Enhancing Bioremediation with Enzymatic Processes: A Review

Phenotypic characterization for bioremediation suitability of isolates from Southern Tunisian tannery effluent

Effluents from the leather tanning industry contain diverse pollutants, including hazardous heavy metals, posing threats to public health and the surrounding environment. Indigenous bacterial isolates can represent an eco-friendly approach for tannery wastewater treatment; however, phenotypic characterization is necessary to determine whether these strains are suitable for bioremediation. In the present study, we analyzed seven new Enterococcus faecium strains and two new Bacillus subtillis strains isolated from effluents from the Southern Tunisian Tannery (ESTT). We evaluated phenotypic features beneficial for bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities. Additionally, we examined characteristics naturally occurring in environmental bacteria but less desirable in strains selected for bioremediation, such as antibiotic resistances and pathogenicity indicators. The observed phenotypes were then compared with whole-genome analysis. We observed biofilm production in two slime-producing bacteria, B. licheniformis RLT6, and E. faecium RLT8. Hydrophobicity of E. faecium strains RLT1, RLT5, RLT8, and RLT9, as well as B. licheniformis RLT6 correlated positively with increasing ESTT concentration. Exoenzyme activities were detected in E. faecium strains RLT2, RLT4, and RLT7, as well as B. licheniformis RLT6. As anticipated, all strains exhibited common resistances to antibiotics and hemolysis, which are widespread in nature and do not hinder their application for bioremediation. Importantly, none of the strains exhibited the pathogenic hypermucoviscosity phenotype. To the best of our knowledge, this is the first report consolidating all these phenotypic characteristics concurrently, providing a complete overview of strains suitability for bioremediation. IMPORTANCE: The study evaluates the bioremediation potential of seven Enterococcus faecium strains and two Bacillus subtillis strains isolated from the effluents from the Southern Tunisian tannery (ESTT), which pose threats to public health and environmental integrity. The analysis primarily examines the phenotypic traits crucial to bioremediation, including biofilm formation, hydrophobicity, and exoenzyme activities, as well as characteristics naturally occurring in environmental bacteria related to heavy metal resistance, such as antibiotic resistances. Several strains were found to have high bioremediation potential and exhibit only antibiotic resistances commonly found in nature, ensuring their application for bioremediation remains uncompromised. The results of the exhaustive phenotypic analysis are contrasted with the whole genome sequences of the nine strains, underscoring the appropriateness of these bacterial strains for eco-friendly interventions in tannery wastewater treatment.

A systematic review on garbage enzymes and their applications in environmental processes

Understanding the new insight on conversion of organic waste into value-added products can improve the environmental activities driven by microorganisms and return the nutrients to environment and earth. Here, we comprehensively review the available knowledge on application of garbage enzyme (GE) for different environmental activities including waste activated sludge, composting process, landfill leachate treatment, soil remediation and wastewater treatment with special focus on their efficiency. To identify peer-reviewed studies published in English-language journals, a comprehensive search was performed across multiple electronic databases including Scopus, Web of Science, Pubmed, and Embase. The search was conducted systematically using relevant keywords. The eligible studies were analyzed to extract data and information pertaining to components of GE, fermentation process operational parameters, type of hydrolytic enzymes and improved environmental performance. The findings derived from this current review demonstrated that GE produced from the fruit and vegetable peels, molasses or brown sugar (carbon source), and water within fermentation process contain different hydrolytic enzymes in order to facilitate the organic waste degradation. Therefore, GE can be considered as a promising and efficient pathway in order to improve the environmental activities depended on microorganism including, composting, wastewater and leachate treatment and bioremediation process.

