Chromate-reducing properties of soluble flavoproteins from Pseudomonas putida and Escherichia coli

Genomic and proteomic analyses reveal the reduction mechanism of hexavalent chromium by the culturing supernatant of strain Pediococcus acidilactici 13-7

This study used lactic acid bacteria with high antioxidative properties to screen for strains capable of reducing hexavalent chromium [Cr (VI)] in their culturing supernatants. The strain Pediococcus acidilactici 13-7 exhibited potent Cr (VI)-reducing capability and remarkable resistance to Cr (VI) even at concentration as high as 24 mM. Comparative genomics analysis revealed a unique gene, ChrR, associated with Cr (VI) reduction in this strain, distinguishing it from four reference strains of P. acidilactici. The proteomic investigation identified proteins linked to the ChrR gene, such as nqo1, frdA, and gshR, indicating significant enrichment in redox-related functions and oxidative phosphorylation pathways. These findings suggest that P. acidilactici 13-7 possesses superior electron transfer capacity compared to other strains, making it more adaptable under highly oxidative conditions by modulating the external environment to mitigate oxidative stress. Collectively, the results demonstrated the potential application of this lactic acid bacterial strain for bioremediation of heavy metals by its ability to reduce Cr (VI), and shed light on the molecular mechanisms underlying Cr (VI) reduction of the strain P. acidilactici 13-7.

Aspergillus niger Ochratoxinase Is a Highly Specific, Metal-Dependent Amidohydrolase Suitable for OTA Biodetoxification in Food and Feed

Microbial enzymes can be used as processing aids or additives in food and feed industries. Enzymatic detoxification of ochratoxin A (OTA) is a promising method to reduce OTA content. Here, we characterize the full-length enzyme ochratoxinase (AnOTA), an amidohydrolase from Aspergillus niger. AnOTA hydrolyzes OTA and ochratoxin B (OTB) mycotoxins efficiently and also other substrates containing phenylalanine, alanine, or leucine residues at their C-terminal position, revealing a narrow specificity profile. AnOTA lacks endopeptidase or aminoacylase activities. The structural basis of the molecular recognition by AnOTA of OTA, OTB, and a wide array of model substrates has been investigated by molecular docking simulation. AnOTA shows maximal hydrolytic activity at neutral pH and high temperature (65 °C) and retained high activity after prolonged incubation at 45 °C. The reduction of OTA levels in food products by AnOTA has been investigated using several commercial plant-based beverages. The results showed complete degradation of OTA with no detectable modification of beverage proteins. Therefore, the addition of AnOTA seems to be a useful procedure to eliminate OTA in plant-based beverages. Moreover, computational predictions of in vivo characteristics indicated that AnOTA is neither an allergenic nor antigenic protein. All characteristics found for AnOTA supported the suitability of its use for OTA detoxification in food and feed.

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.

Role of chromium reductases, antioxidants, and biosorption against oxidative damage of metals by Bacillus cereus

Current research was performed to look for the performance of Bacillus cereus PY3 for metal detoxification. Strain PY3 was recognized as B. cereus using 16 S rRNA. Higher rate of removal of Zn and Cr (VI) by PY3 was obtained between pH 6-8 and 100-500 µg/mL in 24 h. Highest removal of Cr6+ by strain PY3 was achieved at acidic, neutral, and alkaline atmosphere, 100-300 µg Cr6+ /mL and 25-35°C. Supernatant of PY3 detoxified Cr6+ into Cr3+ then cell pellet (debris) adsorbed them. The mechanism of metal removal was due to the release of cytolic extracts. Release of antioxidants and bio-film played a protective role against cell damage. Metals increased antioxidants and bio-film formation. SEM images showed the smooth external structure of PY3 when cells were exposed to metals thus confirming the role of cells for detoxification. Results Above facts conclude that PY3 can remove metallic pollution in polluted soil.

A new and promiscuous α/β hydrolase from Acinetobacter tandoii DSM 14970 T inactivates the mycotoxin ochratoxin A

The presence of ochratoxin A (OTA) in food and feed represents a serious concern since it raises severe health implications. Bacterial strains of the Acinetobacter genus hydrolyse the amide bond of OTA yielding non-toxic OTα and L-β-phenylalanine; in particular, the carboxypeptidase PJ15_1540 from Acinetobacter sp. neg1 has been identified as an OTA-degrading enzyme. Here, we describe the ability to transform OTA of cell-free protein extracts from Acinetobacter tandoii DSM 14970 T, a strain isolated from sludge plants, and also report on the finding of a new and promiscuous α/β hydrolase (ABH), with close homologs highly distributed within the Acinetobacter genus. ABH from A. tandoii (AtABH) exhibited amidase activity against OTA and OTB mycotoxins, as well as against several carboxypeptidase substrates. The predicted structure of AtABH reveals an α/β hydrolase core composed of a parallel, six-stranded β-sheet, with a large cap domain similar to the marine esterase EprEst. Further biochemical analyses of AtABH reveal that it is an efficient esterase with a similar specificity profile as EprEst. Molecular docking studies rendered a consistent OTA-binding mode. We proposed a potential procedure for preparing new OTA-degrading enzymes starting from promiscuous α/β hydrolases based on our results. KEY POINTS: • AtABH is a promiscuous αβ hydrolase with both esterase and amidohydrolase activities • AtABH hydrolyses the amide bond of ochratoxin A rendering nontoxic OTα • Promiscuous αβ hydrolases are a possible source of new OTA-degrading enzymes.

Arbuscular mycorrhizal fungi alter rhizosphere fungal community characteristics of Acorus calamus to improve Cr resistance

To investigate changes in fungal community characteristics under different Cr(VI) concentration stresses and the advantages of adding arbuscular mycorrhizal fungi (AMF), we used high throughput sequencing to characterize the fungal communities. Cr(VI) stress reduced rhizosphere soil SOM (soil organic matter) content and AMF addition improved this stress phenomenon. There were significant differences in fungal community changes under different Cr(VI) concentrations. The fungal community characteristics changed through inhibition of fungal metabolic ability, as fungal abundance increased after AMF addition, and the fungal diversity increased under high Cr(VI) concentration. The dominant phyla were members of the Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. Dominant groups relevant to Cr resistance were Ascomycota and Basidiomycota fungi. Moreover, Fungal community characteristics were analyzed using high-throughput sequencing of the cytochrome c metabolic pathway, NADH dehydrogenase, and NADH: ubiquinone reductase and all these functions were enhanced after AMF addition. Therefore, Cr(VI) stress significantly affects fungal community structure, while AMF addition could increase its SOM content, and metabolic capacity, and improve fungal community tolerance to Cr stress. This study contributed to the understanding response of rhizosphere fungal community in AMF-assisted wetland phytoremediation under Cr stress.

