Contemporary enzyme based technologies for bioremediation: A review

Enzyme aggregation and fragmentation induced by catalysis relevant species

It is usually assumed that enzymes retain their native structure during catalysis. However, the aggregation and fragmentation of proteins can be difficult to detect and sometimes conclusions are drawn based on the assumption that the protein is in its native form. We have examined three model enzymes, alkaline phosphatase (AkP), hexokinase (HK) and glucose oxidase (GOx). We find that these enzymes aggregate or fragment after addition of chemical species directly related to their catalysis. We used several independent techniques to study this behavior. Specifically, we found that glucose oxidase and hexokinase fragment in the presence of D-glucose but not L-glucose, while hexokinase aggregates in the presence of Mg²⁺ ion and either ATP or ADP at low pH. Alkaline phosphatase aggregates in the presence of Zn²⁺ ion and inorganic phosphate. The aggregation of hexokinase and alkaline phosphatase does not appear to attenuate their catalytic activity. Our study indicates that specific multimeric structures of native enzymes may not be retained during catalysis and suggests pathways for different enzymes to associate or separate over the course of substrate turnover.

Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost

Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.

Effective removal of pharmaceutical impurities and nutrients using biocatalyst from the municipal wastewater with moving bed packed reactor

The presence of antibiotics in the wastewater is one of the important issues related to environmental management. In this study, antibiotics-degrading bacteria were screened from the enriched sewage sludge sample. Among the isolated bacterial strains, Bacillus subtilis AQ03 showed maximum antibiotic tolerance (>2000 ppm). The characterized strain B. subtilis AQ03 degraded sulfamethaoxazole and sulfamethoxine and the optimum nutrient and physical-factors were analyzed. B. subtilis AQ03 degraded 99.8 ± 1.3 % sulfamethaoxazole, and 93.3 ± 6.2 % sulfamethoxine. Sodium nitrate and ammonium chloride were improved antibiotics degradation (<90 %). The optimized conditions were maintained in a moving bed bioreactor for the removal of antibiotics and nutrients from the wastewater. The selected strain considerably produced proteases (109.4 U/mL), amylases (55.1 U/mL), cellulase (9.6 U/mL) and laccases (15.2). In moving bed reactor, sulfamethaoxazole degradation was maximum after 8 days (100 ± 1.5 %) and sulfamethoxazole (100 ± 0) was removed completely from wastewater after 10 days. In moving bed reactor, biological oxygen demand (92.1 ± 2.8 %), chemical oxygen demand (79.6 ± 1.2 %), nitrate (89.4 ± 3.9 %) and phosphate (91.8 ± 1.2) were removed from the wastewater along with antibiotics after 10 days of treatment. The findings indicate that the indigenous bacterial communities and the ability to survive in the presence of high antibiotic concentrations and xenobiotics. Moving bed bioreactor is useful for the removal of nutrients and antibiotics from wastewater.

Enhanced HCB removal using bacteria from mangrove as post-treatment after electrochemical oxidation using a laser-prepared Ti/RuO2-IrO2-TiO2 anode

The environmental persistence of hexachlorobenzene (HCB) is a challenge that promotes studies for efficient treatment alternatives to minimize its environmental impact. Here, we evaluated the HCB removal by electrochemical, biological, and combined approaches. The electrochemical treatment of 4 μM HCB solutions was performed using a synthesized Ti/RuO₂-IrO₂-TiO₂ anode, while the biological treatment using mangrove-isolated bacteria was at 24, 48, and 72 h. The HCB degradability was assessed by analyzing chemical oxygen demand (COD), microbial growth capacity in media supplemented with HCB as the only carbon source, gas chromatography, and ecotoxicity assay after treatments. The synthesized anode showed a high voltammetric charge and catalytic activity, favoring the HCB biodegradability. All bacterial isolates exhibited the ability to metabolize HCB, especially Bacillus sp. and Micrococcus luteus. The HCB degradation efficiency of the combined electrochemical-biological treatment was evidenced by a high COD removal percentage, the non-HCB detection by gas chromatography, and a decrease in ecotoxicity tested with lettuce seeds. The combination of electrochemical pretreatment with microorganism degradation was efficient to remove HCB, thereby opening up prospects for in situ studies of areas contaminated by this recalcitrant compound.

A Simple Microextraction Method for Toxic Industrial Dyes Using a Fatty-Acid Solvent Mixture

A mixture of dodecanoic and hexanoic fatty acids was used to perform a simple and efficient microextraction method for industrial dyes such as methylene blue (MB), methyl violet (MV), and malachite green (MG) in aqueous solution. The fatty-acid microextractants were simply mixed and heated until the mixture became homogeneous before adding it to the dye solutions. The fatty-acid solvent and its components were characterized with Fourier transform infrared spectroscopy (FTIR) and proton nuclear magnetic resonance (1H NMR) measurements, while the dye concentrations were measured using UV-Vis spectroscopy. The performance of the extracting mixture was observed to vary across different dye contaminants, dosages of the extractant, concentrations of the dyes, and contact times. High extraction efficiencies of up to ~99% were obtained for MG as well as MV, and ~73% efficiency was achieved for MB. The study shows how a mixture of fatty acids can be used as a simple, efficient, green, and sustainable low-volume method for the removal of toxic industrial dyes in aqueous solutions.

Shape-function of a novel metapyrocatechase, RW4-MPC: Metagenomics to SAXS data based insight into deciphering regulators of function

The oxygenases have attracted considerable attention in enzyme-mediated bioremediation of xenobiotic compounds due to their high specificity, cost-effectiveness, and targeted field applications. Here, we performed a functional metagenomics approach to cope with cultivability limitations to isolate a novel extradiol dioxygenase. Fosmid clone harboring dioxygenase gene was sequenced and analyzed by bioinformatics tools. One ring-cleaving dioxygenase RW4-MPC (metapyrocatechase) was purified and characterized to examine its degradation efficiency. The RW4-MPC was significantly active in the temperature and pH range of 5 to 40 °C, and 7-10, respectively, with an optimum temperature of 25 °C and pH 8. To gain insight into observed differential activity, Small-Angle X-ray Scattering (SAXS) data of the protein samples were analyzed, which brought forth that the RW4-MPC molecules form tight globular tetramers in solution. This native association was stable till 35 °C, and protein started to associate at higher temperatures, explaining heat-induced loss of function. Similarly, RW4-MPC aggregated or lost globular profile below pH 7 or at pH 10, respectively. The kinetic parameters showed the six folds high catalytic efficiency of RW4-MPC towards 2,3-dihydroxy biphenyl than catechol and its derivatives. RW4-MPC molecules showed remarkable retention of functionality in hypersaline conditions with more than 70% activity in a buffer having 3 M NaCl concentration. In concordance, SAXS data analysis showed retention of functional shape profile in hypersaline conditions. The halotolerant and oxygen insensitive nature of this enzyme makes it a potential candidate for bioremediation.