Bioreduction of Cr(VI) using a propane-based membrane biofilm reactor

The strong physiological toxicity of Cr(VI) makes it widely concerned in wastewater treatment. At present, the simplest and harmless method for treating Cr(VI) is known to be biologically reducing it to Cr(III), making it precipitate as Cr(OH)₃(s), and then removing Cr(III) by solid separation technology. Studies have shown that Cr(VI) reduction bacteria can use CH₄ and H₂ as electron donors to reduce Cr(VI). Based on this, in this study, C₃H₈ was used as the only electron donor to investigate the potential of C₃H₈ matrix membrane bioreactor in the Cr(VI) wastewater treatment. The experiment was divided into three stages, each of which run stably for at least 30 days, and the whole process run for 120 days in total. The experiment is divided into three stages, each stage runs stably for at least 30 days, for a total of 120 days. With the increase of the Cr(VI) load, the removal rate gradually decreased. In stage 3, when Cr(VI) concentration was 2.0 mg·L^-1, the removal rate was reduced from 90% in the first stage to 75%. According to X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) analysis, it is known that Cr(III) is the main product during this process and it is adsorbed on the biofilm as Cr(OH)₃ precipitate. During the experiment, the amount of extracellular polymeric substance (EPS) produced by microorganisms increased initially and then decreased, and the amount of polysaccharides (PS) was always more than protein (PN). By analyzing the microbial community structure after inoculating sludge and adding Cr(VI), Nocardia and Rhodococcus dominate the biofilm samples. Chromate reductase, cytochrome c, nitrate reductase, and other functional genes related to chromate reductase increased gradually during the experiment.

Metabolic pathway of Cr(VI) reduction by bacteria: A review

Heavy metal wastes, particularly hexavalent chromium [Cr(VI)], are generated from anthropogenic activities, and their increasing abundance has been a research concern due to their toxicity, genotoxicity, carcinogenicity and mutagenicity. Exposure to these dangerous pollutants could lead to chronic infections and even mortality in humans and animals. Bioremediation using microorganisms, particularly bacteria, has gained considerable interest because it can remove contaminants naturally and is safe to the surrounding environment. Bacteria, such as Pseudomonas putida and Bacillus subtilis, can reduce the toxic Cr(VI) to the less toxic trivalent chromium Cr(III) through mechanisms including biotransformation, biosorption and bioaccumulation. These mechanisms are mostly linked to chromium reductase and nitroreductase enzymes, which are involved in the Cr(VI) reduction pathway. However, relevant data on the nitroreductase route remain insufficient. Thus, this work proposes an alternative metabolic pathway of nitroreductase, wherein nitrate activates the reaction and indirectly reduces toxic chromium. This nitroreductase pathway occurs concurrently with the chromium reduction pathway.

Pilot-scale production and in-situ application of petroleum-degrading enzyme cocktail from Alcanivorax borkumensis

Petroleum degrading enzymes can be used as an alternative way to improve petroleum bioremediation approaches. Alcanivorax borkumensis is an alkane-degrading bacteria that can produce petroleum degrading enzymes such as alkane hydroxylase and lipase. In this study, pilot-scale Alcanivorax borkumensis fermentation was developed for producing large volumes of petroleum degrading enzymes cocktail (∼900 L). Different process conditions, such as inoculum age 72 h and size 4% v/v, temperature 30 ± 1 °C, agitation speed at 150 rpm and, fermentation period 3 days were determined as the optimum for producing alkane hydroxylase and lipase activity. The oxygen transfer capacity was studied for obtaining better bacterial growth and higher enzyme activities in bioreactor process optimization as well as scale-up. Results showed that the maximum values of oxygen mass transfer coefficient (k_La), oxygen uptake rate (OUR), oxygen transfer rate (OTR), alkane hydroxylase, lipase, and cell count were 196.95 h^-1, 0.92 mmol O₂/L/h, 1.8 mmol O₂/L/h, 222.49 U/mL, 325 U/mL, and 8.6 × 10¹⁰ CFU/mL, respectively. Compared with the bench-scale bioreactors, the 150 L fermenter showed a better oxygen transfer rate which affected the cell growth that doubled the number and enzymes production that increased. Then, the enzyme cocktail was used for a field test in a diesel source zone using a 5-spot well pattern. The results showed a significant reduction in concentrations of C10 - C50 (from 36% to > 99%) after one injection of enzyme cocktail, mainly for the contaminated soils located in the saturated zone of the unconfined aquifer. This study confirmed the scaling-up ofalkane-degrading enzyme production to an industrial-scale and its application for effective bioremediation of petroleum contaminated sites.

