Contemporary enzyme based technologies for bioremediation: A review

Simultaneous laccase production and transformation of bisphenol-A and triclosan using Trametes versicolor

New age micro-pollutants, bisphenol-A (BPA) and triclosan (TCA), known for their carcinogenic effects in living organisms can effectively be removed from water using laccase from Trametes versicolor. Laccase was produced from T. versicolor JSRK13 in both submerged and solid-state fermentation (SmF and SSF) conditions. In SmF, T. versicolor JSRK13 gave the maximum production of laccase on the 10th day with an activity of 22 U mL^- 1, whereas, in SSF 185 U g^- 1 of the enzyme was produced on the 17th day. Maximum production of laccase was observed with Parthenium as substrate. Parthenium, with a particle size of 3-5 mm having 60% moisture was found to be a suitable substrate for laccase production and simultaneous transformation (LPST) of BPA in a synergistic manner. A one-step concentration using 85% ammonium sulphate followed by dialysis was sufficient to give 6.7-fold purification of laccase from the crude culture filtrate. Transformation of BPA was achieved in both SmF and SSF conditions along with the production of laccase, whereas TCA was degraded with free enzyme only. Above 90% of BPA (55-5 mg L^- 1) was degraded using the LPST strategy with HBT acting as a mediator in the reaction. LPST strategy did not work for TCA as it completely inhibits the growth of T. versicolor JSRK13. TCA was degraded up to 75% (1.5-0.375 mg L^- 1) by the free enzyme. Our study of simultaneous laccase production and transformation proved to be efficacious in case of BPA. The results indicate that industrial and sewage wastewater containing BPA can potentially be treated with T. versicolor JSRK13 laccase. The described strategy can further be used to develop a bioprocess which can work both on solid and liquid wastes containing BPA.

Acetylacetone extends the working life of laccase in enzymatic transformation of malachite green by interfering with a key intermediate

The potential of acetylacetone (AA) as a mediator of laccase has been tested in the enzymatic transformation of malachite green (MG). AA inhibited the laccase-induced transformation of MG at the beginning of incubation but extended the working life of laccase in long runs. To elucidate the underlying mechanisms, the transformation of MG in the laccase-AA system was systematically investigated. The inhibition of AA on the enzymatic transformation of MG conformed to the partial mixed model. The transformation of N,N,N',N'-tetramethyl-1,1'-biphenyl-4,4'-diamine (NTB) was identified as the rate-controlling step in the laccase system. The generated NTB was oxidized to NTB⁺ by laccase, which acted as a redox mediator to accelerate the transformation of MG. The addition of AA to the enzymatic system quenched the NTB⁺ by forming an intermediate complex of AA-NTB. This quenching reaction led to two contrary effects: the acceleration caused by NTB⁺ in the enzymatic transformation of MG was inhibited whereas the formation of AA-NTB complex enhanced the further transformation at the later stage. As a result, less laccase was consumed, which explained the extended working life of laccase in the long runs. The understanding of these mechanisms are helpful for the better use of laccase as a green biocatalyst.

Antibiotics bioremediation: Perspectives on its ecotoxicity and resistance

Antibiotic is one of the most significant discoveries and have brought a revolution in the field of medicine for human therapy. In addition to the medical uses, antibiotics have broad applications in agriculture and animal husbandry. In developing nations, antibiotics use have helped to increase the life expectancy by lowering the deaths due to bacterial infections, but the risks associated with antibiotics pollution is largely affecting people. Since antibiotics are released partially degraded and undegraded into environment creating antibiotic pollution, and its bioremediation is a challenging task. In the present review, we have discussed the primary antibiotic sources like hospitals, dairy, and agriculture causing antibiotic pollution and their innovative detection methods. The strong commitment towards the resistance prevention and participation, nations through strict policies and their implementations now come to fight against the antibiotic resistance under WHO. The review also deciphers the bacterial evolution based strategies to overcome the effects of antibiotics, so the antibiotic degradation and elimination from the environment and its health benefits. The present review focuses on the environmental sources of antibiotics, it's possible degradation mechanisms, health effects, and bacterial antibiotics resistance mechanisms.

Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review

Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.

Bioinoculants for Bioremediation Applications and Disease Resistance: Innovative Perspectives

Soil microbial species that act as PGPR or bioinoculants have the capability of improving plant health and promoting its growth. They facilitate plants for uptake nutrients from their surroundings. They provide resistivity to pathogenic pests and also play many roles in the bioremediation process. Bioremediation is the biological approach for the elimination of toxic contaminants by the approach of beneficial microbes. By the consortium of beneficial microbes and plant, a large number of heavy metal and organic contaminants can be controlled. With this advancement of bioremediation, microbial species that act as bioinoculants also help in the enhancement of induced systemic resistance (ISR) and their consortium triggers it by controlling SA, JA, ET and hormonal signaling pathways. Here, this review discusses the progress made on these areas and how the beneficial microbes that act as bioinoculants towards triggering bioremediation and ISR mechanism.