Applications of Biocatalysts for Sustainable Oxidation of Phenolic Pollutants: A Review

Phenol and its derivatives are hazardous, teratogenic and mutagenic, and have gained significant attention in recent years due to their high toxicity even at low concentrations. Phenolic compounds appear in petroleum refinery wastewater from several sources, such as the neutralized spent caustic waste streams, the tank water drain, the desalter effluent and the production unit. Therefore, effective treatments of such wastewaters are crucial. Conventional techniques used to treat these wastewaters pose several drawbacks, such as incomplete or low efficient removal of phenols. Recently, biocatalysts have attracted much attention for the sustainable and effective removal of toxic chemicals like phenols from wastewaters. The advantages of biocatalytic processes over the conventional treatment methods are their ability to operate over a wide range of operating conditions, low consumption of oxidants, simpler process control, and no delays or shock loading effects associated with the start-up/shutdown of the plant. Among different biocatalysts, oxidoreductases (i.e., tyrosinase, laccase and horseradish peroxidase) are known as green catalysts with massive potentialities to sustainably tackle phenolic contaminants of high concerns. Such enzymes mainly catalyze the o-hydroxylation of a broad spectrum of environmentally related contaminants into their corresponding o-diphenols. This review covers the latest advancement regarding the exploitation of these enzymes for sustainable oxidation of phenolic compounds in wastewater, and suggests a way forward.

Enzyme polymer engineered structure strategy to enhance cross-linked enzyme aggregate stability: a step forward in laccase exploitation for cannabidiol removal from wastewater

Despite all its advantages and potential, cross-linking enzyme aggregate (CLEA) technology is still not applied at an industrial scale for enzyme insolubilization for bioremediation purposes. In this study, the enzyme polymer engineered structure (EPES) method was used to enhance CLEA stability and reuse. A crude laccase from Trametes hirsuta was successfully insolubilized to form EPES-CLEAs. The polymeric network provided excellent stability (> 90%) to CLEAs after a 24-h incubation in a non-buffered municipal wastewater effluent (WW), and the biocatalysts were recycled using a centrifugation process. While CLEAs activity dropped to 17%, EPES-CLEAs showed a laccase activity retention of 67% after five cycles of 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) oxidation. After 8 h of treatment in WW, the EPES-CLEAs were equally as effective in removing cannabidiol (CBD) as the free-LAC (~ 37%). This research demonstrates that the EPES method is a promising alternative for CLEA stabilization and reuse in environmental conditions.

Single-atom nanozymes and environmental catalysis: A perspective

The nanomaterials intrinsic enzyme-like activity has gained enormous traction since its discovery in 2007 by Gao and colleagues. The wide range of applications with nanozymes made it more attractive among the scientific community across the world. The area of artificial-enzymes is still evolving, with the development of Single-Atom Nanozymes (SANs), and there is a lot of opportunity in the design and development of SANs that has plenty of real-time applications. The irregular active site distribution or truncated densities of active sites present on the surface of nanozymes can be result in the reduced activity and specificity of nanozymes. Individually spreading these active sites evenly on a solid support will help to curtail the uneven distribution of active sites, resulting in the formation of SANs. SANs, like homogeneous catalysts, are very effective and active due to the nearly uniform distribution of active sites on solid support, and their recovery and recyclability, like heterogeneous catalysts, make them green and sustainable. This review provides a brief overview of architecture, synthesis, and implementations of SANs in various fields. Also, the possibility of SANs in environmental catalysis is discussed along with the key challenges and prospects lying ahead in this field.

Effective removal of heavy metals from industrial effluent wastewater by a multi metal and drug resistant Pseudomonas aeruginosa strain RA-14 using integrated sequencing batch reactor

Sequencing batch reactor (SBR) is useful in removal of both non-biodegradable and biodegradable contaminants from wastewater. The main aim of the present investigation was to evaluate the potential of biocatalyst strain RA-14 on heavy metal removal under SBR. The selected strain was screened from the soil sediment contaminated with heavy metals. It was able to survive at different (Hg²⁺, Pb²⁺, Zn²⁺, Cu²⁺, Cd²⁺ and Ni²⁺) heavy metals (>500 ppm). The bacterial strain RA-14 showed maximum bioaccumulation potential than other strains. Heavy metal resistance patterns of Pb²⁺ > Cu² > Cd²⁺ > Hg²⁺, Ni²⁺ and Zn² was observed. Strain RA-14 was resistant to penicillin-G, nalidixic acid, ceftazidime, cefotaxime, kanamycin and ampicillin. The results revealed that bioaccumulation activities were improved at pH 7.0 (83.2 ± 1.8%), 40 °C (89.34 ± 3%) and affected at higher pH values and temperature. The results showed that contact time and initial Lead concentration was also affected Lead accumulation. The heavy metal tolerant strain RA-14 was further investigated towards heavy metal removal in SBR. Heavy metal was removed in SBR within 10 h of hydraulic retention time. Heavy metal removal was high at 2 mg/L (0.33 mg/L Cu²⁺, 0.33 mg/L Hg²⁺, 0.33 mg/L Pb²⁺, 0.33 mg/L Zn²⁺, 0.33 mg/L Cd²⁺ and 0.33 mg/L Ni²⁺) heavy metals. Total nitrogen, biological oxygen demand (BOD) and chemical oxygen demand (COD) of treated water in SBR was removed and the removal efficacy was 91.3 ± 2.1%, 97.6 ± 3.3%, and 94.3 ± 4.4%, respectively in 10 h hydraulic retention time. However, the efficiency of BOD, COD and total nitrogen content removal was decreased, due to the reduced metabolic process of bacteria after 10 h. The SBR reactor proved to be an efficient method for the treatment of various heavy metals from the wastewater.

Subcritical and supercritical water oxidation for dye decomposition

The total annual output of synthetic dyes exceeds 7 × 10⁵ tons. About 1,000 tons of non-biodegradable synthetic dyes are released every year into the natural streams and water sources from textile wastes. The release of these colored wastewater exerts negative impact on aquatic ecology and human beings because of the poisonous and carcinogenic repercussions of dyes involved in coloration production. Therefore, with a growing interest in the environment, efficient technologies need to be developed to eliminate dyes from local and industrial wastewater. Supercritical water oxidation as a promising wastewater treatment technology has many advantages, such as a rapid reaction and pollution-free products. However, due to corrosion, salt precipitation and operational problems, supercritical water oxidation process did not gain expected industrial development. These technical difficulties can be overcome by application of non-corrosive subcritical water as a reaction medium. This work summarizes the negative impacts of dyes and role of subcritical and supercritical water and their efficiencies in dye oxidation processes.

