (VI) activity in the presence of NADH followed by that of formate and acetate, as electron donor. This reduction was highly inhibited by EDTA followed by NaN₃ and KCN, and this activity showed the highest activity at an optimal pH of 7.0 at 37 °C with a protein concentration of 3.62 µg/mL.

Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview

Heavy metals bring long-term hazardous consequences and pose a serious threat to all life forms. Being non-biodegradable, they can remain in the food webs for a long period of time. Metal ions are essential for life and indispensable for almost all aspects of metabolism but can be toxic beyond threshold level to all living beings including microbes. Heavy metals are generally present in the environment, but many geogenic and anthropogenic activities has led to excess metal ion accumulation in the environment. To survive in harsh metal contaminated environments, bacteria have certain resistance mechanisms to metabolize and transform heavy metals into less hazardous forms. This also gives rise to different species of heavy metal resistant bacteria. Herein, we have tried to incorporate the different aspects of heavy metal toxicity in bacteria and provide an up-to-date and across-the-board review. The various aspects of heavy metal biology of bacteria encompassed in this review includes the biological notion of heavy metals, toxic effect of heavy metals on bacteria, the factors regulating bacterial heavy metal resistance, the diverse mechanisms governing bacterial heavy metal resistance, bacterial responses to heavy metal stress, and a brief overview of gene regulation under heavy metal stress.

Biotreatment potential of co-contaminants hexavalent chromium and polychlorinated biphenyls in industrial wastewater: Individual and simultaneous prospects

Co-existence of polychlorinated biphenyls (PCBs) and hexavalent chromium (Cr(VI)) in the environment due to effluent from industries has aggravated the pollution problem. Both contaminants can alter chemical interactions, processes and impair enzymatic activities in the ecosystem that results in negative impacts on aquatic and terrestrial life. Previously, research has been performed for the fate and transfer of these contaminants individually, but simultaneous removal approaches have not received much attention. Cr(VI) exists in a highly toxic form in the environment once released, whereas location of chlorine atoms in the ring determines PCBs toxicity. Lower chlorinated compounds are easily degradable whereas as high chlorinated compounds require sequential strategy for transformation. Microorganisms can develop different mechanism to detoxify both pollutants. However, occurrence of multiple contaminants in single system can alter the bioremediation efficiency of bacteria. Use of metal resistance bacterial for the degradation of organic compounds has been widely used bioaugmentation strategy. Along with that use of sorbents/bio sorbents, biosurfactants and phytoremediation approaches have already been well reported. Bioremediation strategy with dual potential to detoxify the Cr(VI) and PCBs would be a probable option for simultaneous biotreatment. Application of bioreactors and biofilms covered organic particles can be utilized as efficient bioaugmentation approach. In this review, biotreatment systems and bacterial oxidative and reductive enzymes/processes are explained and possible biotransformation pathway has been purposed for bioremediation of co-contaminated waters.

Bioreduction performances and mechanisms of Cr(VI) by Sporosarcina saromensis W5, a novel Cr(VI)-reducing facultative anaerobic bacteria

This study reported a novel facultative anaerobic Cr(VI)-reducing bacteria (Sporosarcina saromensis W5) and investigated its Cr(VI) removal performances and removal mechanisms. The strain W5 was able to grow and reduce Cr(VI) under aerobic and anaerobic environment, and exhibited considerable Cr(VI) reduction capabilities under a wide range of pH (8.0-13.0), temperature (20-40 °C) and initial Cr(VI) concentration (50-800 mg/L). The addition of Cd²⁺ severely inhibited its growth and Cr(VI) removal, while Cu²⁺ and Fe³⁺ significantly enhanced the removal efficiencies. The strain W5 could utilize various electron donors and mediators to accelerate Cr(VI) reduction. Aerobic Cr(VI) reduction mainly occurred in cytoplasm and the final products were soluble organo-Cr(III) complexes. Anaerobic Cr(VI) reduction was located in both cytoplasm and membrane, and the reduction products were soluble organo-Cr(III) complexes and Cr(III) precipitates. The functional groups of hydroxyl, carboxyl and phosphoryl on cell surface participated in the combination with Cr(III). Due to its facultative anaerobic property, S. saromensis W5 offers itself as a promising engineering strain for the bioremediation of Cr(VI)-contaminated areas, especially in hypoxia environments.