Cr(VI) removal from wastewater using nano zero-valent iron and chromium-reducing bacteria

Significant global efforts are currently underway to alleviate the presence of toxic metals in water bodies, aiming to encourage a sustainable environment. Nevertheless, the scientific community has yet to methodically inspect the performance and mechanisms underlying the interaction between nanomaterials and microorganisms in this context. Therefore, this study seeks to address this knowledge gap by developing a novel system that integrates nano zero-valent iron (nZVI) with chromium-reducing bacteria (CrRB) to efficiently remove Cr(VI) from water sources. The combined use of RBC600 and CrRB resulted in a Cr(VI) removal rate of 77.73%, displaying a substantial improvement of 17.61% compared to the use of CrRB alone. The efficacy of Cr(VI) elimination was observed to be affected by several factors within the system, such as the pH value, the quantity of nZVI added, the degree of CrRB inoculation, and the initial concentration of Cr(VI) at the onset of the experiment. When the pH was adjusted to 5, the complete removal of 200 mg/L Cr(VI) was achieved within 36 h. Increasing the dosage of nZVI to above 2 g/L resulted in the complete elimination of Cr(VI) from the solution within 72 h. This can be attributed to the availability of more reaction sites for the reduction of Cr(VI), facilitated by the higher nZVI dose. Additionally, the increased dose of nZVI allowed for the dissolution of more reactive Fe(II) ions. The characterization analysis, high-throughput sequencing, and fluorescence quantitative PCR results have established that CrRB and its extracellular polymer effectively reduce and complex Cr(VI). This process facilitated the dissolution of the passivated layer on the surface of nZVI, thus significantly enhancing the efficiency of nZVI in responding to Cr(VI). Additionally, the presence of nZVI created a favorable living environment for CrRB, resulting in increased richness and diversity within the CrRB community. These findings provide valuable preliminary insights into the mechanism underlying Cr(VI) elimination by the synergistic interaction between nZVI and CrRB. Therefore, this study establishes a solid theoretical foundations for the application of nano-bio synergy in the remediation of Cr(VI).

Facilitating New Chromium Reducing Microbes to Enhance Hexavalent Chromium Reduction by In Situ Sonoporation-Mediated Gene Transfer in Soils

Chromium (Cr) is a heavy metal with a high toxicity and pathogenicity. Microbial reduction is an effective strategy to remove Cr(VI) at contaminated sites but suffers from the low populations and activities of Cr-reducing microorganisms in soils. This study proposed an in situ sonoporation-mediated gene transfer approach, which improved soil Cr(VI) reduction performance by delivering exogenous Cr-transporter chrA genes and Cr-reducing yieF genes into soil microorganisms with the aid of ultrasound. Besides the increasing populations of Cr-resistant bacteria and elevated copy numbers of chrA and yieF genes after sonoporation-mediated gene transfer, three new Cr-reducing strains were isolated, among which Comamonas aquatica was confirmed to obtain Cr-resistant capability. In addition, sonoporation-mediated gene transfer was the main driving force significantly shaping soil microbial communities owing to the predominance of Cr-resistant microbes. This study pioneered and evidenced that in situ soil sonoporation-mediated gene transfer could effectively deliver functional genes into soil indigenous microbes to facilitate microbial functions for enhanced bioremediation, e.g., Cr-reduction in this study, showing its feasibility as a chemically green and sustainable remediation strategy for heavy metal contaminated sites.

An In Silico Bioremediation Study to Identify Essential Residues of Metallothionein Enhancing the Bioaccumulation of Heavy Metals in Pseudomonas aeruginosa

Microorganisms are ubiquitously present in the environment and exert significant influence on numerous natural phenomena. The soil and groundwater systems, precipitation, and effluent outfalls from factories, refineries, and waste treatment facilities are all sources of heavy metal contamination. For example, Madinah, Saudi Arabia, has alarmingly high levels of lead and cadmium. The non-essential minerals cadmium (Cd) and lead (Pb) have been linked to damage to vital organs. Bioremediation is an essential component in the process of cleaning up polluted soil and water where biological agents such as bacteria are used to remove the contaminants. It is demonstrated that Pseudomonas aeruginosa (P. aeruginosa) isolated from activated sludge was able to remove Cd and Pb from water. The protein sequence of metallothionein from P. aeruginosa was retrieved to explore it for physicoparameters, orthologs, domain, family, motifs, and conserved residues. The homology structure was generated, and models were validated. Docking of the best model with the heavy metals was carried out to inspect the intramolecular interactions. The target protein was found to belong to the "metallothionein_pro" family, containing six motifs, and showed a close orthologous relationship with other heavy metal-resistant bacteria. The best model was generated by Phyre2. In this study, three key residues of metallothionein were identified that participate in heavy metal (Pb and Cd) binding, viz., Ala33, Ser34, and Glu59. In addition, the study provides an essential basis to explore protein engineering for the optimum use of metallothionein protein to reduce/remove heavy metals from the environment.

Assessing the Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin Redox Potential Estimation

Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from Clostridium Beijerinckii and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes.

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.

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

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).

The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986T is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity

The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986^T (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.