Biodegradation of aromatic pollutants meets synthetic biology

Ubiquitously distributed microorganisms are natural decomposers of environmental pollutants. However, because of continuous generation of novel recalcitrant pollutants due to human activities, it is difficult, if not impossible, for microbes to acquire novel degradation mechanisms through natural evolution. Synthetic biology provides tools to engineer, transform or even re-synthesize an organism purposefully, accelerating transition from unable to able, inefficient to efficient degradation of given pollutants, and therefore, providing new solutions for environmental bioremediation. In this review, we described the pipeline to build chassis cells for the treatment of aromatic pollutants, and presented a proposal to design microbes with emphasis on the strategies applied to modify the target organism at different level. Finally, we discussed challenges and opportunities for future research in this field.

Green Synthesized of Ag/Ag2O Nanoparticles Using Aqueous Leaves Extracts of Phoenix dactylifera L. and Their Azo Dye Photodegradation

In this study, silver/silver oxide nanoparticles (Ag/Ag2O NPs) were successfully biosynthesized using Phoenix dactylifera L. aqueous leaves extract. The effect of different plant extract/precursor contractions (volume ratio, v/v%) on Ag/Ag2O NP formation, their optical properties, and photocatalytic activity towards azo dye degradation, i.e., Congo red (CR) and methylene blue (MB), were investigated. X-ray diffraction confirmed the crystalline nature of Ag/Ag2O NPs with a crystallite size range from 28 to 39 nm. Scanning electron microscope images showed that the Ag/Ag2O NPs have an oval and spherical shape. UV-vis spectroscopy showed that Ag/Ag2O NPs have a direct bandgap of 2.07-2.86 eV and an indirect bandgap of 1.60-1.76 eV. Fourier transform infrared analysis suggests that the synthesized Ag/Ag2O NPs might be stabilized through the interactions of -OH and C=O groups in the carbohydrates, flavonoids, tannins, and phenolic acids present in Phoenix dactylifera L. Interestingly, the prepared Ag/Ag2O NPs showed high catalytic degradation activity for CR dye. The photocatalytic degradation of the azo dye was monitored spectrophotometrically in a wavelength range of 250-900 nm, and a high decolorization efficiency (84.50%) was obtained after 50 min of reaction. As a result, the use of Phoenix dactylifera L. aqueous leaves extract offers a cost-effective and eco-friendly method.

Fabrication and characterization of purified esterase-embedded zeolitic imidazolate frameworks for the removal and remediation of herbicide pollution from soil

The fragility and high cost of enzymes represent critical challenges limiting their practical application in the removal of pesticides. Herein, an aryloxyphenoxypropionate herbicide-hydrolyzing enzyme, QpeH, was purified via one-step affinity chromatography and embedded into two types of zeolitic imidazolate frameworks (ZIFs) through biomimetic mineralization. The catalytic activity towards the herbicide quizalofop-P-ethyl, the loading capacity and efficiency of the resulting two composites, QpeH@ZIF-10 with cruciate flower-like morphology and QpeH@ZIF-8 with rhombic dodecahedral morphology, were compared. Both composites had excellent stability and reusability after 10 reuse cycles, with QpeH@ZIF-10 having a better performance. More importantly, when applied for the removal of quizalofop-P-ethyl pollution in the watermelon field, QpeH@ZIF-10 (88%) showed a remarkably improved degradation efficiency compared to QpeH@ZIF-8 (84%) despite the latter having a greater loading capacity. Finally, the use of QpeH@ZIF composites was shown to recover the bacterial community in soil. This work provides a new insight into the low-cost synthesis of nanobiocatalysts combining simple purified enzymes and metal-organic frameworks (MOFs) for the remediation of pesticide-contaminated soils.

Succinic anhydride-based chemical modification making laccase@Cu3(PO4)2 hybrid nanoflowers robust in removing bisphenol A in wastewater

To prepare a robust biocatalyst and enhance the removal of bisphenol A in wastewater, succinic anhydride was reacted with laccase to obtain succinic anhydride-modified laccase (SA-laccase) and then co-crystallized with Cu₃(PO₄)₂ to form SA-laccase@Cu₃(PO₄)₂ hybrid nanoflowers (hNFs). The activity of SA-laccase@Cu₃(PO₄)₂ reached 5.27 U/mg, 1.86-, 2.88- and 2.15-fold those of bare laccase@Cu₃(PO₄)₂, laccase@Ca₃(PO₄)₂ and laccase@epoxy resin, respectively. Compared with free laccase, the obtained hNFs present enhanced activity and tolerance to pH and high temperature in the removal of BPA. Under the optimum conditions of pH 6.0 and 35 °C, BPA removal reached 93.2% using SA-laccase@Cu₃(PO₄)₂ hNFs, which was 1.21-fold of that using free laccase. In addition, the obtained SA-laccase@Cu₃(PO₄)₂ hNFs retained nearly 90% of their initial catalytic activity for BPA removal after 8 consecutive batch cycles. This efficient method for preparing immobilized laccase can also be further developed and improved to acquire green biocatalysts for removing persistent organic pollutants in wastewater.

Faster Surface Ligation Reactions Improve Immobilized Enzyme Structure and Activity

During integration into materials, the inactivation of enzymes as a result of their interaction with nanometer size denaturing "hotspots" on surfaces represents a critical challenge. This challenge, which has received far less attention than improving the long-term stability of enzymes, may be overcome by limiting the exploration of surfaces by enzymes. One way this may be accomplished is through increasing the rate constant of the surface ligation reaction and thus the probability of immobilization with reactive surface sites (i.e., ligation efficiency). Here, the connection between ligation reaction efficiency and the retention of enzyme structure and activity was investigated by leveraging the extremely fast reaction of strained trans-cyclooctene (sTCOs) and tetrazines (Tet). Remarkably, upon immobilization via Tet-sTCO chemistry, carbonic anhydrase (CA) retained 77% of its solution-phase activity, while immobilization via less efficient reaction chemistries, such as thiol-maleimide and azide-dibenzocyclooctyne, led to activity retention of only 46% and 27%, respectively. Dynamic single-molecule fluorescence tracking methods further revealed that longer surface search distances prior to immobilization (>0.5 μm) dramatically increased the probability of CA unfolding. Notably, the CA distance to immobilization was significantly reduced through the use of Tet-sTCO chemistry, which correlated with the increased retention of structure and activity of immobilized CA compared to the use of slower ligation chemistries. These findings provide an unprecedented insight into the role of ligation reaction efficiency in mediating the exploration of denaturing hotspots on surfaces by enzymes, which, in turn, may have major ramifications in the creation of functional biohybrid materials.