Chemical-Assisted Microbially Mediated Chromium (Cr) (VI) Reduction Under the Influence of Various Electron Donors, Redox Mediators, and Other Additives: An Outlook on Enhanced Cr(VI) Removal

Chromium (Cr) (VI) is a well-known toxin to all types of biological organisms. Over the past few decades, many investigators have employed numerous bioprocesses to neutralize the toxic effects of Cr(VI). One of the main process for its treatment is bioreduction into Cr(III). Key to this process is the ability of microbial enzymes, which facilitate the transfer of electrons into the high valence state of the metal that acts as an electron acceptor. Many underlying previous efforts have stressed on the use of different external organic and inorganic substances as electron donors to promote Cr(VI) reduction process by different microorganisms. The use of various redox mediators enabled electron transport facility for extracellular Cr(VI) reduction and accelerated the reaction. Also, many chemicals have employed diverse roles to improve the Cr(VI) reduction process in different microorganisms. The application of aforementioned materials at the contaminated systems has offered a variety of influence on Cr(VI) bioremediation by altering microbial community structures and functions and redox environment. The collective insights suggest that the knowledge of appropriate implementation of suitable nutrients can strongly inspire the Cr(VI) reduction rate and efficiency. However, a comprehensive information on such substances and their roles and biochemical pathways in different microorganisms remains elusive. In this regard, our review sheds light on the contributions of various chemicals as electron donors, redox mediators, cofactors, etc., on microbial Cr(VI) reduction for enhanced treatment practices.

Biotreatment of pyrene and Cr(VI) combined water pollution by mixed bacteria

Pyrene and chromium (Cr(VI)) are persistent pollutants and cause serious environmental problems because they are toxic to organisms and difficult to remediate. The toxicity of pyrene and Cr(VI) to three crops (cotton, soybean and maize) was confirmed by the significant decrease in root and shoot biomass during growth in pyrene/Cr(VI) contaminated hydroponic solution. Two bacterial strains capable of simultaneous pyrene biodegradation and Cr(VI) reduction were isolated and identified as Serratia sp. and Arthrobacter sp. A mixture of the isolated strains at a ratio of 1:1 was more efficient for biotreatment of pyrene and Cr(VI) than either strain alone; the mixture effectively carried out bioremediation of contaminated water in a hydroponic system mainly through pyrene biodegradation and Cr(VI) reduction. Application of these isolates shows potential for practical microbial remediation of pyrene and Cr(VI) combined water pollution.

Microbial Cd(II) and Cr(VI) resistance mechanisms and application in bioremediation

The heavy metals cadmium (Cd) and chromium (Cr) are extensively used in industry and result in water and soil contamination. The highly toxic Cd(II) and Cr(VI) are the most common soluble forms of Cd and Cr, respectively. They enter the human body through the food chain and drinking water and then cause serious illnesses. Microorganisms can adsorb metals or transform Cd(II) and Cr(VI) into insoluble or less bioavailable forms, and such strategies are applicable in Cd and Cr bioremediation. This review focuses on the highlighting of novel achievements on microbial Cd(II) and Cr(VI) resistance mechanisms and their bioremediation applications. In addition, the knowledge gaps and research perspectives are also discussed in order to build a bridge between the theoretical breakthrough and the resolution of Cd(II) and Cr(VI) contamination problems.

Cu(II) nonspecifically binding chromate reductase NfoR promotes Cr(VI) reduction

Cu(II)-enhanced microbial Cr(VI) reduction is common in the environment, yet its mechanism is unknown. The specific activity of chromate reductase, NfoR, from Staphylococcus aureus sp. LZ-01 was augmented 1.5-fold by Cu(II). Isothermal titration calorimetry and spectral data show that Cu(II) binds to NfoR nonspecifically. Further, Cu(II) stimulates the nitrobenzene reduction of NfoR, indicating that Cu(II) promotes electron transfer. The crystal structure of NfoR in complex with CuSO₄ (1.46 Å) was determined. The overall structure of NfoR-Cu(II) complex is a dimer that covalently binds with FMN and Cu(II)-binding pocket is located at the interface of the NfoR dimer. Structural superposition revealed that NfoR resembles the structure of class II chromate reductase. Site-directed mutagenesis revealed that Leu⁴⁶ and Phe¹²³ were involved in NADH binding, whereas Trp⁷⁰ and Ser⁴⁵ were the key residues for nitrobenzene binding. Furthermore, His¹⁰⁰ and Asp¹⁷¹ were preferential affinity sites for Cu(II) and that Cys¹⁶³ is an active site for FMN binding. Attenuation reductase activity in C163S can be partially restored to 54% wild type by increasing Cu(II) concentration. Partial restoration indicates dual-channel electron transfer of NfoR via Cu(II) and FMN. We propose a catalytic mechanism for Cu(II)-enhanced NfoR activity in which Cu(I) is formed transiently. Together, the current results provide an insight on Cu (II)-induced enhancement and benefit of Cr(VI) bioremediation.

