Enhanced removal of PAHs by Peniophora incarnata and ascertainment of its novel ligninolytic enzyme genes

A review on bioactivity, plant safety, and metal-reducing potential of lignin, its micro/nanostructures, and composites

Modern science focuses on sustainability-oriented innovation. Structurally sophisticated lignin is a sustainable alternative to non-renewable resources. Over the last several years, a tremendous scientific effort has been made to innovate lignin-based sustainable materials for numerous advanced applications. The lignin's phenolic, methoxyl and aliphatic hydroxyl functional groups are biologically and chemically active, making it conducive to developing state-of-the-art biomedicine, food packaging, crop protection, and catalyst materials. The biocidal effect of lignin rests on the phenolic compounds, specifically the double bond in α, β positions of the side chain, and a methyl group in the γ position. Also, depending on the biomass source and the pulping method, lignins possess different biocidal and antioxidant properties. The abundant hydroxyl groups in lignin are metal reductants and possess capping ability for the nanoparticles (NPs). This review focused on lignin's bioactivity mechanism, including antimicrobial efficacy and antioxidant properties. Lignin-based micro/nanocomposites and their application on food packaging, plant protection, and growth will also be explored. We will also review the application of lignin as a reducing and capping agent for the synthesis of metal NPs.

Degradation of High Concentrations of Anthracene Using White-Rot Wood-Inhabiting Fungi and Investigation of Enzyme Activities

Owing to the production of lignin-modifying enzymes (LMEs), white-rot fungi (WRF) such as polypores are potent organisms in the biodegradation of xenobiotic pollutants. The nonspecific function of LMEs including laccase and manganese peroxidase (MnP), has enabled the use of WRF in biotechnological applications, particularly in bioremediation. In this study, 12 strains from nine white-rot basidiomycete genera viz., Ganoderma, Inocutis, Irpex, Lentinus, Lenzites, Oxyporus, Peniophora, Sanghuangporus, and Trametes were isolated from Iran and identified using morphological and molecular tools. The enzyme activity of laccase and manganese peroxidase that directly correlated with the biodegradation were determined, and the strains with the highest enzyme activities were evaluated for their ability to degrade 400 mg/L of anthracene over 28 days. Gas chromatography with flame ionization detector (GC-FID) revealed that four polypores viz., Trametes versicolor v21te, T. versicolor v22da, T. hirsuta, and Oxyporus sp. degraded 64%, 52%, 34%, and 20% of the anthracene, respectively. According to our analysis, the examined indigenous WRF are potentially useful candidates for the development of new mycoremediation techniques to degrade polycyclic aromatic hydrocarbons (PAHs).

Microbes and microbial strategies in carcinogenic polycyclic aromatic hydrocarbons remediation: a systematic review

Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation-related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem.

Enhancement of MBBR reactor efficiency using effective microorganism for treatment of wastewater containing diazinon by engineered Pseudomonas putida KT2440 with manganese peroxidase 2 gene

Pesticides not only are harmful to humans but they are noxious for water reservoirs, soil, and air quality as well. In this research, diazinon was removed from aqueous solutions by Moving Bed Biofilm Reactor (MBBR). The MBBR was spiked with transgenic Pseudomonas putida KT2440 with Pleurotus ostreatus fungus manganese peroxidase 2 gene to enhance the capabilities of Pseudomonas putida KT2440 in the degradation of diazinon. Although the amount of diazinon and COD and diazinon removal in the reactor including transgenic P. putida KT2440 was 95.46% and 97.47% and they were greater than the control and wild type (non-modified) P. putida KT2440 reactors, the surprising result was related to the adaptation pace of transgenic P. putida KT2440. The produced metabolites and the quantity of diazinon were assessed by HPLC and LC/MS. The metabolite hydroxyisopropyl diazinon was not found in the transgenic P. putida KT2440 reactor. Furthermore, a new sequence of cloned manganese peroxidase 2 gene has been recorded in GenBank with the accession number MT185558. According to bacterial identification of provided sludge the most frequent genus belonged to Aeromonas. Therefore, it seems that the MBBR in the presence of transgenic P. putida KT2440 with manganese peroxidase 2 gene can effectively remove the diazinon.