Antibiotic and metal resistance of Stenotrophomonas maltophilia isolates from Eboling permafrost of the Tibetan Plateau

Whole-genome sequencing of pathogenic bacteria Stenotrophomonas maltophilia from a less polluted environment of permafrost can help understand the intrinsic resistome of both antibiotics and metals. This study aimed to examine the maximum minimum inhibitory concentration (MIC) of both antibiotics and metals, as well as antibiotic resistance genes and metal resistance genes annotated from whole-genome sequences. The permafrost S. maltophilia was sensitive to ciprofloxacin, tetracycline, streptomycin, and bacitracin, and resistant to chloramphenicol, trimethoprim-sulfamethoxazole, erythromycin, Zn²⁺, Ni²⁺, Cu²⁺, and Cr⁶⁺, with a lower maximum MIC, compared with clinical S. maltophilia. The former strain belonged to the lower antibiotic resistance gene (ARG) and metal resistance gene (MRG) clusters compared with the latter ones. The permafrost strain contained no or only one kind of ARG or MRG on a single genomic island, which explained the aforementioned lower maximum MIC and less diversity of ARGs or MRGs. The result indicated that the co-occurrence of antibiotic and metal resistance was due to a certain innate ability of S. maltophilia. The continuous human use of antibiotics or metals induced selective pressure, resulting in higher MIC and more diverse ARGs and MRGs in human-impacted environments.

The degradation of an aromatic organic compound by Aspergillus niger var tubingensis Ed8 produces metabolites that reduce Cr (VI)

Chromium Cr(VI) is a highly toxic environmental contaminant for any organism, its presence in the environment is mainly due to anthropogenic activities. The use of biotechnology has been implemented for the treatment of effluents contaminated with Cr(VI).Our working group has isolated several fungi and bacteria capable of removing Cr(VI) from the culture medium. Aspergillus niger var tubingensis Ed8 is a strain that can produce metabolites which reduce Cr (VI) to Cr (III). The objective of this work was to determine the effect of sodium salicylate on the growth of this strain and on the Cr(VI) reduction system, as well as to identify the metabolites that are produced from sodium salicylate. Our results show that the Culture medium containing sodium salicylate (20 mM) inhibits strain growth compared to the control condition (0 mM). However, it increases the specific reduction capacity of Cr (VI) red/mg Biomass in order of magnitude. Analysis of the culture medium corresponding to 48 h of incubation shows the presence of catechol and salicylate diminution. In addition, as a product of the enzymatic activity of a cell-free cellular extract, after 24 h of incubation, the consumption of salicylate is detected, as well as the presence of peaks corresponding to resorcinol and catechol. Our results show that it is possible to increase the Cr(VI) reducing capacity of the Ed8 strain, depending on the composition of the culture medium.

Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case

Determining the redox potentials of protein cofactors and how they are influenced by their molecular neighborhoods is essential for basic research and many biotechnological applications, from biosensors and biocatalysis to bioremediation and bioelectronics. The laborious determination of redox potential with current experimental technologies pushes forward the need for computational approaches that can reliably predict it. Although current computational approaches based on quantum and molecular mechanics are accurate, their large computational costs hinder their usage. In this work, we explored the possibility of using more efficient QSPR models based on machine learning (ML) for the prediction of protein redox potential, as an alternative to classical approaches. As a proof of concept, we focused on flavoproteins, one of the most important families of enzymes directly involved in redox processes. To train and test different ML models, we retrieved a dataset of flavoproteins with a known midpoint redox potential (Em) and 3D structure. The features of interest, accounting for both short- and long-range effects of the protein matrix on the flavin cofactor, have been automatically extracted from each protein PDB file. Our best ML model (XGB) has a performance error below 1 kcal/mol (∼36 mV), comparing favorably to more sophisticated computational approaches. We also provided indications on the features that mostly affect the Em value, and when possible, we rationalized them on the basis of previous studies.

Strategy for enhancing Cr(VI)-contaminated soil remediation and safe utilization by microbial-humic acid-vermiculite-alginate immobilized biocomposite

Bioreduction is an efficient approach to in-situ remediate Cr(VI)-contaminated soil, but further strengthening methods are still urgently needed. Herein, a novel immobilized biocomposite (B-HA-VE-SA) was successfully synthesized by embedding a efficient strain Bacillus sp. CRB-7 with humic acid (HA) combined vermiculite (VE) and sodium alginate (SA). The performance and enhancement mechanism of the immobilized biocomposite on remediating Cr(VI)-contaminated soil were also investigated by analyzing the whole-genome of CRB-7, Cr(VI) detoxification, soil microecological regulation, and subsequent crop growth response. Genomic annotation demonstrated that CRB-7 contains multiple genes contributed to Cr(VI) tolerance, Cr(VI) reduction and other metals resistance. Results showed that embedded CRB-7 biocomposites exhibited more effective reduction of Cr(VI) in soil compared with control and free CRB-7 treatment, especially B-HA-VE-SA achieved the highest Cr(VI) removal efficiency (96.18%) and the residual Cr proportion (49.04%) via multiple mechanisms including carrier effects, nutrient sustained-release, and electron-shuttle effect enhanced the bioremediation process. Furthermore, the synergies of CRB-7 and immobilizers (HA, VE and SA) significantly improved soil microecology (soil enzyme activities, microbial quantity and diversity), and engendered the evolution of microbial community composition and functional pathways. Consequently, pot experiments (Brassica napus L.) verified the plant-growth-promoting (12.00-18.00% and 43.82-69.00% higher in emergence rate and biomass) and Cr-accumulation-reducing effects (19.47-91.09% and 29.11-89.80% lower in root and aerial parts) of free and immobilized CRB-7. Taken together, these findings highlighted the superiority of B-HA-VE-SA in simultaneous remediation, microecological improvement and safe utilization of Cr(VI)-contaminated soil.