Bioremediation potential of new cadmium, chromium, and nickel-resistant bacteria isolated from tropical agricultural soil

Soil management using fertilizers can modify soil chemical, biochemical and biological properties, including the concentration of trace-elements as cadmium (Cd), chromium (Cd) and nickel (Ni). Bacterial isolates from Cd, Cr, and Ni-contaminated soil were evaluated for some characteristics for their use in bioremediation. Isolates (592) were obtained from soil samples (19) of three areas used in three maize cultivation systems: no-tillage and conventional tillage with the application of mineral fertilizers; minimum tillage with the application of sewage sludge. Four isolates were resistant to Cr³⁺ (3.06 mmol dm^-3) and Cd²⁺ (2.92 mmol dm^-3). One isolate was resistant to the three metals at 0.95 mmol dm^-3. All isolates developed in a medium of Cd²⁺, Cr³⁺ and Ni²⁺ at 0.5 mmol dm^-3, and removed Cd²⁺ (17-33%) and Cr⁶⁺ (60-70%). They were identified by sequencing of the gene 16S rRNA, as bacteria of the genera Paenibacillus, Burkholderia, Ensifer, and two Cupriavidus. One of the Cupriavidus isolate was able to remove 60% of Cr⁶⁺ from the culture medium and showed high indole acetic acid production capacity. We evaluated it in a microbe-plant system that could potentially be deployed in bioremediation by removing toxic metals from contaminated soil.

Novel Biochemical Properties and Physiological Role of the Flavin Mononucleotide Oxidoreductase YhdA from Bacillus subtilis

Cr(VI) is mutagenic and teratogenic and considered an environmental pollutant of increasing concern. The use of microbial enzymes that convert this ion into its less toxic reduced insoluble form, Cr(III), represents a valuable bioremediation strategy. In this study, we examined the Bacillus subtilis YhdA enzyme, which belongs to the family of NADPH-dependent flavin mononucleotide oxide reductases and possesses azo-reductase activity as a factor that upon overexpression confers protection on B. subtilis from the cytotoxic effects promoted by Cr(VI) and counteracts the mutagenic effects of the reactive oxygen species (ROS)-promoted lesion 8-OxoG. Further, our in vitro assays unveiled catalytic and biochemical properties of biotechnological relevance in YhdA; a pure recombinant His10-YhdA protein efficiently catalyzed the reduction of Cr(VI) employing NADPH as a cofactor. The activity of the pure oxidoreductase YhdA was optimal at 30°C and at pH 7.5 and displayed Km and Vmax values of 7.26 mM and 26.8 μmol·min-1·mg-1 for Cr(VI), respectively. Therefore, YhdA can be used for efficient bioremediation of Cr(VI) and counteracts the cytotoxic and genotoxic effects of oxygen radicals induced by intracellular factors and those generated during reduction of hexavalent chromium.IMPORTANCE Here, we report that the bacterial flavin mononucleotide/NADPH-dependent oxidoreductase YhdA, widely distributed among Gram-positive bacilli, conferred protection to cells from the cytotoxic effects of Cr(VI) and prevented the hypermutagenesis exhibited by a MutT/MutM/MutY-deficient strain. Additionally, a purified recombinant His10-YhdA protein displayed a strong NADPH-dependent chromate reductase activity. Therefore, we postulate that in bacterial cells, YhdA counteracts the cytotoxic and genotoxic effects of intracellular and extracellular inducers of oxygen radicals, including those caused by hexavalent chromium.

Biosorption of Cr(VI) by Halomonas sp. DK4, a halotolerant bacterium isolated from chrome electroplating sludge

This study evaluated Cr(VI) biosorption by a halotolerant gram-negative bacterium Halomonas sp. DK4 isolated from chrome electroplating sludge. The bacterium could withstand high concentrations of Cr(VI) exhibiting a minimal inhibitory concentration (MIC) of 250 mg/L. Plackett-Burman design confirmed glucose, KH₂PO₄, NaCl, inoculum size, and initial Cr(VI) concentration as significant variables influencing the Cr(VI) removal ability of the bacterium. The suspended culture of Halomonas sp. DK4 was able to remove 81% (100 mg/L) of Cr(VI) in optimized MSM medium from aqueous solutions within 48 h. The bacterium also removed 59% Cr(VI) in the presence of 15% NaCl concentration within 72 h. The main mechanism involved in Cr(VI) removal by Halomonas sp. DK4 was determined to be biosorption which was best explained using the Langmuir isotherm model, wherein the maximum adsorption of 150.7 mg/g was observed under equilibrium conditions. Kinetic studies reveal that chemisorption of Cr(VI) by Halomonas sp. DK4 was a rate-limiting process which followed pseudo-second-order kinetics (R² = 0.99). Bacterial biomass exhibited maximum adsorption of 70.3% Cr(VI) at an initial concentration of 100 mg/L under optimal conditions. Fourier transform infrared spectroscopy (FTIR) analysis confirmed the presence of hydroxyl, carboxyl, amide, and phosphate groups on the bacterial surface which may be involved in Cr(VI) adsorption. Scanning electron microscopy coupled energy dispersive X-ray (SEM-EDX) analysis revealed morphological changes in the bacterial cell and accumulation of Cr(VI) on the cell surface. These results suggest the potential application of Halomonas sp. DK4 in the removal of Cr(VI) from saline chromium-containing industrial wastewaters.