Pyrene remediation by Trametes maxima: an insight into secretome response and degradation pathway

The rapid pace of economic development has resulted in the release of several polycyclic aromatic hydrocarbons (PAHs) into the environment. Microbial degradation using white-rot fungi is a promising method for the removal of PAHs from the environment. In the present study, biodegradation of recalcitrant PAH by a white-rot fungus, Trametes maxima IIPLC-32, was investigated using pyrene. The pyrene concentration decreased by 79.80%, 65.37%, and 56.37% within 16 days from the initial levels of 10 mg L^-1, 25 mg L^-1, and 50 mg L^-1, respectively. Gas chromatographic-mass spectrometric identification of prominent metabolites 1-hydroxypyrene, 2-methyl-1-naphthyl acetic acid, di-n-butyl phthalate, and diethyl phthalate helped in determining the pyrene degradation pathway. The presence of 81 extracellular proteins was revealed by secretome analysis. The identified proteins up-regulated in response to pyrene degradation were classified into detoxification proteins (6.12%), redox proteins (6.12%), stress proteins (4.08%), metabolic-related proteins (26.53%), translation and transcriptional proteins (49%), catalytic proteins (49%), and other proteins (8.16%). Knowledge of secretome analysis in pyrene degradation helped to understand the degradation mechanism of pyrene. Also, the study suggests that T. maxima IIPLC-32 has the potential to be used in the bioremediation of PAH contaminated aquatic environment.

Succession of diversity, functions, and interactions of the fungal community in activated sludge under aromatic hydrocarbon stress

Although fungi are regarded as the important degraders of aromatic hydrocarbons (AHs) in various environments, the dynamic succession and interaction of their community under aromatic hydrocarbon stress has been rarely reported. In this study, we systematically investigated the responses of the fungal community and the associations among fungal species when facing the continuous stress of two typical AHs, benzene and naphthalene. Using high-throughput sequencing technology, we demonstrated that fungal diversity displayed a significant downward trend during six weeks of continuous aromatic hydrocarbon treatment. Community succession was observed during the operational period, and the relative abundance of some typical degraders, such as Exophiala sp. and Candida sp., increased during the later period of operation. Meanwhile, by predicting the functions of the fungal community through PICRUSt2, we found that some relevant enzymes, such as peroxidase, dioxygenase, and monooxygenase, may play an important role in the degradation process and maintaining overall community multifunctionality. Furthermore, the measurement of modified normalized stochasticity ratio (MST) indicated that continuous aromatic hydrocarbon stress resulted in a stronger deterministic process in community assembly over time, suggesting environmental selection dominated succession of the fungal community in activated sludge. Finally, molecular ecological network analysis (MENA) demonstrated that, the cooperative behaviors among members, the network keystone genera related to biodegradation, such as Exophiala sp. and Haglerozyma sp., and a well-organized topological structure, together, maintained the structural stability of the fungal community under AH stress. Our study provides new insights for understanding the stability of fungal communities during the degradation of contaminants in activated sludge.

Current perspective of innovative strategies for bioremediation of organic pollutants from wastewater

Organic contaminants in water are a growing environmental threat to sustainable development, with detrimental effects on the biosphere. In recent years, researchers have increasingly focused their attention on the area of bioremediation as an important tool to eliminate harmful pollutants from the environment. This review examines the application of bioremediation technologies to the removal of organic pollutants, with an emphasis on hydrocarbons and textile dyes. It applies a descriptive bibliometric analysis to study statistical practicality-vs-applicability of bioremediation of emerging organic pollutants. The paper identifies efficient pathways for bioremediation of different types of organic pollutants and outlines the potential for an eco-friendly and economical approach for the biological remediation of micropollutants by microalgae. Facts and figures on various hazardous pollutants, constraints in their current removal from water at an industrial level, and promising future solutions are carefully presented here.