Degradation and defluorination of 6:2 fluorotelomer sulfonamidoalkyl betaine and 6:2 fluorotelomer sulfonate by Gordonia sp. strain NB4-1Y under sulfur-limiting conditions

6:2 fluorotelomer sulfonamidoalkyl betaine (6:2 FTAB) is a major component of aqueous film-forming foams (AFFFs) used for firefighting and is frequently detected, along with one of its suspected transformation products, 6:2 fluorotelomer sulfonate (6:2 FTSA), in terrestrial and aquatic ecosystems impacted by AFFF usage. Biochemical processes underlying bacterial biodegradation of these compounds remain poorly understood due to a lack of pure culture studies. Here, we characterized the water-soluble and volatile breakdown products of 6:2 FTSA and 6:2 FTAB produced using Gordonia sp. strain NB4-1Y cultures over seven days under sulfur-limited conditions. After 168 h, 99.9% of 60 μM 6:2 FTSA was degraded into ten major breakdown products, with a mol% recovery of 88.2, while 70.4% of 60 μM 6:2 FTAB was degraded into ten major breakdown products, with a mol% recovery of 84.7. NB4-1Y uses two pathways for 6:2 FTSA metabolism, with 55 mol% of breakdown products assigned to a major pathway and <1.0 mol% assigned to a minor pathway. This work indicates that rapid transformation of 6:2 FTSA and 6:2 FTAB can be achieved under controlled conditions and improves the bacterial metabolism of these compounds.

Nanomaterials with enzyme-like characteristics (nanozymes): next-generation artificial enzymes (II)

An updated comprehensive review to help researchers understand nanozymes better and in turn to advance the field.

Diesel degrading bacterial endophytes with plant growth promoting potential isolated from a petroleum storage facility

Thirteen (13) endophytic bacterial strains were isolated from Echinochloa crus-galli (Cockspur grass) and Cynodon dactylon (Bermuda grass) growing in an oil-contaminated site at a petroleum storage and transportation facility. Of the 13 strains assessed for their potential to degrade monoaromatic compounds (phenol, toluene, and xylene) and diesel and for their plant growth promoting (PGP) ability (phosphate solubilization, siderophores and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production), isolate J10 (identified as Pseudomonas sp. by 16S rRNA gene sequencing) was found to the best diesel biodegrader with the best PGP traits. The Monod model used for Pseudomonas sp. J10 growth kinetics on diesel fuel as the sole carbon source showed that the maximum specific bacterial growth rate was 0.0644 h- 1 and the half velocity constant (K s ) was estimated as 4570 mg L- 1. The overall growth yield coefficient and apparent growth yield were determined to be 0.271 g h- 1 and 0.127 g cells/g substrate, respectively. Pseudomonas sp. J10 removed 69% diesel in four days as determined by gas chromatographic (GC) analysis. These findings could assist in developing an endophyte assisted efficient diesel biodegradation system using Pseudomonas sp. J10 isolated from Echinochloa crus-galli.

A promising laccase immobilization approach for Bisphenol A removal from aqueous solutions

The immobilization of crude laccase from Trametes pubescens by glutaraldehyde crosslinking prior to entrapment into Ca-alginate beads increased the immobilization yield by 30% and reduced the leaking by 7-fold compared to the immobilization with no crosslinking. The performance of the newly developed biocatalyst to degrade Bisphenol A (BPA) from aqueous solutions was tested. Thus, operating at optimal conditions (i.e. pH 5, 30 °C, 20 mg L^-1 BPA and 1500 U L^-1 laccase), a BPA removal higher than 99% in 2 h was achieved. This value is higher than those reported to date for BPA removal by immobilized laccases. In addition, the biocatalyst was able to remove BPA in 10 successive batches with an efficiency higher than 70% at the end of the last batch. BPA adsorption on the alginate beads was negligible, therefore BPA removal was only due to laccase action. Moreover, Fourier-transform Infrared (FTIR) spectroscopy suggested BPA transformation by laccase.

Decolorization and detoxification of textile wastewaters by recombinant Myceliophthora thermophila and Trametes trogii laccases

Laccases are multi-copper oxidoreductases with broad biotechnological applications. Here, we report detailed biochemical characterization of purified recombinant laccases originating from Myceliophthora thermophila (MtL) and Trametes trogii (TtL). We identified optimal conditions for decolorization of commercial dyes and textile wastewater samples. We also tested the toxicity of decolorized wastewater samples using human peripheral blood mononuclear cells. MtL and TtL were expressed in Saccharomyces cerevisiae, and secreted enzymes were purified by consecutive hydrophobic and gel chromatography. The molecular masses of TtL (~ 65 kDa) and MtL (> 100 kDa) suggested glycosylation of the recombinant enzymes. Deglycosylation of MtL and TtL led to 25% and 10% decreases in activity, respectively. In a thermal stability assay, TtL retained 61% and MtL 86% of the initial activity at 40 °C. While TtL retained roughly 50% activity at 60 °C, MtL lost stability at temperatures higher than 40 °C. MtL and TtL preferred syringaldazine as a substrate, and the catalytic efficiencies for ABTS oxidation were 7.5 times lower than for syringaldazine oxidation. In the presence of the mediator HBT, purified TtL almost completely decolorized dyes within 30 min and substantially decolorized wastewater samples from a textile factory (up to 74%) within 20 h. However, products of TtL-catalyzed decolorization were more toxic than MtL-decolorized products, which were almost completely detoxified.