Column tests for evaluation of the enzymatic biodegradation capacity of hydrocarbons (C10-C50) contaminated soil

Though many studies pertaining to soil bioremediation have been performed to study the microbial kinetics in shake flasks, the process efficiency in column tests is seldom. In the present study, soil columns tests were carried out to study the biodegradation of soil contaminated with a high concentration of diesel (≈19.5 g/kg) petroleum hydrocarbons expressed as C₁₀-C₅₀. Experiments were done with crude enzymatic cocktail produced by the hydrocarbonoclastic bacterium, Alcanivorax borkumensis. A. borkumensis was grown on a media with 3% (v/v) motor oil as the sole carbon and energy source. The effects of the enzyme concentration, treatment time and oxidant on the bioremediation efficiency of C₁₀-C₅₀ were investigated. A batch test was also carried out in parallel to investigate the stability of the enzymes and the effect of the biosurfactants on the desorption and the bioconversion of C₁₀-C₅₀. Batch tests indicated that the biosurfactants significantly affected the desorption and alkane hydroxylase and lipase enzymes, maintained their catalytic activity during the 20-day test, with a half-life of 7.44 days and 8.84 days, respectively. The crude enzyme cocktail, with 40 U/mL of lipase and 10 U/mL of alkane hydroxylase, showed the highest conversion of 57.36% after 12 weeks of treatment with a degradation rate of 0.0218 day^-1. The results show that the soil column tests can be used to optimize operating conditions for hydrocarbon degradation and to assess the performance of the overall bioremediation process.

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi

Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.

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.

Enhanced adsorption of hexavalent chromium and the microbial effect on quartz sand modified with Al-layered double hydroxides

To enhance the hexavalent chromium (Cr(VI)) removal performance of simulated constructed rapid infiltration systems (CRIS) with quartz sand (QS) substrate, QS coated with Al-layered double hydroxides (Al-LDHs@QS) was prepared by the co-precipitation method under alkaline conditions. A scanning electron microscope (SEM), energy dispersive spectrometer (EDS) and X-ray diffractometer (XRD) were used to characterize QS before and after modification. The result showed that the Al-LDHs were successfully coated on the surface of the QS. The isotherm adsorption experiment indicated that compared with the original QS, the adsorption property of the modified QS changed from monolayered chemical adsorption to multilayered physical adsorption, perhaps because of different types of adsorption forces. Moreover, the adsorption capacity of modified QS was significantly enhanced and ZnAl-LDHs@QS had a maximum adsorption capacity (1428.57 mg·kg^-1) nearly 6 times greater than that of the original QS (232.56 mg·kg^-1). Adsorption experiments at different pH showed that the adsorption capacity of ZnAl-LDHs@QS gradually increased as acidity decreased. High-throughput sequencing revealed that the relative abundance of chrome-tolerant microorganisms at the phylum and family levels were increased in modified QS compared with original QS. Hemocytometer counting revealed enhanced microbial quantity on the surface of QS after modification. The content of extracellular polymeric substances (EPS) and the enzymatic activity of the microorganisms adhered to the surface of modified and original QS were detected, results showed that Al-LDHs had an obvious influence on the promotion of EPS secretion and enhanced the enzymatic activity of microorganisms. These changes indicated that the modified QS created better conditions for microorganism growth, and the improved microbial effect caused strong biosorption, resulting in greatly enhanced Cr(VI) removal. Thus, ZnAl-LDHs@QS is a better choice for CRIS to remove Cr(VI).

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.

Biodegradation of slop oil by endophytic Bacillus cereus EN18 coupled with lipase from Rhizomucor miehei (Palatase®)

Removal of slop oil, a by-product of oil refining, also obtained in cleaning up of oil tanks and filters is a difficult issue. High content of hydrocarbons (C3-C40) and other organic compounds makes this waste difficult to eliminate from the environment. The purpose of this investigation was to combine bacterial degradation by endophytic Bacillus cereus EN18 with biotransformation performed using lipase enzyme preparation (Palatase®) to remove recalcitrant compounds present in slop oil from the environment. Endophytic B. cereus EN18 was able to biodegrade up to 40% of slop oil while supplementation with lipase improved the efficiency of contamination removal in about one third. Also the use of lipase enzyme preparation resulted in higher microbial activity of B. cereus EN18 bacterial strain, as well as higher concentration of fatty acids in the culture medium, which indicates higher degradation efficiency. Obtained results suggest that lipase preparation from Rhizomucor miehei (Palatase®) may be a useful agent to improve microbial degradation of recalcitrant pollutants, like slop oil in water environments. GC and spectrometric analysis revealed that hydrocarbons from slop oil were effectively degraded while using both microbial degradation and lipase catalysis.