PAHs biodegradation in soil washing effluent by native mixed bacteria embedded in polyvinyl alcohol-sodium alginate-nano alumina gel beads

In this study, the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in soil washing solution containing Tween 80 was conducted using native mixed bacteria (Pseudomonas sp. Z1, Sphingobacterium sp. Z2, and Klebsiella sp. K) embedded in polyvinyl alcohol-sodium alginate-nano alumina (PVA-SA-ALNPs) gel beads. The optimal dosage of immobilized beads and embedded biomass for the biodegradation of phenanthrene (PHE), fluoranthene (FLU), and pyrene (PYR) were 10 % (v/v) and 20 % (v/v), respectively. SEM analysis showed that the porous structure of the immobilized beads was a cross-linked network with abundant pores that provided many potential adhesion sites for microorganisms. The beads with the immobilized mixed bacteria maintained a high activity during batch experiments and could even be reused for 3 cycles (90 d). Compared with the beads containing individual immobilized strain, the immobilized mixed bacteria showed a more efficient biodegradation of PHE (91.67 %), FLU (88.6 %), and PYR (88.5 %) in synthetic soil washing effluent within 30 d. The first-order kinetic model suitably described the degradation process of the three target PAHs. By adding Tween 80 to the synthetic eluent, the degradation of PHE, FLU, and PYR increased by 16.39 %, 22.25 %, and 21.29 %, respectively, indicating that Tween 80 promoted PAHs biodegradation, even though it was also rapidly degraded during the reaction cycle. These findings suggest that the developed mixed bacteria embedded in PVA-SA-ALNPs gel beads has great potential for PAHs remediation.

Selective delignification of poplar wood with a newly isolated white-rot basidiomycete Peniophora incarnata T-7 by submerged fermentation to enhance saccharification

BACKGROUND

Pretreatment is a critical step required for efficient conversion of woody biomass into biofuels and platform chemicals. Fungal pretreatment is regarded as one of the most promising technology for woody biomass conversion but remains challenging for industrial application. The exploration of potential fungus strain with high efficient delignification and less processing time for woody biomass pretreatment will be valuable for development of biorefinery industry. Here, a newly isolated white-rot basidiomycete Peniophora incarnate T-7 was employed for poplar wood pretreatment.

RESULTS

The chemical component analysis showed that cellulose, hemicellulose and lignin from poplar wood declined by 16%, 48% and 70%, respectively, after 7 days submerged fermentation by P. incarnate T-7. Enzymatic saccharification analysis revealed that the maximum yields of glucose and xylose from 7 days of P. incarnate T-7 treated poplar wood reached 33.4% and 27.6%, respectively, both of which were enhanced by sevenfold relative to the untreated group. Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), X-ray diffraction (XRD) and pyrolysis gas chromatography-mass spectrometry (Py-GC/MS) characterization confirmed that lignocellulosic structure of poplar wood was largely broken by P. incarnate T-7, including delignification and de-crystalline of cellulose. Meanwhile, lignin component of poplar wood was selectively degraded by P. incarnate T-7, and G-type unit of lignin was preferentially attacked by the strain. Furthermore, quantitative proteomic analysis revealed that a considerable amount of lignocellulolytic enzymes were detected in the secretory proteins of P. incarnate T-7, especially with high abundance of lignin-degrading enzymes and hemicellulases. Combination of quantitative proteomic with transcriptomic analysis results showed that most of those lignocellulolytic enzymes were highly upregulated on poplar wood substrate compared to glucose substrate.

CONCLUSIONS

This study showed that P. incarnate T-7 could selectively delignify poplar wood by submerged fermentation with short time of 7 days, which greatly improved its enzymatic saccharification efficiency. Our results suggested that P. incarnate T-7 might be a promising candidate for industrial woody biomass pretreatment.

Purification and Characterization of Two Novel Laccases from Peniophora lycii

Although, currently, more than 100 laccases have been purified from basidiomycete fungi, the majority of these laccases were obtained from fungi of the Polyporales order, and only scarce data are available about the laccases from other fungi. In this article, laccase production by the white-rot basidiomycete fungus Peniophora lycii, belonging to the Russulales order, was investigated. It was shown that, under copper induction, this fungus secreted three different laccase isozymes. Two laccase isozymes—Lac5 and LacA—were purified and their corresponding nucleotide sequences were determined. Both purified laccases were relatively thermostable with periods of half-life at 70 °C of 10 and 8 min for Lac5 and LacA, respectively. The laccases demonstrated the highest activity toward ABTS (97 U·mg⁻¹ for Lac5 and 121 U·mg⁻¹ for LacA at pH 4.5); Lac5 demonstrated the lowest activity toward 2,6-DMP (2.5 U·mg⁻¹ at pH 4.5), while LacA demonstrated this towards gallic acid (1.4 U·mg⁻¹ at pH 4.5). Both Lac5 and LacA were able to efficiently decolorize such dyes as RBBR and Bromcresol Green. Additionally, phylogenetic relationships among laccases of Peniophora spp. were reconstructed, and groups of orthologous genes were determined. Based on these groups, all currently available data about laccases of Peniophora spp. were systematized.