Cloning of Nitrate Reductase and Nitrite Reductase Genes and Their Functional Analysis in Regulating Cr(VI) Reduction in Ectomycorrhizal Fungus Pisolithus sp.1

Assimilatory-type nitrate reductase (NR) and nitrite reductase (NiR) are the key enzymes that involve in nitrate assimilation and nitrogen cycling in microorganisms. NR and NiR with NADH or NADPH and FMN or FAD domains could be coupled to the reduction process of hexavalent chromium [Cr(VI)] in microorganisms. A new assimilatory-type NR gene (named niaD) and a new assimilatory-type NiR gene (named niiA) are cloned, identified, and functionally characterized by 5′ and 3′ RACE, alignment, annotation, phylogenetic tree, and yeast mutant complementation analyses from Pisolithus sp.1, a dominant symbiotic ectomycorrhizal fungi (EMF) that can assist in phytoremediation. Assimilatory-type niaD and niiA were 2,754 bp and 3,468 bp and encode a polypeptide with 917 and 1,155 amino acid residues, respectively. The isoelectric points of NR (Pisolithus sp.1 NR) and NiR (Pisolithus sp.1 NiR) of Pisolithus sp.1 are 6.07 and 6.38, respectively. The calculated molecular mass of Pisolithus sp.1 NR and Pisolithus sp.1 NiR is 102.065 and 126.914 kDa, respectively. Yeast mutant complementation analysis, protein purification, and activities of NR and NiR under Cr treatment suggest that Pisolithus sp.1 NR is a functional NR that mediates Cr(VI) tolerance and reduction. The multiple alignment demonstrates that Pisolithus sp.1 NR is potentially a nicotinamide adenine dinucleotide phosphate-dependent flavin mononucleotide reductase and also Class II chromate reductase. Our results suggest that Pisolithus sp.1 NR plays a key role in Cr(VI) reduction in the EMF Pisolithus sp.1.

A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance

Background

Acidophilic microorganisms like Leptospirillum sp. CF-1 thrive in environments with extremely low pH and high concentrations of dissolved heavy metals that can induce the generation of reactive oxygen species (ROS). Several hypothetical genes and proteins from Leptospirillum sp. CF-1 are known to be up-regulated under oxidative stress conditions.

Results

In the present work, the function of hypothetical gene ABH19_09590 from Leptospirillum sp. CF-1 was studied. Heterologous expression of this gene in Escherichia coli led to an increase in the ability to grow under oxidant conditions with 5 mM K₂CrO₄ or 5 mM H₂O₂. Similarly, a significant reduction in ROS production in E. coli transformed with a plasmid carrying ABH19_09590 was observed after exposure to these oxidative stress elicitors for 30 min, compared to a strain complemented with the empty vector. A co-transcriptional study using RT-PCR showed that ABH19_09590 is contained in an operon, here named the “och” operon, that also contains ABH19_09585, ABH19_09595 and ABH19_09600 genes. The expression of the och operon was significantly up-regulated in Leptospirillum sp. CF-1 exposed to 5 mM K₂CrO₄ for 15 and 30 min. Genes of this operon potentially encode a NADH:ubiquinone oxidoreductase, a CXXC motif-containing protein likely involved in thiol/disulfide exchange, a hypothetical protein, and a di-hydroxy-acid dehydratase. A comparative genomic analysis revealed that the och operon is a characteristic genetic determinant of the Leptospirillum genus that is not present in other acidophiles.

Conclusions

Altogether, these results suggest that the och operon plays a protective role against chromate and hydrogen peroxide and is an important mechanism required to face polyextremophilic conditions in acid environments.

Identification of a Novel Chromate and Selenite Reductase FesR in Alishewanella sp. WH16-1

A ferredoxin protein (AAY72_06850, named FesR) was identified to associate with chromate [Cr(VI)] resistance in Alishewanella sp. WH16-1. FesR and its similar proteins were phylogenetically separated from other reductase families. Unlike the reported Cr(VI) and selenite [Se(IV)] reductases, two 4Fe-4S clusters and one flavin adenine dinucleotide (FAD) -binding domain were found in the FesR sequence. The experiment in vivo showed that the mutant strain ΔfesR had lost partial Cr(VI) and Se(IV) reduction capacities compared to the wild-type and complemented strains. Furthermore, overexpression in Escherichia coli and enzymatic tests in vitro showed FesR were involved in Cr(VI) and Se(IV) reduction. 4Fe-4S cluster in purified FesR was detected by ultraviolet-visible spectrum (UV-VIS) and Electron Paramagnetic Resonance (EPR). The Km values of FesR for Cr(VI) and Se(IV) reduction were 1682.0 ± 126.2 and 1164.0 ± 89.4 μmol/L, and the Vmax values for Cr(VI) and Se(IV) reduction were 4.1 ± 0.1 and 9.4 ± 0.3 μmol min^–1 mg^–1, respectively. Additionally, site-directed mutagenesis and redox potential analyses showed that 4Fe-4S clusters were essential to FesR, and FAD could enhance the enzyme efficiencies of FesR as intracellular electron transporters. To the best of our knowledge, FesR is a novel Cr(VI) and Se(IV) reductase.

Immobilization pathways of heavy metals in composting: Interactions of microbial community and functional gene under varying C/N ratios and bulking agents

Excessive heavy metals (HMs) in livestock manure due to additives over-use limits its recycling through composting. However, few studies have investigated the interactive influence of microbial communities, functional genes, and environmental factors in HM immobilization during composting. Therefore, treatments with different C/N ratios (15:1, 20:1, 25:1) and bulking agents (maize straw, green waste, vinasse) were conducted to explore the HMs immobilization pathways using structural equation model (SEM). Results confirmed the promoting effect of C/N ratio of 20:1 and vinasse on microbial diversity, thus leading to greater HMs immobilization rate. Meanwhile, the dominant microbial phyla of Cu/Zn, Cd, As, and Cr were identified as Proteobacteria, Firmicutes, Chytridiomycota, and Bacteroidota, respectively. Moreover, the significant correlation between functional genes (copC, mt, cbh1, aoxB, yieF) and HMs illustrated potential immobilization effects of metal-binding proteins on Cu and Zn, humus complexation on Zn, and oxidase/reductase on As/Cr. Finally, SEM indicated that the redistribution of Cu, Zn, As, and Cr fractions was interactively influenced by environmental factors (organic matter, pH, electrical conductivity, and total phosphorus), microbial communities, and functional genes, while Cd was directly regulated by organic matter and total phosphorus. These results may provide a deeper understanding of HM immobilization pathways during swine manure composting.