Preparation and Characterization of Chitosan-Coated Manganese-Ferrite Nanoparticles Conjugated with Laccase for Environmental Bioremediation

Bioremediation with immobilized enzymes has several advantages, such as the enhancement of selectivity, activity, and stability of biocatalysts, as well as enzyme reusability. Laccase has proven to be a good candidate for the removal of a wide range of contaminants. In this study, naked or modified MnFe₂O₄ magnetic nanoparticles (MNPs) were used as supports for the immobilization of laccase from Trametes versicolor. To increase enzyme loading and stability, MNPs were coated with chitosan both after the MNP synthesis (MNPs-CS) and during their formation (MNPs-CS_{in situ}). SEM analysis showed different sizes for the two coated systems, 20 nm and 10 nm for MNPs-CS and MNPs-CS_{in situ}, respectively. After covalent immobilization of laccase by glutaraldehyde, the MNPs-CS_{in situ}-lac and MNPs-CS-lac systems showed a good resistance to temperature denaturation and storage stability. The most promising system for use in repeated batches was MNPs-CS_{in situ}-lac, which degraded about 80% of diclofenac compared to 70% of the free enzyme. The obtained results demonstrated that the MnFe₂O₄-CS_{in situ} system could be an excellent candidate for the removal of contaminants.

Immobilising Microalgae and Cyanobacteria as Biocomposites: New Opportunities to Intensify Algae Biotechnology and Bioprocessing

There is a groundswell of interest in applying phototrophic microorganisms, specifically microalgae and cyanobacteria, for biotechnology and ecosystem service applications. However, there are inherent challenges associated with conventional routes to their deployment (using ponds, raceways and photobioreactors) which are synonymous with suspension cultivation techniques. Cultivation as biofilms partly ameliorates these issues; however, based on the principles of process intensification, by taking a step beyond biofilms and exploiting nature inspired artificial cell immobilisation, new opportunities become available, particularly for applications requiring extensive deployment periods (e.g., carbon capture and wastewater bioremediation). We explore the rationale for, and approaches to immobilised cultivation, in particular the application of latex-based polymer immobilisation as living biocomposites. We discuss how biocomposites can be optimised at the design stage based on mass transfer limitations. Finally, we predict that biocomposites will have a defining role in realising the deployment of metabolically engineered organisms for real world applications that may tip the balance of risk towards their environmental deployment.

Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation

Simple Summary

Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions.

Abstract

The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.

Mycoremediation of oxytetracycline by marine fungi mycelium isolated from salmon farming areas in the south of Chile

Antibiotics are extensively used for growth promotion purposes in intensive aquaculture. In Chile, the use of antibiotics in salmon farming is excessive, approximately 62 times more than is used in Norway. In the salmon industry, antibiotics such as oxytetracycline (OTC) are administered in the diet, both in the juvenile stage in freshwater and in the fattening process of salmon in marine sectors. We have investigated the fjords of Chile, where many salmon farms are located, searching for fungi able to degrade this tetracycline antibiotic. We have evaluated the OTC degradation ability of the following; Penicillium commune, Epicoccum nigrum, Trichoderma harzianum, Aspergillus terreus and Beauveria bassiana, isolated from sediments in salmon farms from southern Chile. In all these fungal strains, the amount of OTC decreased in the culture medium, as adsorbed in the mycelia, after the third day of exposure. These strains were capable of degrading OTC at remarkable rates up to 78%, by the 15th day. This is the first study showing that the mycelium of these fungal strains has the ability to degrade OTC. We believe the knowledge produced by these results has the potential to serve as a basis for implementing a bioremediation process in the near future.

Tailoring Next Generation Plant Growth Promoting Microorganisms as Versatile Tools beyond Soil Desalinization: A Road Map towards Field Application

Plant growth promoting bacteria (PGPB) have been the target of intensive research studies toward their efficient use in the field as biofertilizers, biocontrol, and bioremediation agents among numerous other applications. Recent trends in the field of PGPB research led to the development of versatile multifaceted PGPB that can be used in different field conditions such as biocontrol of plant pathogens in metal contaminated soils. Unfortunately, all these research efforts lead to the development of PGPB that failed to perform in salty environments. Therefore, it is urgently needed to address this drawback of these PGPB toward their efficient performance in salinity context. In this paper we provide a review of state-of-the-art research in the field of PGPB and propose a road map for the development of next generation versatile and multifaceted PGPB that can perform in salinity. Beyond soil desalinization, our study paves the way towards the development of PGPB able to provide services in diverse salty environments such as heavy metal contaminated, or pathogen threatened. Smart development of salinity adapted next generation biofertilizers will inevitably allow for mitigation and alleviation of biotic and abiotic threats to plant productivity in salty environments.

Emerging Roles of PETase and MHETase in the Biodegradation of Plastic Wastes

Polyethylene terephthalate (PET) is extensively used in plastic products, and its accumulation in the environment has become a global concern. Being a non-degradable pollutant, a tremendous quantity of PET-bearing plastic materials have already accumulated in the environment, posing severe challenges towards the existence of various endangered species and consequently threatening the ecosystem and biodiversity. While conventional recycling and remediation methodologies so far have been ineffective in formulating a "green" degradation protocol, the bioremediation strategies-though nascent-are exhibiting greater promises towards achieving the target. Very recently, a novel bacterial strain called Ideonella sakaiensis 201-F6 has been discovered that produces a couple of unique enzymes, polyethylene terephthalate hydrolase and mono(2-hydroxyethyl) terephthalic acid hydrolase, enabling the bacteria to utilize PET as their sole carbon source. With a detailed understanding of the protein structure of these enzymes, possibilities for their optimization as PET degrading agents have started to emerge. In both proteins, several amino acids have been identified that are not only instrumental for catalysis but also provide avenues for the applications of genetic engineering strategies to improve the catalytic efficiencies of the enzymes. In this review, we focused on such unique structural features of these two enzymes and discussed their potential as molecular tools that can essentially become instrumental towards the development of sustainable bioremediation strategies. Degradation PET by wild type and genetically engineered PETase and MHETase. Effect of the MHETase-PETase chimeric protein and PETase expressed on the surface of yeast cells on PET degradation is also shown.