Ligninolytic enzyme involved in removal of high molecular weight polycyclic aromatic hydrocarbons by Fusarium strain ZH-H2

The capacity of Fusarium sp. strain ZH-H2 to secret lignin peroxidase (LiP), laccase (Lac), and manganese peroxidase (MnP) and degrade high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) was studied. When the fungus was grown in control mineral salt medium for 4 days, LiP and Lac activities were detected at 8871 U L^-1 and 5123 U L^-1, respectively. In the presence of HMW-PAHs as the sole carbon source, only LiP activity was detectable, and LiP activity had significantly reduced HMW-PAHs at day 7, with a maximum decrease of 85.9%. A strong correlation between LiP activity and HMW-PAHs removal efficiency could be fit into various models, with the highest correlation coefficients obtained for quadratic functions (P < 0.01). When a specific enzyme inhibitor was added, the ability of Fusarium to remove HMW-PAHs was reduced from 85.9 to 66.7%, depending on the inhibitor's concentration. Meanwhile, the determined activity of LiP was reduced from 11.4 to 48.6%. We conclude that in the presence of HMW-PAHs as the only carbon source to support growth, Fusarium ZH-H2 mainly produces LiP but not Lac or MnP for HMW-PAHs degradation. To our knowledge, it was the first time to propose a metabolic lignin peroxidase characterization of HMW-PAHs degradation by Fusarium sp. strains.

Degradation of the Organochlorinated Herbicide Diuron by Rainforest Basidiomycetes

The main organochlorinated compounds used on agricultural crops are often recalcitrant, affecting nontarget organisms and contaminating rivers or groundwater. Diuron (N-(3,4-dichlorophenyl)-N',N'-dimethylurea) is a chlorinated herbicide widely used in sugarcane plantations. Here, we evaluated the ability of 13 basidiomycete strains of growing in a contaminated culture medium and degrading the xenobiotic. Dissipation rates in culture medium with initial 25 mg/L of diuron ranged from 7.3 to 96.8%, being Pluteus cubensis SXS 320 the most efficient strain, leaving no detectable residues after diuron metabolism. Pycnoporus sanguineus MCA 16 removed 56% of diuron after 40 days of cultivation, producing three metabolites more polar than parental herbicide, two of them identified as being DCPU and DCPMU. Despite of the strong inductive effect of diuron upon laccase synthesis and secretion, the application of crude enzymatic extracts of P. sanguineus did not catalyzed the breakdown of the herbicide in vitro, indicating that diuron biodegradation was not related to this oxidative enzyme.

Identification of culturable petroleum-degrading bacteria and fungi from petroleum-contaminated sites in Brunei Darussalam

Microbes that can be cultured and degrade petroleum are of particular interest for biotechnology such as bioremediation. This study aims to isolate and identify culturable petroleum-degrading bacteria and fungi from Brunei Darussalam, which has not previously been explored. A total of eight bacterial and nine fungal isolates that could degrade petroleum were obtained from petroleum-contaminated water or soil samples. DNA barcoding using 16S rRNA gene sequence identified five different bacterial genera which were Bacillus, Enterobacter, Micrococcus, Pseudoaltermonas and Pseudomonas. DNA barcoding using rRNA-ITS gene sequence identified nine different fungal taxa which were Aspergillus, Cladosporium, Exophiala, Flavodon, Hypocreales, Nectriaceae, Penicillium, Peniophora and Trichoderma. Biolog provided additional support to the identification of some isolates. This study is the first to report these unique microbes from Brunei Darussalam, which are of ecological and biotechnological value.