Electricity production of microbial fuel cells by degrading cellulose coupling with Cr(VI) removal

A facultative exoelectrogen strain Lsc-8 belonging to the Cellulomonas genus with the ability to degrade carboxymethyl cellulose (CMC) coupled with the reduction of Cr(VI), was successfully isolated from rumen content. The maximum output power density of the microbial fuel cells (MFCs) inoculated strain Lsc-8 was 9.56 ± 0.37 mW·m^-2 with CMC as the sole carbon source. From the biomass analysis it can be seen that the electricity generation of the MFCs was primarily attributed to the planktonic cells of strain Lsc-8 rather than the biofilm attached on the electrode, which was different from Geobacter sulfurreducens. Especially, during electricity generation of the MFCs using CMC as carbon source in the anode chamber, the Cr(VI) reduction were simultaneously realized. And it is also found that the Cr(VI) reduction ratio by strain Lsc-8 is directly related to the initial Cr(VI) concentration, and it increased with the increase of initial Cr(VI) concentration at first, then started to decrease when the Cr(VI) concentration was above 21 mg ·L^-1. Meanwhile, the highest output power density of 3.47 ± 0.28 mW·m^-2 was observed coupling with 95.22 ± 2.72 % of Cr(VI) reduction. These data suggested that the strain Lsc-8 could reduce high toxicity Cr(VI) to low toxicity Cr(III) coupled with electricity generation in MFCs with CMC as the carbon source. Our results also suggested that this study will provide a possibility to simultaneously degrade Cr(VI) and generate electricity by using cellulose as the carbon source via MFCs.

The Role of Microbial Mats in the Removal of Hexavalent Chromium and Associated Shifts in Their Bacterial Community Composition

Microbial mats are rarely reported for chromium-polluted ecosystems, hence information on their bacterial diversity and role in chromium removal are very scarce. We investigated the role of nine microbial mats, collected from three quarry sumps of chromium mining sites, in the removal of hexavalent chromium [Cr(VI)]. Bacterial diversity in these mats and community shifts after incubation with Cr(VI) have been investigated using MiSeq sequencing. In nature, a chromium content of 1,911 ± 100 mg kg^–1 was measured in the microbial mats, constituting the third highest source of environmentally available chromium. The mats were able to remove 1 mg l^–1 of Cr(VI) in 7 days under aerobic conditions. MiSeq sequencing of the original mats yielded 46–99% of the sequences affiliated to Proteobacteria, Firmicutes and Actinobacteria. When the mats were incubated with Cr(VI), the bacterial community shifted in the favor of Alphaproteobacteria and Verrucomicrobiae. We conclude that microbial mats in the quarry sumps harbor diverse microorganisms with the ability to remove toxic Cr(VI), hence these mats can be potentially used to remove chromium from polluted waters.

Optimizing the Management of Cadmium Bioremediation Capacity of Metal-Resistant Pseudomonas sp. Strain Al-Dhabi-126 Isolated from the Industrial City of Saudi Arabian Environment

In this study, 23 bacterial strains were isolated from a Cadmium (Cd) contaminated soil in the industrial city, Riyadh of Saudi Arabia. Among these isolates six strains were found to withstand cadmium contamination and grow well. From the six isolates Pseudomonas sp. strain Al-Dhabi-122-127 were found to resist cadmium toxicity to a higher level. The isolates were subjected to biochemical and 16S rDNA gene sequence characterization to confirm their identification. The bacterial strain Al-Dhabi-124 showed 1.5 times higher Cd-degrading activity than Al-Dhabi-122 and Al-Dhabi-123, and Al-Dhabi-126 exhibited 3.5 times higher Cd-degrading activity, higher than the other strains. An atomic absorption spectrophotometer study showed that the strain Al-Dhabi-126 absorbed Cd, and that the bacterial strain Al-Dhabi-126 was found to tolerate cadmium level up to 2100 µg/mL. The bacterial strain Al-Dhabi-126 showed a maximum Cd removal efficacy at pH between 6.0 and 8.0. The efficacy decreased sharply after an increase in pH (9.0). An optimum temperature of 50 °C and pH 6.0 were found to be effective for the Cd removal process by the isolate. The study indicated that the bacterial strain Al-Dhabi-126 can be used effectively for the bioremediation of heavy metals like cadmium, a major toxic pollutant in industrial effluents.