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils-Case of Sulfamethazine-Degrading Microbacterium sp. C448

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion of antibiotrophs in contaminated environments. A microcosm experiment was conducted to test this hypothesis in an agroecosystem context. The sulfonamide-degrading and resistant bacterium Microbacterium sp. C448 was inoculated in four different soil types with and without added sulfamethazine and/or swine manure. After 1 month of incubation, Microbacterium sp. (and its antibiotrophic gene sadA) was detected only in the sulfamethazine-treated soils, suggesting a low competitiveness of the strain without antibiotic selection pressure. In the absence of manure and despite the presence of Microbacterium sp. C448, only one of the four sulfamethazine-treated soils exhibited mineralization capacities, which were low (inferior to 5.5 ± 0.3%). By contrast, manure addition significantly enhanced sulfamethazine mineralization in all the soil types (at least double, comprised between 5.6 ± 0.7% and 19.5 ± 1.2%). These results, which confirm that the presence of functional genes does not necessarily ensure functionality, suggest that sulfamethazine does not necessarily confer a selective advantage on the degrading strain as a nutritional source. 16S rDNA sequencing analyses strongly suggest that sulfamethazine released trophic niches by biocidal action. Accordingly, manure-originating bacteria and/or Microbacterium sp. C448 could gain access to low-competition or competition-free ecological niches. However, simultaneous inputs of manure and of the strain could induce competition detrimental for Microbacterium sp. C448, forcing it to use sulfamethazine as a nutritional source. Altogether, these results suggest that the antibiotrophic strain studied can modulate its sulfamethazine-degrading function depending on microbial competition and resource accessibility, to become established in an agricultural soil. Most importantly, this work highlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, as antibiotics can not only release existing trophic niches but also form new ones.

Dynamic consolidated bioprocessing for innovative lab-scale production of bacterial alkaline phosphatase from Bacillus paralicheniformis strain APSO

To meet the present and forecasted market demand, bacterial alkaline phosphatase (ALP) production must be increased through innovative and efficient production strategies. Using sugarcane molasses and biogenic apatite as low-cost and easily available raw materials, this work demonstrates the scalability of ALP production from a newfound Bacillus paralicheniformis strain APSO isolated from a black liquor sample. Mathematical experimental designs including sequential Plackett–Burman followed by rotatable central composite designs were employed to select and optimize the concentrations of the statistically significant media components, which were determined to be molasses, (NH₄)₂NO₃, and KCl. Batch cultivation in a 7-L stirred-tank bioreactor under uncontrolled pH conditions using the optimized medium resulted in a significant increase in both the volumetric and specific productivities of ALP; the alkaline phosphatase throughput 6650.9 U L⁻¹, and µ = 0.0943 h⁻¹; respectively, were obtained after 8 h that, ameliorated more than 20.96, 70.12 and 94 folds compared to basal media, PBD, and RCCD; respectively. However, neither the increased cell growth nor enhanced productivity of ALP was present under the pH-controlled batch cultivation. Overall, this work presents novel strategies for the statistical optimization and scaling up of bacterial ALP production using biogenic apatite.

Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria

An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.

Machine learning for enzyme engineering, selection and design

Machine learning is a useful computational tool for large and complex tasks such as those in the field of enzyme engineering, selection and design. In this review, we examine enzyme-related applications of machine learning. We start by comparing tools that can identify the function of an enzyme and the site responsible for that function. Then we detail methods for optimizing important experimental properties, such as the enzyme environment and enzyme reactants. We describe recent advances in enzyme systems design and enzyme design itself. Throughout we compare and contrast the data and algorithms used for these tasks to illustrate how the algorithms and data can be best used by future designers.

Degradation of polylactic acid/polybutylene adipate-co-terephthalate by coculture of Pseudomonas mendocina and Actinomucor elegans

A cocultivation of the Pseudomonas mendocina with Actinomucor elegans was developed and investigated to improve the biodegradation of polylactic acid/polybutylene adipate-co-terephthalate (PLA/PBAT). And the coculture system could produce an efficient PLA/PBAT-degrading enzymes system to degrade PLA/PBAT films. The results showed that the protease activity (11.50 U/mL) and lipase activity (40.46 U/mL) of the coculture exceeded that of the monoculture (P. mendocina of 7.31 U/mL, A. elegans of 32.47 U/mL). The degradation rate of PLA/PBAT films using the coculture system was 18.95 w_t% within 5 days, which was considerably higher than that of P. mendocina (12.94 w_t%) and A. elegans (9.27 w_t%) individually, suggesting that P. mendocina and A. elegans had synergistic degradation. In addition, P. mendocina and A. elegans could secrete proteases and lipases, respectively, which could catalyze the ester bonds of PLA¹ and PBAT in PLA/PBAT films, respectively, and hydrolyze them into different monomers and oligomers as nutrition sources. Therefore, the PLA/PBAT films could be completely degraded. In this study, the PLA/PBAT films were efficiently degraded in the coculture system for the first time, which significantly improved the biodegradation of PLA/PBAT films.

Nanozymes for Environmental Pollutant Monitoring and Remediation

Nanozymes are advanced nanomaterials which mimic natural enzymes by exhibiting enzyme-like properties. As nanozymes offer better structural stability over their respective natural enzymes, they are ideal candidates for real-time and/or remote environmental pollutant monitoring and remediation. In this review, we classify nanozymes into four types depending on their enzyme-mimicking behaviour (active metal centre mimic, functional mimic, nanocomposite or 3D structural mimic) and offer mechanistic insights into the nature of their catalytic activity. Following this, we discuss the current environmental translation of nanozymes into a powerful sensing or remediation tool through inventive nano-architectural design of nanozymes and their transduction methodologies. Here, we focus on recent developments in nanozymes for the detection of heavy metal ions, pesticides and other organic pollutants, emphasising optical methods and a few electrochemical techniques. Strategies to remediate persistent organic pollutants such as pesticides, phenols, antibiotics and textile dyes are included. We conclude with a discussion on the practical deployment of these nanozymes in terms of their effectiveness, reusability, real-time in-field application, commercial production and regulatory considerations.