A proposed stepwise screening framework for the selection of polycyclic aromatic hydrocarbon (PAH)-degrading white rot fungi

This study suggests a simple three-step screening protocol for the selection of white rot fungi (WRF) capable of degrading polycyclic aromatic hydrocarbons (PAHs), which combines easily applicable bioassay techniques, and verifies that protocol by evaluating the PAH degradation activity, ligninolytic enzyme secretion, and relevant gene expressions of the selected PAH-degraders. Using 120 fungal strains, a sequence of bioassay techniques was applied: Bavendamm's reaction (Step 1), remazol brilliant blue R (RBBR) decolorization (Step 2); assays for tolerance to four mixed PAHs-phenanthrene, anthracene, fluoranthene, and pyrene (Step 3). This stepwise protocol selected 14 PAH-degrading WRF, including Microporus vernicipes, Peniophora incarnata, Perenniporia subacida, Phanerochaete sordida, Phlebia acerina, and Phlebia radiata. Of these, P. incarnata exhibited the highest PAH degradative activity, ranging from 40 to > 90%, which was related to the time-variable secretions of three extracellular ligninolytic enzymes: laccase, manganese-dependent peroxidase (MnP) and lignin peroxidase (LiP). Laccase and MnP production by P. incarnata tended to be greater in the early stages of PAH degradation, whereas its LiP production became intensified with decreasing laccase and MnP production. Pilc1 and pimp1 genes encoding laccase and MnP were expressed, indicating the occurrence of extracellular enzyme-driven biodegradation of PAH by the fungal strains.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) by fungal enzymes: A review

Polycyclic aromatic hydrocarbons (PAHs) are a large group of chemicals. They represent an important concern due to their widespread distribution in the environment, their resistance to biodegradation, their potential to bioaccumulate and their harmful effects. Several pilot treatments have been implemented to prevent economic consequences and deterioration of soil and water quality. As a promising option, fungal enzymes are regarded as a powerful choice for degradation of PAHs. Phanerochaete chrysosporium, Pleurotus ostreatus and Bjerkandera adusta are most commonly used for the degradation of such compounds due to their production of ligninolytic enzymes such as lignin peroxidase, manganese peroxidase and laccase. The rate of biodegradation depends on many culture conditions, such as temperature, oxygen, accessibility of nutrients and agitated or shallow culture. Moreover, the addition of biosurfactants can strongly modify the enzyme activity. The removal of PAHs is dependent on the ionization potential. The study of the kinetics is not completely comprehended, and it becomes more challenging when fungi are applied for bioremediation. Degradation studies in soil are much more complicated than liquid cultures because of the heterogeneity of soil, thus, many factors should be considered when studying soil bioremediation, such as desorption and bioavailability of PAHs. Different degradation pathways can be suggested. The peroxidases are heme-containing enzymes having common catalytic cycles. One molecule of hydrogen peroxide oxidizes the resting enzyme withdrawing two electrons. Subsequently, the peroxidase is reduced back in two steps of one electron oxidation. Laccases are copper-containing oxidases. They reduce molecular oxygen to water and oxidize phenolic compounds.

Simultaneous removal of PAHs and metal contaminants from water using magnetic nanoparticle adsorbents

Many industrial wastewaters are contaminated with both heavy metal ions and organic compounds, posing a major threat to public health and the environment. In this study, magnetic nanoparticle adsorbents, namely Mag-PCMA-T, which contain a maghemite core and a silica mesoporous layer that permanently confines surfactant micelles within the mesopores, were synthesized to achieve simultaneous removal of polycyclic aromatic hydrocarbons (PAHs) (1mg/L) and metal contaminants (1mg/L). The individual removal efficiency of Cd(2+) and acenaphthene using Mag-PCMA-T was evaluated under a range of initial ion concentrations and adsorbent dosages, as well as the competitive adsorption with Cd(2+) and acenaphthene simultaneously present. The isotherms and kinetics of Cd(2+) and acenaphthene sorption onto Mag-PCMA-T were determined. Mag-PCMA-T removed >85% of the acenaphthene in <30min, with relatively high sorption capacity (up to 1060mg/kg). Mag-PCMA-T also exhibited high sorption capacity for Cd(2+) (up to 2250mg/kg). The simultaneous sorption performance was stable across a wide pH range (4-9) as well as in the presence of competitive metal ions (Ca(2+) and Mg(2+)) or natural organic matters. The Mag-PCMA-T can be regenerated and reused, providing a sustainable, fast, convenient, and efficient approach for water treatment.