Recent advances in glyphosate biodegradation

Glyphosate has emerged as the most widespread herbicide to control annual and perennial weeds. Massive use of glyphosate for decades has resulted in its ubiquitous presence in the environment, and poses a threat to humans and ecosystem. Different approaches such as adsorption, photocatalytic degradation, and microbial degradation have been studied to break down glyphosate in the environment. Among these, microbial degradation is the most effective and eco-friendly method. During its degradation, various microorganisms can use glyphosate as a sole source of phosphorus, carbon, and nitrogen. Major glyphosate degradation pathways and its metabolites have been frequently investigated, but the related enzymes and genes have been rarely studied. There are many reviews about the toxicity and fate of glyphosate and its major metabolite, aminomethylphosphonic acid. However, there is lack of reviews on biodegradation and bioremediation of glyphosate. The aims of this review are to summarize the microbial degradation of glyphosate and discuss the potential of glyphosate-degrading microorganisms to bioremediate glyphosate-contaminated environments. This review will provide an instructive direction to apply glyphosate-degrading microorganisms in the environment for bioremediation.

Controlling Redox Enzyme Orientation at Planar Electrodes

Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations.

Bioremediation of piggery slaughterhouse wastewater using the marine protist, Thraustochytrium kinney VAL-B1

Industrial wastewaters from pig slaughtering plants (PSPs) generated in the slaughtering process could have an environmental impact, if discharged to a receiving water body without any treatment. In this study, a Chilean Thraustochytrid (TH) strain, a class of marine protist, was used for the bioremediation of piggery slaughterhouse wastewater (SWW). According to the physicochemical analysis of the residue, it was characterized by an initial chemical oxygen demand (COD) of 9610 mg L⁻¹, 18,625 mg L⁻¹ of oil and grease, 1639 mg L⁻¹ of total nitrogen, 149 mg L⁻¹ of total phosphorus, and 82.41 mg L⁻¹ of total iron. Growth studies were conducted to evaluate the growth and biomass production of the strain on residue-based media and its subsequent bioremediation ability. After 5–7 days of fermentation, the results showed that COD of the medium supernatant was reduced by 56.29% (4200 mg L⁻¹), while oil and grease had a significant decrease about 99% (18 mg L⁻¹), and the content of total nitrogen, total phosphorus, and total iron were also decreased by 63.27% (602 mg L⁻¹), 97.55% (3.65 mg L⁻¹) and 60.35% (30.88 mg L⁻¹), respectively. With these results, it was concluded that VAL-B1 can be used for the bioremediation of industrial wastewater from PSPs, and therefore THs could contribute to regulate the environmental pollution.

Self-assembled 2,4-dichlorophenol hydroxylase-inorganic hybrid nanoflowers with enhanced activity and stability

2,4-Dichlorophenol hydroxylase (2,4-DCP hydroxylase) is a key enzyme in the degradation of 2,4-dichlorophenoxyacetic acid in the hydroxylation step in many bacteria. Our previous study demonstrated that a cold-adapted 2,4-DCP hydroxylase (tfdB-JLU) exhibits broad substrate specificity for chlorophenols, biphenyl derivatives and their homologues. However, the stability of this enzyme is not satisfactory in practical use. There have been no reports of immobilizing a cold-adapted enzyme to improve its activity and stability so far. This study for the first time reports a facile approach for the synthesis of hybrid nanoflowers (hNFs) formed from cold-adapted 2,4-dichlorophenol hydroxylase (tfdB-JLU) and Cu₃(PO₄)₂·3H₂O. The influence of experimental factors, such as the pH of the solution mixture and the enzyme and Cu²⁺ concentrations, on the activity of the prepared tfdB-JLU-hNFs is investigated. The morphologies of the tfdB-JLU-hNFs are further analyzed by SEM and TEM. Compared to the free enzyme, the tfdB-JLU-hNFs exhibit up to 162.46 ± 1.53% enhanced 2,4-dichlorophenol degradation activity when encapsulated at different enzyme concentrations. The tfdB-JLU-hNFs exhibit excellent durability with 58.34% residual activity after six successive cycles, and up to 90.58% residual activity after 20 days of storage. These results demonstrate that this multistage and hierarchical flower-like structure can effectively increase enzyme activity and stability with respect to those of the free enzyme. The satisfactory removal rate of 2,4-dichlorophenol catalyzed by tfdB-JLU-hNFs suggests that this immobilized enzyme exhibits great potential for application in bioremediation.

Highly stable and active hydroxylase-inorganic hybrid nanoflowers with great potential for application in bioremediation were obtained.