The toxicity of hexavalent chromium to soil microbial processes concerning soil properties and aging time

Chromium (Cr) pollution has attracted much attention due to its biological toxicity. However, little is known regarding Cr toxicity to soil microorganisms. The present study assesses the toxicity of Cr(VI) on two microbial processes, potential nitrification rate (PNR) and substrate-induced respiration (SIR), in a wide range of agricultural soils and detected the abundance of soil bacteria, fungi, ammonia-oxidizing bacteria and archaea. The toxicity thresholds of 10% and 50% effective concentrations (EC₁₀ and EC₅₀) for PNR varied by 32.18- and 38.66-fold among different soils, while for SIR they varied by 391.21- and 16.31-fold, respectively. Regression model analysis indicated that for PNR, CEC as a single factor explained 27% of the variation in EC₁₀, with soil clay being the key factor explaining 47.3% of the variation in EC₅₀. For SIR, organic matter and pH were found to be the most vital predictors for EC₁₀ and EC₅₀, explaining 34% and 61.1% of variation, respectively. In addition, extended aging time was found to significantly attenuate the toxicity of Cr on PNR. SIR was mainly driven by total bacteria rather than fungi, while PNR was driven by both AOA and AOB. These results were helpful in deriving soil Cr toxicity threshold based on microbial processes, and provided a theoretical foundation for ecological risk assessments and establishing a soil environmental quality criteria for Cr.

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.

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.

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.

Recent Advances in Enzymes for the Bioremediation of Pollutants

Nowadays, pollution of the environment is a huge problem for humans and other organisms' health. Conventional methods of pollutant removal like membrane filtration or ion exchange are not efficient enough to lower the number of pollutants to standard levels. Biological methods, because of their higher efficiency and biocompatibility, are preferred for the remediation of pollutants. These cost-effective and environment-friendly methods of reducing pollutants are called bioremediation. In bioremediation methods, enzymes play the most crucial role. Enzymes can remedy different types of organic and inorganic pollutants, including PAHs, azo dyes, polymers, organocyanides, lead, chromium, and mercury. Different enzymes isolated from various species have been used for the bioremediation of pollutants. Discovering new enzymes and new subtypes with specific physicochemical characteristics would be a promising way to find more efficient and cost-effective tools for the remediation of pollutants.

Enhanced biostimulation coupled with a dynamic groundwater recirculation system for Cr(VI) removal from groundwater: A field-scale study

A large gap exists between laboratory findings and successful implementation of bioremediation technologies for the treatment of chromium (Cr)-contaminated sites. This work conducted the enhanced bioremediation of Cr(VI) in situ via the addition of organic carbon (ethanol) coupled with a dynamic groundwater recirculation (DGR)-based system in a field-scale study. The DGR system was applied to successfully (1) remove Cr(VI) from groundwater via enhanced flushing by the recirculation system and (2) deliver the biostimulant to the heterogeneous subsurface environment, including a sand/cobble aquifer and a fractured bedrock aquifer. The results showed that the combined extraction and bioreduction of Cr(VI) were able to reduce Cr(VI) concentrations from 1000 to 2000 mg/L to below the clean-up goal of 0.1 mg/L within the operation period of 52 days. The effectiveness of Cr(VI) bioremediation and the relationship between microbial communities and geochemical parameters were evaluated. Multiple-line of evidence demonstrated that the introduction of ethanol significantly stimulated a variety of bacteria, including those responsible for denitrification, sulfate reduction and reduction of Cr(VI), which contributed to the establishment of reducing conditions in both aquifers. Cr(VI) was removed from groundwater via combined mechanisms of physical removal through the DGR system and the bioreduction of Cr(VI) followed by precipitation. In particular, it was found competitive growth among Cr(VI)-reducing bacteria (such as the enrichment of Geobacter, along with the reduced relative abundance of Acinetobacter and Pseudomonas) was induced by ethanol injection. Furthermore, Cr(VI), total organic carbon, NO₂^-, and SO₄^2- played important roles in shaping the composition of the microbial community and its functions.

Metabolic potentials of members of the class Acidobacteriia in metal-contaminated soils revealed by metagenomic analysis

The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriia-associated MAGs from five additional metal-contaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites.

Remediation of soil contaminated with high levels of hexavalent chromium by combined chemical-microbial reduction and stabilization

In order to solve the problem of re-oxidation after chemical remediation of soil contaminated with high levels of hexavalent chromium (Cr(VI)), we investigated the use of chemical reduction combined with microbial stabilization to remediate soils contaminated with high Cr(VI) concentration. The leaching toxicity and microbial diversity of Cr(VI)-contaminated soil and the leaching toxicity of remediated soil oxidized by potassium permanganate (KMnO₄) were measured. The results indicate that the conversion rate of Cr(VI) reached 97 %, and the concentration of Cr(VI) in toxic solutions leaching can be reduced by 95 % after 40 days of microbial stabilization. Sterilization experiments showed that the reduction of Cr(VI) by microorganisms is stable. The results of microbial diversity analysis indicate that bacterial community changed more than fungal community during the reduction process of Cr(VI), and the species abundance and species evenness of bacteria decreased. Bacillus spp. and Halomonas spp. were the dominant species in this study.

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.

Detoxification, Active Uptake, and Intracellular Accumulation of Chromium Species by a Methane-Oxidizing Bacterium

M. capsulatus Bath is a well-characterized aerobic methane-oxidizing bacterium that has become a model system for biotechnological development of methanotrophs to perform useful reactions for environmental cleanup and for making valuable chemicals and biological products using methane gas. Interest in such technology has increased recently owing to increasing availability of low-cost methane from fossil and biological sources. Here, it is demonstrated that this versatile methanotroph can reduce the toxic contaminating heavy metal chromium(VI) to the less toxic form chromium(III) while accumulating the chromium(III) within the cells. This is expected to diminish the bioavailability of the chromium and make it less likely to be reoxidized to chromium(VI). Thus, M. capsulatus has the capacity to perform methane-driven remediation of chromium-contaminated water and other materials and to accumulate the chromium in the low-toxicity chromium(III) form within the cells.