Lead bioaccumulation mediated by Bacillus cereus BPS-9 from an industrial waste contaminated site encoding heavy metal resistant genes and their transporters

This study explores the soil microorganisms for their Lead bioremediation capability. The MIC values of the six Lead resistant bacteria were evaluated, and the AAS studies of these isolates estimated their Lead accumulation percentage. The results showed that the isolate namely Bacillus cereus BPS-9 as identified based on 16S rDNA gene sequences was shown to have the highest Lead accumulation potential (79.26 %) and also selected for bioaccumulation studies. Despite the reduction in growth rate, the superoxide dismutase activity of B. cereus BPS-9 was increased with a rise in the concentration of Lead manifested through increased nitro-blue tetrazolium (NBT) reduction from 3.94 % to 77.48 %. Moreover, the biosorption capacity of B. cereus BPS-9 was 193.93 mg/g and the Langmuir isotherm model showed a value of R² = 0.9. Furthermore, the FTIR analysis also established the role of C-H, C=C, N=N, N-H, and C-O functional groups in Lead adsorption and the SEM micrographs showed that the cells of B. cereus BPS-9 became dense, adhered and distorted after Lead adsorption. Finally, the In-silico results obtained by functional analysis through SEED viewer of the whole genome of B. cereus deciphered the presence of genes encoding heavy metal resistant proteins and transporters for the efflux of heavy metals.

A comprehensive review on the integration of advanced oxidation processes with biodegradation for the treatment of textile wastewater containing azo dyes

The threat of dye contamination has achieved an unsurpassed abnormal state lately due to their massive consumption in several enterprises including textile, leather, cosmetic, plastic, and paper industries. This review focuses on the integrations of various advanced oxidation processes (AOPs), such as Fenton, photocatalysis, and ozonation, with biodegradation for the treatment of textile azo dyes. Such integrations have been explored lately by researchers to bring down the processing cost and improve the degree of mineralization of the treated dyeing wastewater. The review refers to the basic mechanisms, the influence of various process parameters, outcomes of recent works, and future research directions. All the three AOPs, independently, demonstrated substantial color reduction of 54–100%. The ozonation process, stand-alone, showed the most efficient decolorization (of 88–100%) consistently in all reviewed research works. In contrast, all three AOPs independently offered varied and inadequate COD reduction in the range of 16–80%. The AOPs, after getting integrated with biodegradation, yielded an additional reduction (of 11–70%) in the COD-levels and (of 16–80%) in the TOC-levels. Further, the integration of AOPs with biodegradation has potential to significantly reduce the treatment costs. The review suggests further research efforts in the direction of sequencing chemical and biological routes such that their synergistic utilization yield complete detoxification of the textile azo dyes economically at large-scale.

A critical review on advances in the practices and perspectives for the treatment of dye industry wastewater

Rapid industrialization has provided comforts to mankind but has also impacted the environment harmfully. There has been severe increase in the pollution due to several industries, in particular due to dye industry, which generate huge quantities of wastewater containing hazardous chemicals. Although tremendous developments have taken place for the treatment and management of such wastewater through chemical or biological processes, there is an emerging shift in the approach, with focus shifting on resource recovery from such wastewater and also their management in sustainable manner. This review article aims to present and discuss the most advanced and state-of-art technical and scientific developments about the treatment of dye industry wastewater, which include advanced oxidation process, membrane filtration technique, microbial technologies, bio-electrochemical degradation, photocatalytic degradation, etc. Among these technologies, microbial degradation seems highly promising for resource recovery and sustainability and has been discussed in detail as a promising approach. This paper also covers the challenges and future perspectives in this field.

A Facile Strategy for Immobilizing GOD and HRP onto Pollen Grain and Its Application to Visual Detection of Glucose

Pollen grain was explored as a new carrier for enzyme immobilization. After being modified with boric acid-functionalized titania, the pollen grain was able to covalently immobilize glycosylated enzymes by boronate affinity interaction under very mild experimental conditions (e.g., pH 7.0, ambient temperature and free of organic solvent). The glucose oxidase and horse radish peroxidase-immobilized pollen grain became a bienzyme system. The pollen grain also worked as an indicator of the cascade reaction by changing its color. A rapid, simple and cost-effective approach for the visual detection of glucose was then developed. When the glucose concentration exceeded 0.5 mM, the color change was observable by the naked eye. The assay of glucose in body fluid samples exhibited its great potential for practical application.

Futuristic avenues of metabolic engineering techniques in bioremediation

Bioremediation is a promising technology for the treatment of environmental contaminants and paving new avenues for the betterment of the environment. Over the last some years, several approaches have been employed to optimize the genetic machinery of microorganisms relevant to bioremediation. Metabolic engineering is one of them that provides a new insight for bioremediation. This review envisages the critical role of these techniques toward exploring the possibilities of the creation of a new pathway, leading to pathway expansion to new substrates by assembling of catabolic modules from different origins in the same microbial cell. The recombinant DNA technology and gene editing tools were also explored for the construction of metabolically engineered microbial strains for the degradation of complex pollutants. Moreover, the importance of CRISPR-Cas system for knock-in and knock-out of genes was described by using recent studies. Further, the idea of the cocultivation of more than one metabolic engineered microbial communities is also discussed, which can be crucial in the bioremediation of multiple and complex pollutants. Finally, this review also elucidates the effective application of metabolic engineering in bioremediation through these techniques and tools.

Microbial Polyethylene Terephthalate Hydrolases: Current and Future Perspectives

Plastic has rapidly transformed our world, with many aspects of human life now relying on a variety of plastic materials. Biological plastic degradation, which employs microorganisms and their degradative enzymes, has emerged as one way to address the unforeseen consequences of the waste streams that have resulted from mass plastic production. The focus of this review is microbial hydrolase enzymes which have been found to act on polyethylene terephthalate (PET) plastic. The best characterized examples are discussed together with the use of genomic and protein engineering technologies to obtain PET hydrolase enzymes for different applications. In addition, the obstacles which are currently limiting the development of efficient PET bioprocessing are presented. By continuing to study the possible mechanisms and the structural elements of key enzymes involved in microbial PET hydrolysis, and by assessing the ability of PET hydrolase enzymes to work under practical conditions, this research will help inform large-scale waste management operations. Finally, the contribution of microbial PET hydrolases in creating a potential circular PET economy will be explored. This review combines the current knowledge on enzymatic PET processing with proposed strategies for optimization and use, to help clarify the next steps in addressing pollution by PET and other plastics.