Monitoring Cr toxicity and remediation processes - combining a whole-cell bioreporter and Cr isotope techniques

Bioremediation is a sustainable and cost-effective means of contaminant detoxification. Although Cr(VI) is toxic at high concentrations, various microbes can utilise it as an electron accepter in the bioremediation process, and reduce it to the less toxic form Cr(III). During remediation, it is important to monitor the level of toxicity and effectiveness of Cr(VI) reduction in order to optimize the conditions. This study employed a whole-cell bioreporter Acinetobacter baylyi ADPWH-recA to access the degree of toxicity of different species of Cr over a range of initial concentrations. It also investigated whether Cr isotope fractionation factors were impacted by different levels of Cr toxicity (related to its concentration) and Cr(VI) reduction rates by Cr resistant bacteria Pseudomonas fluorescens LB 300. The results show that, of both Cr₂O₇^2- and CrO₄^2-, the whole-cell bioreporter was efficient in indicating the level of genotoxicity of Cr(VI) at low concentrations and cytotoxicity at high concentrations via variations of bioluminescence. High concentrations (> 100 mg/L) of Cr(III) could also strongly induce the luminescence in the bioreporter, indicating DNA damage at such abundance. Pseudomonas fluorescens LB 300 was found to be effective in reducing Cr(VI) even when the concentration was high (40 mg/L); however, complete Cr(VI) reduction was only observed at low concentrations (< 5 mg/L), since the toxicity of high concentrations of Cr(VI) impacted the effectiveness of reduction by the bacteria. During reduction, the C53r/C52r ratio of remaining Cr(VI) increased from its initial value, and the calculated fractionation factor by bacterial Cr(VI) reduction (ε) was -3.1±0.3‰. The fractionation factor was independent of the initial Cr(VI) concentration. Therefore, a single Cr isotope fractionation factor can be effectively applied in indicating the extent of bioremediation processing of Cr(VI) over a wide range of concentrations. This significantly simplified monitoring of Cr(VI) depletion in bioremediation, since variations of ε normally indicate a change in the reduction mechanism and therefore would complicate the elucidation of processes driving the remediation.

Cr(VI) reduction by an extracellular polymeric substance (EPS) produced from a strain of Pseudochrobactrum saccharolyticum

A better understanding of the Cr(VI) reduction position and mechanisms by a Cr(VI)-reducing strain is important for the bioremediation of Cr pollution in the environment. In the present study, we were interested in figuring out the role of extracellular polymeric substances (EPS) as the main area for Cr(VI) reduction in the newly reported strain of Pseudochrobactrum saccharolyticum LY10. We investigated the subcellular distribution and reduction capability of each cellular component as the main area of Cr(VI) reduction by scanning electron microscopy and soft X-ray spectromicroscopy. The results suggested that most of Cr was presented in the supernatants as Cr(III) after reduction. In the cells, Cr was mostly distributed in the EPS and cell wall, while the EPS had the maximum Cr(VI) reduction rate (81.5%) as compared with the cell wall (30.1%). Soft X-ray spectromicroscopy analysis indicated that Cr accumulated more in the EPS. Therefore, the results suggested that the EPS were the main area for Cr(VI) reduction in the bacteria of P. saccharolyticum LY10.

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics

A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5–20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0–16 μg ml⁻¹, chloramphenicol 0–24 μg ml⁻¹, and vancomycin 0–24 μg ml⁻¹). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates’ ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.

Draft Genome Sequences of Two Bacillus sp. Strains and Four Cellulomonas sp. Strains Isolated from Heavy-Metal-Contaminated Soil

We present the draft genome sequence for Bacillus sp. strain PF3, Bacillus sp.

We present the draft genome sequence for Bacillus sp. strain PF3, Bacillus sp. strain K6W, Cellulomonas sp. strain B12, Cellulomonas sp. strain K38, Cellulomonas sp. strain K39, and Cellulomonas sp. strain K42B. These bacteria were isolated from contaminated soils, and their genomes contain genes related to chromate transport and reduction.

Draft Genome Sequence of Shewanella algidipiscicola H1, a Highly Chromate-Resistant Strain Isolated from Mediterranean Marine Sediments

The ability of different Shewanella spp. to convert heavy metals and toxic substances into less toxic products by using them as electron acceptors has led to their use in environmental clean-up strategies.

The ability of different Shewanella spp. to convert heavy metals and toxic substances into less toxic products by using them as electron acceptors has led to their use in environmental clean-up strategies. We present here the draft genome sequence of Shewanella algidipiscicola H1, a strain resistant to high concentrations of chromates.

Co-expression of YieF and PhoN in Deinococcus radiodurans R1 improves uranium bioprecipitation by reducing chromium interference

Overexpression of the enzyme phosphatase (PhoN/PhoK) in the radiation-resistant bacterium Deinococcus radiodurans could be an efficient strategy for uranium remediation. However, the presence of other metals in nuclear wastes often interferes with uranium bioprecipitation. In our study, the uranium-precipitating ability of the PhoN-expressing D. radiodurans strain (Deino-phoN) significantly decreased by 45.4% in 13 h in the presence of chromium (VI); however, it was partially recovered after supplementation with chromium (III). Therefore, the reduction of chromium (VI) to chromium (III) was obtained by the co-expression of the YieF protein and PhoN in D. radiodurans (Deino-phoN-yieF). As a result, an increase in the chromium (VI) reduction (25.1%) rate was observed in 24 h. Furthermore, uranium precipitation also increased by 28.0%. For the decontamination of groundwater, we immobilized Deino-phoN-yieF cells using Polyvinyl alcohol (PVA)-sodium alginate (SA) beads, followed by incubation in a bioreactor. Approximately 99% of chromium (VI) and uranium (VI) was removed after 4 continuous cycles operated for a period of over 20 days at room temperature (25 °C). Therefore, Deino-phoN-yieF could be used as a potential biological agent for mixed radioactive nuclear waste remediation.