Despite the wide-ranging proscription of hexavalent chromium, chromium(VI) remains among the major polluting heavy metals worldwide. Aerobic methane-oxidizing bacteria are widespread environmental microorganisms that can perform diverse reactions using methane as the feedstock. The methanotroph Methylococcus capsulatus Bath, like many other microorganisms, detoxifies chromium(VI) by reduction to chromium(III). Here, the interaction of chromium species with M. capsulatus Bath was examined in detail by using a range of techniques. Cell fractionation and high-performance liquid chromatography–inductively coupled plasma mass spectrometry (HPLC–ICP-MS) indicated that externally provided chromium(VI) underwent reduction and was then taken up into the cytoplasmic and membranous fractions of the cells. This was confirmed by X-ray photoelectron spectroscopy (XPS) of intact cultures that indicated negligible chromium on the surfaces of or outside the cells. Distribution of chromium and other elements within intact and sectioned cells, as observed via transmission electron microscopy (TEM) combined with energy-dispersive X-ray spectroscopy (EDX) and electron energy loss spectroscopy (EELS), was consistent with the cytoplasm/membrane location of the chromium(III), possibly as chromium phosphate. The cells could also take up chromium(III) directly from the medium in a metabolism-dependent fashion and accumulate it. These results indicate a novel pattern of interaction with chromium species distinct from that observed previously with other microorganisms. They also suggest that M. capsulatus and similar methanotrophs may contribute directly to chromium(VI) reduction and accumulation in mixed communities of microorganisms that are able to perform methane-driven remediation of chromium(VI).

IMPORTANCEM. capsulatus Bath is a well-characterized aerobic methane-oxidizing bacterium that has become a model system for biotechnological development of methanotrophs to perform useful reactions for environmental cleanup and for making valuable chemicals and biological products using methane gas. Interest in such technology has increased recently owing to increasing availability of low-cost methane from fossil and biological sources. Here, it is demonstrated that this versatile methanotroph can reduce the toxic contaminating heavy metal chromium(VI) to the less toxic form chromium(III) while accumulating the chromium(III) within the cells. This is expected to diminish the bioavailability of the chromium and make it less likely to be reoxidized to chromium(VI). Thus, M. capsulatus has the capacity to perform methane-driven remediation of chromium-contaminated water and other materials and to accumulate the chromium in the low-toxicity chromium(III) form within the cells.

Evaluation of Cr(VI) Reducing Capability of Shewanella putrefaciens (MTTC8410) and Optimization of Operational Parameters

Bioremediation is an important technology to remediate the chromium (Cr) contaminated soil and water. In this study, Shewanella putrefaciens (MTTC8410) was used to investigate the influence of carbon concentration, pH, and temperature on reduction of hexavalent chromium [Cr(VI)] into trivalent chromium [Cr(III)]. The increased bacterial growth rate was significantly reduced the Cr(VI) concentration. In batch mode experiments, 1% starch recorded the highest reduction of Cr(VI) (90%) followed by 1% glucose (88% reduction) and a reduction of 77% was by 1% cellulose. By using various pH conditions the maximum Cr(VI) reduction was achieved at pH 7.0. In this experiment the maximum Cr(VI) reduction (75%) was observed at 35°C, followed by 30°C with 62% of Cr(VI) reduction. Bioreactor analysis revealed the highest reduction of Cr(VI) (88%) in unsterile tannery effluent. The significant levels of physico- chemical parameters were reduced in unsterile tannery effluent, as compared to the sterile tannery effluent. The experimental results revealed that the S. putrefaciens (MTTC8410) could be used as a potential bacterial strain for reduction of Cr(VI) from contaminated groundwater.

Recent advances in exploring the heavy metal(loid) resistant microbiome

Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.

NfoR: Chromate Reductase or Flavin Mononucleotide Reductase?

Soil bacteria can detoxify Cr(VI) ions by reduction. Within the last 2 decades, numerous reports of chromate reductase enzymes have been published. These reports describe catalytic reduction of chromate ions by specific enzymes. These enzymes each have sequence similarity to known redox-active flavoproteins. We investigated the enzyme NfoR from Staphylococcus aureus, which was reported to be upregulated in chromate-rich soils and to have chromate reductase activity (H. Han, Z. Ling, T. Zhou, R. Xu, et al., Sci Rep 7:15481, 2017, https://doi.org/10.1038/s41598-017-15588-y). We show that NfoR has structural similarity to known flavin mononucleotide (FMN) reductases and reduces FMN as a substrate. NfoR binds FMN with a dissociation constant of 0.4 μM. The enzyme then binds NADPH with a dissociation constant of 140 μM and reduces the flavin at a rate of 1,350 s^-1 Turnover of the enzyme is apparently limited by the rate of product release that occurs, with a net rate constant of 0.45 s^-1 The rate of product release limits the rate of observed chromate reduction, so the net rate of chromate reduction by NfoR is orders of magnitude lower than when this process occurs in solution. We propose that NfoR is an FMN reductase and that the criterion required to define chromate reduction as enzymatic has not been met. That NfoR expression is increased in the presence of chromate suggests that the survival adaption was to increase the net rate of chromate reduction by facile, adventitious redox processes.IMPORTANCE Chromate is a toxic by-product of multiple industrial processes. Chromate reduction is an important biological activity that ameliorates Cr(VI) toxicity. Numerous researchers have identified chromate reductase activity by observing chromate reduction. However, all identified chromate reductase enzymes have flavin as a cofactor or use a flavin as a substrate. We show here that NfoR, an enzyme claimed to be a chromate reductase, is in fact an FMN reductase. In addition, we show that reduction of a flavin is a viable way to transfer electrons to chromate but that it is unlikely to be the native function of enzymes. We propose that upregulation of a redox-active flavoprotein is a viable means to detoxify chromate that relies on adventitious reduction that is not catalyzed.