Exploring novel Cr(VI) remediation genes for Cr(VI)-contaminated industrial wastewater treatment by comparative metatranscriptomics and metagenomics

Microbial remediation is a promising method to treat Cr(VI) in industrial wastewater. The remediation efficiency and stress-resistance ability of Cr(VI) remediation genes in microbes are the limiting factors for their application in industrial wastewater treatment. To screen novel highly efficient Cr(VI) remediation genes, comparative metatranscriptomic and metagenomic analyses were performed on long-term Cr(VI)-contaminated riparian soil with/without additional Cr(VI) treatment. The most suitable Cr(VI) treatment time was determined to be 30 min according to the high quality RNA yield and fold changes in gene expression. Six novel genes, which had complete open reading frames (ORFs) in metagenomic libraries, were identified from unculturable microbes. In the phenotypic functional assay, all novel genes enhanced the Cr(VI) resistance/reduction ability of E. coli. In the industrial wastewater treatment, E-mcr and E-gsr presented at least 50% Cr(VI) removal efficiencies in the presence of 200-600 μM of Cr(VI), without a decrease in efficiency over 17 days. The stress resistance assay showed that gsr increased the growth rate of E. coli by at least 30% under different extreme conditions, and thus, gsr was identified as a general stress-response gene. In the Cr valence distribution assay, E-mcr presented ~40 μM higher extracellular Cr (III) compared to E-yieF. Additionally, transmission electron microscopy (TEM) of E-mcr showed bulk black agglomerates on the cell surface. Thus, mcr was identified as a membrane chromate reductase gene. This research provides a new idea for studying novel highly efficient contaminant remediation genes from unculturable microbes.

Removal of dye using peroxidase-immobilized Buckypaper/polyvinyl alcohol membrane in a multi-stage filtration column via RSM and ANFIS

The feasibility and performance of Jicama peroxidase (JP) immobilized Buckypaper/polyvinyl alcohol (BP/PVA) membrane for methylene blue (MB) dye removal was investigated in a customized multi-stage filtration column under batch recycle mode. The effect of independent variables, such as influent flow rate, ratio of H₂O₂/MB dye concentration, and contact time on the dye removal efficiency, were investigated using response surface methodology (RSM). To capture the inherent characteristics and better predict the removal efficiency, a data-driven adaptive neuro-fuzzy inference system (ANFIS) is implemented. Results indicated that the optimum dye removal efficiency of 99.7% was achieved at a flow rate of 2 mL/min, 75:1 ratio of H₂O₂/dye concentration with contact time of 183 min. The model predictions of ANFIS are significantly good compared with RSM, thus resulting in R² values of 0.9912 and 0.9775, respectively. The enzymatic kinetic parameters, K_m and V_max, were evaluated, which are 1.98 mg/L and 0.0219 mg/L/min, respectively. Results showed that JP-immobilized BP/PVA nanocomposite membrane can be promising and cost-effective biotechnology for the practical application in the treatment of industrial dye effluents.

Current Development in Decolorization of Synthetic Dyes by Immobilized Laccases

The world today is in a quest for new means of environmental remediation as the methods currently used are not sufficient to halt the damage. Mostly, a global direction is headed toward a shift from traditional chemical-based methods to a more ecofriendly alternative. In this context, biocatalysis is seen as a cost-effective, energy saving, and clean alternative. It is meant to catalyze degradation of recalcitrant chemicals in an easy, rapid, green, and sustainable manner. One already established application of biocatalysis is the removal of dyes from natural water bodies using enzymes, notably oxidoreductases like laccases, due to their wide range of substrate specificity. In order to boost their catalytic activity, various methods of enhancements have been pursued including immobilization of the enzyme on different support materials. Aside from increased catalysis, immobilized laccases have the advantages of higher stability, better durability against harsh environment conditions, longer half-lives, resistance against protease enzymes, and the ability to be recovered for reuse. This review briefly outlines the current methods used for detoxification and decolorization of dye effluents stressing on the importance of laccases as a revolutionary biocatalytic solution to this environmental problem. This work highlights the significance of laccase immobilization and also points out some of the challenges and opportunities of this technology.

Lignocellulolytic Enzymes in Biotechnological and Industrial Processes: A Review

Tons of anthropological activities contribute daily to the massive amount of lignocellulosic wastes produced annually. Unfortunately, their full potential usually is underutilized, and most of the biomass ends up in landfills. Lignocellulolytic enzymes are vital and central to developing an economical, environmentally friendly, and sustainable biological method for pre-treatment and degradation of lignocellulosic biomass which can lead to the release of essential end products such as enzymes, organic acids, chemicals, feed, and biofuel. Sustainable degradation of lignocellulosic biomass via hydrolysis is achievable by lignocellulolytic enzymes, which can be used in various applications, including but not limited to biofuel production, the textile industry, waste treatment, the food and drink industry, personal care industry, health and pharmaceutical industries. Nevertheless, for this to materialize, feasible steps to overcome the high cost of pre-treatment and lower operational costs such as handling, storage, and transportation of lignocellulose waste need to be deployed. Insight on lignocellulolytic enzymes and how they can be exploited industrially will help develop novel processes that will reduce cost and improve the adoption of biomass, which is more advantageous. This review focuses on lignocellulases, their use in the sustainable conversion of waste biomass to produce valued-end products, and challenges impeding their adoption.

A Bacillus Spore-Based Display System for Bioremediation of Atrazine

Owing to human activities, a large number of organic chemicals, including petroleum products, industrial solvents, pesticides, herbicides (including atrazine [ATR]), and pharmaceuticals, contaminate soil and aquatic environments. Remediation of these pollutants by conventional approaches is both technically and economically challenging. Bacillus endospores are highly resistant to most physical assaults and are capable of long-term persistence in soil. Spores can be engineered to express, on their surface, important enzymes for bioremediation purposes. We have developed a Bacillus thuringiensis spore platform system that can display a high density of proteins on the spore surface. The spore surface-tethered enzymes exhibit enhanced activity and stability relative to free enzymes in soil and water environments. In this study, we evaluated a B. thuringiensis spore display platform as a bioremediation tool against ATR. The Pseudomonas sp. strain ADP atzA determinant, an ATR chlorohydrolase important to the detoxification of ATR, was expressed as a fusion protein linked to the attachment domain of the BclA spore surface nap layer protein and expressed in B. thuringiensis Spores from this strain are decorated with AtzA N-terminally linked on the surface of the spores. The recombinant spores were assayed for ATR detoxification in liquid and soil environments, and enzyme kinetics and stability were assessed. We successfully demonstrated the utility of this spore-based enzyme display system to detoxify ATR in water and laboratory soil samples.IMPORTANCE Atrazine is one of the most widely applied herbicides in the U.S. midwestern states. The long environmental half-life of atrazine has contributed to the contamination of surface water and groundwater by atrazine and its chlorinated metabolites. The toxic properties of ATR have raised public health and ecological concerns. However, remediation of ATR by conventional approaches has proven to be costly and inefficient. We developed a novel B. thuringiensis spore platform system that is capable of long-term persistence in soil and can be engineered to surface express a high density of enzymes useful for bioremediation purposes. The enzymes are stably attached to the surface of the spore exosporium layer. The spore-based system will likely prove useful for remediation of other environmental pollutants as well.