The Cytochrome bd Complex Is Essential for Chromate and Sulfide Resistance and Is Regulated by a GbsR-Type Regulator, CydE, in Alishewanella Sp. WH16-1

Sulfate-reducing bacteria are a group of microorganisms that use sulfate as an electron acceptor. These bacteria are useful in the bioremediation of heavy metal pollution since they can reduce/precipitate metals. Previously, we identified the Alishewanella strain WH16-1 from soil of a copper and iron mine and determined that it can reduce sulfate and chromate and that it was tolerant to many heavy metals. In this study, we investigated the chromate reduction mechanism of strain WH16-1 through Tn5 transposon mutagenesis. A cytochrome bd (cytbd) Tn5 mutant was generated (Δcytbd), and a detail analysis showed that the following: (1) gene cydE (coding for a GbsR-type regulator) was co-transcribed with the two subunits coding genes of the Cytochrome bd complex (Cytbd), namely, cydA and cydB, based on RT-PCR analysis, and similar gene arrangements were also found in other Alteromonadaceae family strains; (2) the chromate resistance level was dramatically decreased and chromate reduction efficiency also decreased in strain Δcytbd compared to the wild-type and a complemented strain (Δcytbd-C); (3) Cytbd could catalyze the decomposition of H₂O₂ according to the analyses of H₂O₂ decomposition ability, cellular H₂O₂ contents, H₂O₂ inhibition zone, and H₂O₂ sensitivity tests; (4) surprisingly, chromate was not an inducer of the expression of Cytbd, but sulfate induced expression of Cytbd, and sulfate/sulfide resistance levels were also decreased in the Δcytbd strain; (5) the addition of sulfate enhanced the chromate resistance level and reduction efficiency; (6) Cytbd expression was repressed by CydE and derepressed by sulfate based on an in vivo bacterial one hybrid system and in vitro EMSA tests; and (7) DNA footprinting and short-fragment EMSA tests revealed two binding sites of CydE in its promoter region. All these results showed that Cytbd is negatively regulated by CydE and derepressed by sulfate. In addition, Cytbd contributes to the resistance of sulfate and sulfide, and sulfide could be used as a reductant to reduce chromate. Moreover, Cytbd is essential to decompose H₂O₂ to decrease cellular oxidative stress. Thus, the regulation and function of Cytbd may explain why sulfate could enhance chromate reduction.

The effect of electron competition on chromate reduction using methane as electron donor

We studied the effect of electron competition on chromate (Cr(VI)) reduction in a methane (CH₄)-based membrane biofilm reactor (MBfR), since the reduction rate was usually limited by electron supply. A low surface loading of SO₄^2- promoted Cr(VI) reduction. The Cr(VI) removal percentage increased from 60 to 70% when the SO₄^2- loading increased from 0 to 4.7 mg SO₄^2-/m²-d. After the SO₄^2- loading decreased back to zero, the Cr(VI) removal further increased to 90%, suggesting that some sulfate-reducing bacteria (SRB) stayed in the reactor to reduce Cr(VI). However, a high surface loading of SO₄^2- (26.6 mg SO₄^2-/m²-d) significantly slowed down the Cr(VI) reduction to 40% removal, which was probably due to competition between Cr(VI) and SO₄^2- reduction. Similarly, when 0.5 mg/L of Se(VI) was introduced into the MBfR, Cr(VI) removal percentage slightly decreased to 60% and then increased to 80% when input Se(VI) was removed again. The microbial community strongly depended on the loadings of Cr(VI) and SO₄^2-. In the sulfate effect experiment, three genera were dominant. Based on the correlation between the abundances of the three genera and the loadings of Cr(VI) and SO₄^2-, we conclude that Methylocystis, a type II methanotroph, reduced both Cr(VI) and sulfate, Meiothermus only reduced Cr(VI), and Ferruginibacter only reduced SO₄^2-.

Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula

The Psychrobacter genus is a cosmopolitan and diverse group of aerobic, cold-adapted, Gram-negative bacteria exhibiting biotechnological potential for low-temperature applications including bioremediation. Here, we present the draft genome sequence of a bacterium from the Psychrobacter genus isolated from a sediment sample from King George Island, Antarctica (3,490,622 bp; 18 scaffolds; G + C = 42.76%). Using phylogenetic analysis, biochemical properties and scanning electron microscopy the bacterium was identified as Psychrobacter glacincola BNF20, making it the first genome sequence reported for this species. P. glacincola BNF20 showed high tellurite (MIC 2.3 mM) and chromate (MIC 6.0 mM) resistance, respectively. Genome-wide nucleotide identity comparisons revealed that P. glacincola BNF20 is highly similar (>90%) to other uncharacterized Psychrobacter spp. such as JCM18903, JCM18902, and P11F6. Bayesian multi-locus phylogenetic analysis showed that P. glacincola BNF20 belongs to a polyphyletic clade with other bacteria isolated from polar regions. A high number of genes related to metal(loid) resistance were found, including tellurite resistance genetic determinants located in two contigs: Contig LIQB01000002.1 exhibited five ter genes, each showing putative promoter sequences (terACDEZ), whereas contig LIQB1000003.2 showed a variant of the terZ gene. Finally, investigating the presence and taxonomic distribution of ter genes in the NCBI’s RefSeq bacterial database (5,398 genomes, as January 2017), revealed that 2,623 (48.59%) genomes showed at least one ter gene. At the family level, most (68.7%) genomes harbored one ter gene and 15.6% exhibited five (including P. glacincola BNF20). Overall, our results highlight the diverse nature (genetic and geographic diversity) of the Psychrobacter genus, provide insights into potential mechanisms of metal resistance, and exemplify the benefits of sampling remote locations for prospecting new molecular determinants.

Reduction of Hexavalent Chromium and Detection of Chromate Reductase (ChrR) in Stenotrophomonas maltophilia

An Gram negative strain of S. maltophilia, indigenous to environments contaminated by Cr(VI) and identified by biochemical methods and 16S rRNA gene analysis, reduced chromate by 100%, 98-99% and 92% at concentrations in the 10-70, 80-300, and 500 mg/L range, respectively at pH 7 and temperature 37 °C. Increasing concentrations of Cr(VI) in the medium lowered the growth rate but could not be directly correlated with the amount of Cr(VI) reduced. The strain also exhibited multiple resistance to antibiotics and tolerance and resistance to various heavy metals (Ni, Zn and Cu), with the exception of Hg. Hexavalent chromium reduction was mainly associated with the soluble fraction of the cell evaluated with crude cell-free extracts. A protein of molecular weight around 25 kDa was detected on SDS-PAGE gel depending on the concentration of hexavalent chromium in the medium (0, 100 and 500 mg/L). In silico analysis in this contribution, revealed the presence of the chromate reductase gene ChrR in S. maltophilia, evidenced through a fragment of around 468 bp obtained experimentally. High Cr(VI) concentration resistance and high Cr(VI) reducing ability of the strain make it a suitable candidate for bioremediation.

Relationship of Biodiversity with Heavy Metal Tolerance and Sorption Capacity: A Meta-Analysis Approach

Microbial remediation of metals can alleviate the concerns of metal pollution in the environment. The microbial remediation, however, can be a complex process since microbial metal resistance and biodiversity can play a direct role in the bioremediation process. This study aims to understand the relationships among microbial metal resistance, biodiversity, and metal sorption capacity. Meta-analyses based on 735 literature data points of minimum inhibitory concentrations (MIC) of Plantae, Bacteria, and Fungi exposed to As, Cd, Cr Cu, Ni, Pb, and Zn showed that metal resistance depends on the microbial Kingdom and the type of heavy metal and that consortia are significantly more resistant to heavy metals than pure cultures. A similar meta-analysis comparing 517 MIC values from different bacterial genera (Bacillus, Cupriavidus, Klebsiella, Ochrobactrum, Paenibacillus, Pseudomonas, and Ralstonia) confirmed that metal tolerance depends on the type of genus. Another meta-analysis with 195 studies showed that the maximum sorption capacity is influenced by microbial Kingdoms, the type of biosorbent (whether consortia or pure cultures), and the type of metal. This study also suggests that bioremediation using microbial consortia is a valid option to reduce environmental metal contaminations.

ChrASO, the chromate efflux pump of Shewanella oneidensis, improves chromate survival and reduction

The chromate efflux pump encoding gene chrASO was identified on the chromosome of Shewanella oneidensis MR1. Although chrASO is expressed without chromate, its expression level increases when Cr(VI) is added. When deleted, the resulting mutant ΔchrASO exhibits a chromate sensitive phenotype compared to that of the wild-type strain. Interestingly, heterologous expression of chrASO in E. coli confers resistance to high chromate concentration. Moreover, expression of chrASO in S. oneidensis and E. coli significantly improves Cr(VI) reduction. This effect could result either from extracytoplasmic chromate reduction or from a better cell survival leading to enhanced Cr(VI) reduction.