Microbial insights into the biogeochemical features of thallium occurrence: A case study from polluted river sediments

Thallium (Tl) is a trace element with extreme toxicity. Widespread Tl pollution in riverine systems, mainly due to escalating mining and smelting activities of Tl-bearing sulfide minerals, has attracted increasing attention. Insights into the function of the microbial communities with advanced characterization tools are critical for understanding the biogeochemical cycle of Tl. Herein, microbial communities and their adaptive evolution strategies in river sediments from a representative Tl-bearing pyrite mine area in southern China were profiled via 16S rRNA gene sequence analysis and shotgun metagenomic analysis. In total, 64 phyla and 778 genera of microorganisms were observed in the studied sediments. The results showed that pH, Tl, Pb, Zn and total organic carbon (TOC) had a significant influence on microbial community structure. Some important reductive microorganisms (such as Erysipelothrix, Geobacter, desulfatiferula, desulfatihabadium and fusibacter) were involved in the biogeochemical cycle of Tl. The ruv, rec, ars and other resistance genes enhanced the tolerance of microorganisms to Tl. The study suggested that relevant C, N and S cycle genes were the main metabolic paths of microorganisms surviving in the high Tl-polluted environment. The findings were critical for establishment, operation and regulation in the microbial treatment of Tl containing or related wastewater.

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.

Mechanistic and Crystallographic Studies of Azoreductase AzoA from Bacillus wakoensis A01

The azoreductase AzoA from the alkali-tolerant Bacillus wakoensis A01 has been studied to reveal its structural and mechanistic details. For this, a recombinant expression system was developed which yields impressive amounts of fully active enzyme. The purified holo enzyme is remarkably solvent-tolerant and thermostable with an apparent melting temperature of 71 °C. The dimeric enzyme contains FMN as a prosthetic group and is strictly NADH dependent. While AzoA shows a negligible ability to use molecular oxygen as an electron acceptor, it is efficient in reducing various azo dyes and quinones. The kinetic and catalytic mechanism has been studied in detail using steady state kinetic analyses and stopped-flow studies. The data show that AzoA performs quinone and azo dye reductions via a two-electron transfer. Moreover, quinones were shown to be much better substrates (kcat values of 100-400 s-1 for several naphtoquinones) when compared with azo dyes. This suggests that the physiological role of AzoA and sequence-related microbial reductases is linked to quinone reductions and that they can better be annotated as quinone reductases. The structure of AzoA has been determined in complex with FMN at 1.8 Å resolution. AzoA displays unique features in the active site providing clues for explaining its catalytic and thermostability features. An uncommon loop, when compared with sequence-related reductases, forms an active site lid with Trp60 acting as an anchor. Several Trp60 mutants have been analyzed disclosing an important role of this residue in the stability of AzoA, while they retained activity. Structural details are discussed in relation to other azo and quinone reductases. This study provides new insights into the molecular functioning of AzoA and sequence-related reductases.

Progress Towards Bioelectrochemical Remediation of Hexavalent Chromium

Chromium is one of the most frequently used metal contaminants. Its hexavalent form Cr(VI), which is exploited in many industrial activities, is highly toxic, is water-soluble in the full pH range, and is a major threat to groundwater resources. Alongside traditional approaches to Cr(VI) treatment based on physical-chemical methods, technologies exploiting the ability of several microorganisms to reduce toxic and mobile Cr(VI) to the less toxic and stable Cr(III) form have been developed to improve the cost-effectiveness and sustainability of remediating hexavalent chromium-contaminated groundwater. Bioelectrochemical systems (BESs), principally investigated for wastewater treatment, may represent an innovative option for groundwater remediation. By using electrodes as virtually inexhaustible electron donors and acceptors to promote microbial oxidation-reduction reactions, in in situ remediation, BESs may offer the advantage of limited energy and chemicals requirements in comparison to other bioremediation technologies, which rely on external supplies of limiting inorganic nutrients and electron acceptors or donors to ensure proper conditions for microbial activity. Electron transfer is continuously promoted/controlled in terms of current or voltage application between the electrodes, close to which electrochemically active microorganisms are located. Therefore, this enhances the options of process real-time monitoring and control, which are often limited in in situ treatment schemes. This paper reviews research with BESs for treating chromium-contaminated wastewater, by focusing on the perspectives for Cr(VI) bioelectrochemical remediation and open research issues.

Expression of Rice Metallothionein Isoforms in Escherichia coli Enhances the Accumulation of Trivalent and Hexavalent Chromium

INTRODUCTION

Metallothioneins (MTs) are members of a family of low molecular weight and cysteine-rich proteins that are involved in heavy metal homeostasis and detoxification in living organisms. Plants have multiple MT types that are generally divided into four subgroups according to the arrangement of Cys residues.

METHODS

In the present study the E. coli cells which heterologously express four different rice MT (OsMT) isoforms were analyzed for the accumulation of two forms of chromium, Cr3+ and Cr6+.

RESULTS

The results show that the transgenic bacteria were more tolerant than control cells when they were grown up in the medium comprising Cr(NO3)3.9H2O or Na2CrO4. The cells expressing OsMT1, OsMT2, OsMT3 and OsMT4 give rise to 6.5-, 2.7-, 5.5- and 2.1-fold improvements on the accumulation capacity for Cr3+ and 9-, 3-, 5- and 3- fold Cr6+ respectively compared with comparison to the control strain. Furthermore, the purified recombinant GST-OsMTs were tested for their binding ability to Cr+3 and Cr+6 in vitro.

DISCUSSION

The data show that the recombinant GST-OsMT1 and GST-OsMT2 were able to bind both Cr3+ and Cr6+, in vitro. However, their binding strength was low with respect to previous tested divalent ions like Cd2+.

Arsenic Oxidation by Flavin-Derived Reactive Species under Oxic and Anoxic Conditions: Oxidant Formation and pH Dependence

Flavins are ubiquitous redox-active compounds capable of producing reactive oxygen (O₂^•-, ^•OH, and H₂O₂) and flavin radical species in natural environments, yet their roles in the redox transformations of environmental contaminants, such as arsenic (As), remain to be investigated. Here, we show that reduced flavins can be a source of effective oxidants for As(III) under both oxic and anoxic conditions. For instance, in the presence of 15 μM reduced riboflavin (RBFH₂), 22% of 30 μM As(III) is oxidized in aerated solution at pH 7.0. The co-oxidation of As(III) with RBFH₂ is pH-dependent, with a faster reaction rate under mildly acidic relative to alkaline conditions. Quencher tests with 2-propanol (for ^•OH) and catalase (for H₂O₂) indicate that As(III) oxidation under oxic conditions is likely controlled by flavin-derived ^•OH at pH 5.2 and 7.0, and by H₂O₂ at pH 9.0. Kinetic modeling further implies that flavin-derived reactive oxygen species are mainly responsible for As(III) oxidation under oxic conditions, whereas oxidation of As(III) under anoxic conditions at pH 9.0 is attributed to riboflavin radicals (RBFH^•) generated from co-existing oxidized and reduced riboflavin. The demonstrated ability of flavins to catalyze As(III) oxidation has potential implications for As redox cycling in the environment.