Bench-scale production of enzymes from the hydrocarbonoclastic bacteria Alcanivorax borkumensis and biodegradation tests

This study investigates motor oil (3, 5, 7.5 and 10% (v v^-1)) as a sole carbon source for the production of Alcanivorax borkumensis in shake flasks and a 5 L bench-scale fermenter in comparison to the standard media. Shake flask studies showed a significant and higher cell growth (p=0.000038), lipase (p = 0.006900) and alkane hydroxylase production (p = 0.000921) by Alcanivorax borkumensis when motor oil was used as the substrate. Based on Tukey post-hoc tests, 5% motor oil concentration was selected as the optimal substrate concentration. The 5 L fermenter experiments conducted using motor oil at 5% (v v^-1) concentration, under controlled conditions exhibited significant and higher alkane hydroxylase and lipase activities (55.6 U mL^-1 (p = 0.018418) and 208.30 U mL^-1 (p =  0.020087), respectively) as compared with those of motor oil at 3% (v v^-1) and n-hexadecane at 3% (v v^-1) concentration which was used as control. Cell growth was significantly higher when motor oil (3 or 5%) was used as a substrate (p =  0.024705). Enzymatic degradation tested on two different polycyclic aromatic hydrocarbons (PAHs) contaminated groundwaters showed 37.4% removal after 5 days with a degradation rate of 196.6 ppb day^-1 and 82.8% removal after 10 days with a degradation rate of 217.54 ppb day^-1 for the 1st site and an almost complete biodegradation with 95% removal and 499.02 ppb day^-1 removal rate after only 5 days for the 2nd site.

Contemporary enzyme based technologies for bioremediation: A review

The persistent disposal of xenobiotic compounds like insecticides, pesticides, fertilizers, plastics and other hydrocarbon containing substances is the major source of environmental pollution which needs to be eliminated. Many contemporary remediation methods such as physical, chemical and biological are currently being used, but they are not sufficient to clean the environment. The enzyme based bioremediation is an easy, quick, eco-friendly and socially acceptable approach used for the bioremediation of these recalcitrant xenobiotic compounds from the natural environment. Several microbial enzymes with bioremediation capability have been isolated and characterized from different natural sources, but less production of such enzymes is a limiting their further exploitation. The genetic engineering approach has the potential to get large amount of recombinant enzymes. Along with this, enzyme immobilization techniques can boost the half-life, stability and activity of enzymes at a significant level. Recently, nanozymes may offer the potential bioremediation ability towards a broad range of pollutants. In the present review, we have described a brief overview of the microbial enzymes, different enzymes techniques (genetic engineering and immobilization of enzymes) and nanozymes involved in bioremediation of toxic, carcinogenic and hazardous environmental pollutants.

Microbially-induced Carbonate Precipitation for Immobilization of Toxic Metals

Rapid urbanization and industrialization resulting from growing populations contribute to environmental pollution by toxic metals and radionuclides which pose a threat to the environment and to human health. To combat this threat, it is important to develop remediation technologies based on natural processes that are sustainable. In recent years, a biomineralization process involving ureolytic microorganisms that leads to calcium carbonate precipitation has been found to be effective in immobilizing toxic metal pollutants. The advantage of using ureolytic organisms for bioremediating metal pollution in soil is their ability to immobilize toxic metals efficiently by precipitation or coprecipitation, independent of metal valence state and toxicity and the redox potential. This review summarizes current understanding of the ability of ureolytic microorganisms for carbonate biomineralization and applications of this process for toxic metal bioremediation. Microbial metal carbonate precipitation may also be relevant to detoxification of contaminated process streams and effluents as well as the production of novel carbonate biominerals and biorecovery of metals and radionuclides that form insoluble carbonates.