The naphthalene catabolic protein NahG plays a key role in hexavalent chromium reduction in Pseudomonas brassicacearum LZ-4

Soil contamination by PAH and heavy metals is a growing problem. Here, we showed that a new isolate, Pseudomonas brassicacearum strain LZ-4, can simultaneously degrade 98% of 6 mM naphthalene and reduce 92.4% of 500 μM hexavalent chromium [Cr (VI)] within 68 h. A draft genome sequence of strain LZ-4 (6,219,082 bp) revealed all the genes in the naphthalene catabolic pathway and some known Cr (VI) reductases. Interestingly, genes encoding naphthalene pathway components were upregulated in the presence of Cr (VI), and Cr (VI) reduction was elevated in the presence of naphthalene. We cloned and expressed these naphthalene catabolic genes and tested for Cr (VI) reduction, and found that NahG reduced 79% of 100 μM Cr (VI) in 5 minutes. Additionally, an nahG deletion mutant lost 52% of its Cr (VI) reduction ability compared to that of the wild-type strain. As nahG encodes a salicylate hydroxylase with flavin adenine dinucleotide (FAD) as a cofactor for electron transfer, Cr (VI) could obtain electrons from NADH through NahG-associated FAD. To the best of our knowledge, this is the first report of a protein involved in a PAH-degradation pathway that can reduce heavy metals, which provides new insights into heavy metal-PAH contamination remediation.

Detoxification of hexavalent chromate by growing Paecilomyces lilacinus XLA

In the study, the capability of Paecilomyces lilacinus XLA (CCTCC: M2012135) to reduce Cr⁶⁺ and its main antagonistic mechanisms to Cr⁶⁺ were experimentally evaluated. Activated growing fungus XLA efficiently reduced over 90% Cr⁶⁺ in the media with Cr⁶⁺ concentration below 100 mg L^-1 at pH 6 after 14 days. After 1-day exposure to 100 mg L^-1 Cr⁶⁺, nearly 50% of Cr⁶⁺ was reduced. Moreover, SO₄^2- stimulated Cr⁶⁺ reduction, whereas other interferential ions inhibited Cr⁶⁺ reduction. The interaction mechanisms between XLA and Cr⁶⁺ mainly involve biotransformation, biosorption, and bioaccumulation, as detected by electron microscopy and chemical methods. The lower concentrations of Cr⁶⁺ (5 and 50 mg L^-1) stimulated the activities of superoxide dismutase (SOD), catalase (CAT) and glutathione (GSH) level in XLA, respectively, but the higher concentration of Cr⁶⁺ (150 mg L^-1) decreased the enzymatic activities and GSH concentration. The results implied that SOD, CAT and GSH were defensive guards to the oxidant stress produced by Cr⁶⁺. All these extracellular/intracellular defense systems endowed XLA with the ability to resist and detoxify Cr⁶⁺ by transforming its valent species. The fungus XLA could efficiently reduce Cr⁶⁺ under different environmental conditions (pH, interferential ions, and concentration). Moreover, XLA could endure the high concentration of Cr⁶⁺ probably due to its high biotransformation capability of Cr⁶⁺ and intracellular antioxidant systems for the detoxification of ROS generated by external Cr⁶⁺. All these results suggested that the fungus XLA can be applied to remediation of Cr⁶⁺-contaminated environments.

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site

Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.

Cr(VI) reduction and Cr(III) immobilization by resting cells of Pseudomonas aeruginosa CCTCC AB93066: spectroscopic, microscopic, and mass balance analysis

The aim of this study was to investigate the mechanism of Cr(VI) reduction and Cr(III) immobilization by resting cells of Pseudomonas aeruginosa using batch experiments and analysis techniques. Data showed that resting cells of this strain (3.2 g/L dry weight) reduced 10 mg/L of Cr(VI) by 86% in Tris-HCl buffer solution under optimized conditions of 5 g/L of sodium acetate as an electron donor, pH of 7.0 and temperature of 37 °C within 24 h. Cr(VI) was largely converted to nontoxic Cr(III), and both soluble crude cell-free extracts and membrane-associated fractions were responsible for Cr(VI) reduction. While remnant Cr(VI) existed only in the supernatant, the content of resultant Cr(III) in supernatant, on cell surface and inside cells was 2.62, 1.06, and 5.07 mg/L, respectively, which was an indicative of extracellular and intracellular reduction of chromate. Scanning electron microscopy analysis combined with energy dispersive X-ray spectroscopy revealed the adsorption of chromium on the bacterial surface. Interaction between Cr(III) and cell surface functional groups immobilized Cr(III) as indicated by Fourier transform infrared analyses and X-ray photoelectron spectroscopy. Transmission electron microscopy revealed Cr(III) precipitates in bacterial interior suggesting that Cr(II) could also be intracellularly accumulated. Thus, it can be concluded that interior and exterior surfaces of resting P. aeruginosa cells were sites for reduction and immobilization of Cr(VI) and Cr(III), respectively. This is further insight into the underlying mechanisms of microbial chromate reduction.