Genome-Wide and Functional View of Proteolytic and Lipolytic Bacteria for Efficient Biogas Production through Enhanced Sewage Sludge Hydrolysis

In this study, we used a multifaceted approach to select robust bioaugmentation candidates for enhancing biogas production and to demonstrate the usefulness of a genome-centric approach for strain selection for specific bioaugmentation purposes. We also investigated the influence of the isolation source of bacterial strains on their metabolic potential and their efficiency in enhancing anaerobic digestion. Whole genome sequencing, metabolic pathway reconstruction, and physiological analyses, including phenomics, of phylogenetically diverse strains, Rummeliibacillus sp. POC4, Ochrobactrum sp. POC9 (both isolated from sewage sludge) and Brevundimonas sp. LPMIX5 (isolated from an agricultural biogas plant) showed their diverse enzymatic activities, metabolic versatility and ability to survive under varied growth conditions. All tested strains display proteolytic, lipolytic, cellulolytic, amylolytic, and xylanolytic activities and are able to utilize a wide array of single carbon and energy sources, as well as more complex industrial by-products, such as dairy waste and molasses. The specific enzymatic activity expressed by the three strains studied was related to the type of substrate present in the original isolation source. Bioaugmentation with sewage sludge isolates–POC4 and POC9–was more effective for enhancing biogas production from sewage sludge (22% and 28%, respectively) than an approach based on LPMIX5 strain (biogas production boosted by 7%) that had been isolated from an agricultural biogas plant, where other type of substrate is used.

Multi-omics response of Pannonibacter phragmitetus BB to hexavalent chromium

The release of hexavalent chromium [Cr(VI)] into water bodies poses a major threat to the environment and human health. However, studies of the biological response to Cr(VI) are limited. In this study, a toxic bacterial mechanism of Cr(VI) was investigated using Pannonibacter phragmitetus BB (hereafter BB), which was isolated from chromate slag. The maximum Cr(VI) concentrations with respect to the resistance and reduction by BB are 4000 mg L^-1 and 2500 mg L^-1, respectively. In the BB genome, more genes responsible for Cr(VI) resistance and reduction are observed compared with other P. phragmitetus strains. A total of 361 proteins were upregulated to respond to Cr(VI) exposure, including enzymes for Cr(VI) uptake, intracellular reduction, ROS detoxification, DNA repair, and Cr(VI) efflux and proteins associated with novel mechanisms involving extracellular reduction mediated by electron transfer, quorum sensing, and chemotaxis. Based on metabolomic analysis, 174 metabolites were identified. Most of the upregulated metabolites are involved in amino acid, glucose, lipid, and energy metabolisms. The results show that Cr(VI) induces metabolite production, while metabolites promote Cr(VI) reduction. Overall, multi-enzyme expression and metabolite production by BB contribute to its high ability to resist/reduce Cr(VI). This study provides details supporting the theory of Cr(VI) reduction and a theoretical basis for the efficient bioremoval of Cr(VI) from the environment.

Chromate tolerance and removal of bacterial strains isolated from uncontaminated and chromium-polluted environments

Investigation of bacterial chromate tolerance has mostly focused on strains originating from polluted sites. In the present study, we isolated 33 chromate tolerant strains from diverse environments harbouring varying concentrations of chromium (Cr). All of these strains were able to grow on minimal media with at least 2 mM hexavalent chromium (Cr(VI)) and their classification revealed that they belonged to 12 different species and 8 genera, with a majority (n = 20) being affiliated to the Bacillus cereus group. Selected B. cereus group strains were further characterised for their chromate tolerance level and the ability to remove toxic Cr(VI) from solution. A similar level of chromate tolerance was observed in isolates originating from environments harbouring high or low Cr. Reference B. cereus strains exhibited the same Cr(VI) tolerance which indicates that a high chromate tolerance could be an intrinsic group characteristic. Cr(VI) removal varied from 22.9% (strain PCr2a) to 98.5% (strain NCr4). Strains NCr1a and PCr12 exhibited the ability to grow to the greatest extent in Cr(VI) containing media (maximum growth of 65.3% and 64.9% relative to that in the absence of Cr(VI), respectively) accompanied with high chromate removal activity (73.7% and 74.4%, respectively), making them prime candidates for the investigation of chromate tolerance mechanisms in Gram-positive bacteria and Cr(VI) bioremediation applications.

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 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.

Distribution of Extracellular Flavins in a Coastal Marine Basin and Their Relationship to Redox Gradients and Microbial Community Members

The flavins (including flavin mononucleotide (FMN) and riboflavin (RF)) are a class of organic compounds synthesized by organisms to assist in critical redox reactions. While known to be secreted extracellularly by some species in laboratory-based cultures, flavin concentrations are largely unreported in the natural environment. Here, we present pore water and water column profiles of extracellular flavins (FMN and RF) and two degradation products (lumiflavin and lumichrome) from a coastal marine basin in the Southern California Bight alongside ancillary geochemical and 16S rRNA microbial community data. Flavins were detectable at picomolar concentrations in the water column (93-300 pM FMN, 14-40 pM RF) and low nanomolar concentrations in pore waters (250-2070 pM FMN, 11-210 pM RF). Elevated pore water flavin concentrations displayed an increasing trend with sediment depth and were significantly correlated with the total dissolved Fe (negative) and Mn (positive) concentrations. Network analysis revealed a positive relationship between flavins and the relative abundance of Dehalococcoidia and the MSBL9 clade of Planctomycetes, indicating possible secretion by members of these lineages. These results suggest that flavins are a common component of the so-called shared extracellular metabolite pool, especially in anoxic marine sediments where they exist at physiologically relevant concentrations for metal oxide reduction.