Purification and characterization of a highly active chromate reductase from endophytic Bacillus sp. DGV19 of Albizzia lebbeck (L.) Benth. actively involved in phytoremediation of tannery effluent-contaminated sites

Phytoremediation using timber-yielding tree species is considered to be the most efficient method for chromium/tannery effluent-contaminated sites. In this study, we have chosen Albizzia lebbeck, a chromium hyperaccumulator plant, and studied one of its chromium detoxification processes operated by its endophytic bacterial assemblage. Out of the four different groups of endophytic bacteria comprising Pseudomonas, Rhizobium, Bacillus, and Salinicoccus identified from A. lebbeck employed in phytoremediation of tannery effluent-contaminated soil, Bacillus predominated with three species, which exhibited not only remarkable chromium accumulation ability but also high chromium reductase activity. A chromate reductase was purified to homogeneity from the most efficient chromium accumulator, Bacillus sp. DGV 019, and the purified 34.2-kD enzyme was observed to be stable at temperatures from 20°C to 60°C. The enzyme was active over a wide range of pH values (4.0-9.0). Furthermore, the enzyme activity was enhanced with the electron donors NADH, followed by NADPH, not affected by glutathione and ascorbic acid. Cu(2+) enhanced the activity of the purified enzyme but was inhibited by Zn(2+) and etheylenediamine tetraacetic acid (EDTA). In conclusion, due to its versatile adaptability the chromate reductase can be used for chromium remediation.

Bacterial chromate reductase, a potential enzyme for bioremediation of hexavalent chromium: a review

Hexavalent chromium is mobile, highly toxic and considered as a priority environmental pollutant. Chromate reductases, found in chromium resistant bacteria are known to catalyse the reduction of Cr(VI) to Cr(III) and have recently received particular attention for their potential use in bioremediation process. Different chromate reductases such as ChrR, YieF, NemA and LpDH, have been identified from bacterial sources which are located either in soluble fractions (cytoplasm) or bound to the membrane of the bacterial cell. The reducing conditions under which these enzymes are functional can either be aerobic or anaerobic or sometimes both. Enzymatic reduction of Cr(VI) to Cr(III) involves transfer of electrons from electron donors like NAD(P)H to Cr(VI) and simultaneous generation of reactive oxygen species (ROS). Based on the steps involved in electron transfer to Cr(VI) and the subsequent amount of ROS generated, two reaction mechanisms, namely, Class I "tight" and Class II "semi tight" have been proposed. The present review discusses on the types of chromate reductases found in different bacteria, their mode of action and potential applications in bioremediation of hexavalent chromium both under free and immobilize conditions. Besides, techniques used in characterization of the Cr (VI) reduced products were also discussed.

Enzymes as useful tools for environmental purposes

In the environment enzymes may play important and different roles at least in three cases: as main agents (as isolated, cell-bound or immobilized enzymes) in charge of either the transformation and/or degradation of compounds polluting the environment and the restoration of the polluted environment; as reliable and sensitive tools to detect and measure the amount and concentration of pollutants before, during and after the restoration process; as reliable, easy and sensitive indicators of quality and health status of the environment subjected to the restoration process. To our knowledge papers or reviews integrating findings on these three functions of enzymes are missing in literature. Therefore the main scope of the present paper is to briefly encompass general and specific concepts about roles of enzymes as decontaminating agents, pollutant assaying agents and indicators of environment safety. Examples chosen among those published very recently, supporting and confirming peculiarities, features, and performance of enzymatic agents will be illustrated.

Novel insights into enzymatic-enhanced anaerobic digestion of waste activated sludge by three-dimensional excitation and emission matrix fluorescence spectroscopy

In our previous study, it has been proposed that the hydrolysis of waste activated sludge (WAS) can be enhanced by hydrolytic enzymes. In this study, fluorescence spectral characteristics of extracellular polymeric substances (EPSs) and dissolved organic matter (DOM) during anaerobic digestion were investigated using three-dimensional excitation-emission matrix (EEM) fluorescence spectroscopy to explore the destruction mechanisms of WAS enhanced by additional enzymes (protease, α-amylase and the mixture). Two individual fluorescence peaks associated with protein-like fluorophores (aromatic and tryptophan protein-like substances) were identified in the EEM fluorescence spectra of the EPS after 1 and 6d, and only aromatic protein-like substances were observed after 12d of anaerobic digestion for all treatments. As for the DOM, three individual fluorescence peaks were identified, but the peaks associated with visible humic acid-like fluorophores disappeared after 12d. The EEM fluorescence intensity of EPS decreased during the entire anaerobic process, whereas that of the DOM increased at 1d and then decreased till the end. In the EPS, the residual protein-like substances were found to be the lowest during the entire anaerobic process when treated with protease. Correspondingly, the protein-like substances in the DOM increased rapidly from 1 to 6d, and decreased to the lowest level after 12d for the protease treatment.