Degradation and detoxification of azo dyes with recombinant ligninolytic enzymes from Aspergillus sp. with secretory overexpression in Pichia pastoris

Ligninolytic enzymes, including laccase (Lac), manganese peroxidase (MnP) and lignin peroxidase (LiP), have attracted much attention in the degradation of contaminants. Genes of Lac (1827 bp), MnP (1134 bp) and LiP (1119 bp) were cloned from Aspergillus sp. TS-A, and the recombinant Lac (69 kDa), MnP (45 kDa) and LiP (35 kDa) were secretory expressed in Pichia pastoris GS115, with enzyme activities of 34, 135.12 and 103.13 U l-1, respectively. Dyes of different structures were treated via the recombinant ligninolytic enzymes under the optimal degradation conditions, and the result showed that the decolourization rate of Lac on Congo red (CR) in 5 s was 45.5%. Fourier-transform infrared spectroscopy, gas chromatography-mass spectrometry analysis and toxicity tests further proved that the ligninolytic enzymes could destroy the dyes, both those with one or more azo bonds, and the degradation products were non-toxic. Moreover, the combined ligninolytic enzymes could degrade CR more completely compared with the individual enzyme. Remarkably, besides azo dyes, ligninolytic enzymes could also degrade triphenylmethane and anthracene dyes. This suggests that ligninolytic enzymes from Aspergillus sp. TS-A have the potential for application in the treatment of contaminants.

Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?

Petroleum is the major energy matrix in the world whose refining generates chemical byproducts that may damage the environment. Among such waste, polycyclic aromatic hydrocarbons (PAH) are considered persistent pollutants. Sixteen of these are considered priority for remediation, and among them is benzo(a)pyrene. Amid remediation techniques, bioremediation stands out. The genus Burkholderia is amongst the microorganisms known for being capable of degrading persistent compounds; its strains are used as models to study such ability. High-throughput sequencing allows researchers to reach a wider knowledge about biodegradation by bacteria. Using transcripts and mRNA analysis, the genomic regions involved in this aptitude can be detected. To unravel these processes, we used the model B. vietnamiensis strain G4 in two experimental groups: one was exposed to benzo(a)pyrene and the other one (control) was not. Six transcriptomes were generated from each group aiming to compare gene expression and infer which genes are involved in degradation pathways. One hundred fifty-six genes were differentially expressed in the benzo(a)pyrene exposed group, from which 33% are involved in catalytic activity. Among these, the most significant genomic regions were phenylacetic acid degradation protein paaN, involved in the degradation of organic compounds to obtain energy; oxidoreductase FAD-binding subunit, related to the regulation of electrons within groups of dioxygenase enzymes with potential to cleave benzene rings; and dehydrogenase, described as accountable for phenol degradation. These data provide the basis for understanding the bioremediation of benzo(a)pyrene and the possible applications of this strain in polluted environments.

Aromatic Hydrocarbon Removal by Novel Extremotolerant Exophiala and Rhodotorula Spp. from an Oil Polluted Site in Mexico

Since Aromatic hydrocarbons are recalcitrant and toxic, strategies to remove them are needed. The aim of this work was to isolate fungi capable of using aromatic hydrocarbons as carbon sources. Two isolates from an oil polluted site in Mexico were identified through morphological and molecular markers as a novel Rhodotorula sp. and an Exophiala sp. Both strains were able to grow in a wide range of pH media, from 4 to 12, showing their optimal growth at alkaline pH's and are both halotolerant. The Exophiala strain switched from hyphae to yeast morphotype in high salinity conditions. To the best of our knowledge, this is the first report of salt triggering dimorphism. The Rhodotorula strain, which is likely a new undescribed species, was capable of removing singled ringed aromatic compounds such as benzene, xylene, and toluene, but could not remove benzo[a] pyrene nor phenanthrene. Nevertheless, these hydrocarbons did not impair its growth. The Exophiala strain showed a different removal capacity. It could remove the polyaromatic hydrocarbons but performed poorly at removing toluene and xylene. Nevertheless, it still could grow well in the presence of the aromatic compounds. These strains could have a potential for aromatic compounds removal.

Microbial biofilm ecology, in silico study of quorum sensing receptor-ligand interactions and biofilm mediated bioremediation

Biofilms are structured microbial communities of single or multiple populations in which microbial cells adhere to a surface and get embedded in extracellular polymeric substances (EPS). This review attempts to explain biofilm architecture, development phases, and forces that drive bacteria to promote biofilm mode of growth. Bacterial chemical communication, also known as Quorum sensing (QS), which involves the production, detection, and response to small molecules called autoinducers, is highlighted. The review also provides a brief outline of interspecies and intraspecies cell-cell communication. Additionally, we have performed docking studies using Discovery Studio 4.0, which has enabled our understanding of the prominent interactions between autoinducers and their receptors in different bacterial species while also scoring their interaction energies. Receptors, such as LuxN (Phosphoreceiver domain and RecA domain), LuxP, and LuxR, interacted with their ligands (AI-1, AI-2, and AHL) with a CDocker interaction energy of - 31.6083 kcal/mole; - 34.5821 kcal/mole, - 48.2226 kcal/mole and - 41.5885 kcal/mole, respectively. Since biofilms are ideal for the remediation of contaminants due to their high microbial biomass and their potential to immobilize pollutants, this article also provides an overview of biofilm-mediated bioremediation.

Bioremediation of intertidal zones polluted by heavy oil spilling using immobilized laccase-bacteria consortium

Heavy oil pollution in the intertidal zones has become a worldwide environmental problem. In this study, bioremediation on heavy oil pollutants in the intertidal zones using an immobilized laccase-bacteria consortium system was evaluated with the aid of intertidal experimental pools built in the coastal area. It is found that degradation efficiency of the immobilized laccase-bacteria consortium for heavy oil was 66.5% after 100 days remediation, with the reaction rate constant of 0.018 d^-1. Gas Chromatograph-Mass Spectrometer analysis shows that degradation efficiency of saturated hydrocarbons and aromatic hydrocarbons were 79.2% and 78.7%, which were 64.9% and 65.1% higher than control. It is further seen that degradation of long-chain n-alkanes of C26-C35 and polycyclic aromatic hydrocarbons with more than three rings were significant. Metagenomic analysis indicates that the immobilized laccase-bacterial consortium has not only increased the biodiversity of heavy oil degrading bacteria, but also accelerated the degradation of heavy oil.