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

Biodegradation mechanisms of polycyclic aromatic hydrocarbons: Combination of instrumental analysis and theoretical calculation

Polycyclic aromatic hydrocarbons (PAHs) are a common class of petroleum hydrocarbons, widely encountered in both environment and industrial pollution sources. Owing to their toxicity, environmental persistence, and potential bioaccumulation properties, a mounting interest has been kindled in addressing the remediation of PAHs. Biodegradation is widely employed for the removal and remediation of PAHs due to its low cost, lack of second-contamination and ease of operation. This paper reviews the degradation efficiency of degradation and the underlying mechanisms exhibited by algae, bacteria, and fungi in remediation. Additionally, it delved into the application of modern instrumental analysis techniques and theoretical investigations in the realm of PAH degradation. Advanced instrumental analysis methods such as mass spectrometry provide a powerful tool for identifying intermediates and metabolites throughout the degradation process. Meanwhile, theoretical calculations could guide the optimization of degradation processes by revealing the reaction mechanisms and energy changes in PAH degradation. The combined use of instrumental analysis and theoretical calculations allows for a comprehensive understanding of the degradation mechanisms of PAHs and provides new insights and approaches for the development of environmental remediation technologies.

Biodegradation of Benzo[a]pyrene by a White-Rot Fungus Phlebia acerina: Surfactant-Enhanced Degradation and Possible Genes Involved

Polycyclic aromatic hydrocarbons (PAHs) are persistent environmental pollutants that pose a threat to human health. Among these PAHs, benzo[a]pyrene (BaP), a five-ring compound, exhibits high resistance to biodegradation. White-rot fungus Phlebia acerina S-LWZ20190614-6 has demonstrated higher BaP degradation capabilities compared with Phanerochaete chrysosporium and P. sordida YK-624, achieving a degradation rate of 57.7% after 32 days of incubation under a ligninolytic condition. To further enhance the biodegradation rate, three nonionic surfactants were used, and the addition of 1 or 2 g·L-1 of polyethylene glycol monododecyl ether (Brij 30) resulted in nearly complete BaP biodegradation by P. acerina S-LWZ20190614-6. Interestingly, Brij 30 did not significantly affect the activity of manganese peroxidase and lignin peroxidase, but it did decrease laccase activity. Furthermore, the impact of cytochrome P450 on BaP degradation by P. acerina S-LWZ20190614-6 was found to be relatively mild. Transcriptomic analysis provided insights into the degradation mechanism of BaP, revealing the involvement of genes related to energy production and the synthesis of active enzymes crucial for BaP degradation. The addition of Brij 30 significantly upregulated various transferase and binding protein genes in P. acerina S-LWZ20190614-6. Hence, the bioremediation potential of BaP by the white-rot fungus P. acerina S-LWZ20190614-6 holds promise and warrants further exploration.

Endophytic, extremophilic and entomophilic fungi strains biodegrade anthracene showing potential for bioremediation

Anthropogenic activities have been increasing Polycyclic Aromatic Hydrocarbons (PAHs) release, promoting an urgent need for decontamination methods. Therefore, anthracene biodegradation by endophytic, extremophilic, and entomophilic fungi was studied. Moreover, a salting-out extraction methodology with the renewable solvent ethanol and the innocuous salt K₂HPO₄ was employed. Nine of the ten employed strains biodegraded anthracene in liquid medium (19-56% biodegradation) after 14 days at 30 °C, 130 rpm, and 100 mg L^-1. The most efficient strain Didymellaceae sp. LaBioMMi 155, an entomophilic strain, was employed for optimized biodegradation, aiming at a better understanding of how factors like pollutant initial concentration, pH, and temperature affected this process. Biodegradation reached 90 ± 11% at 22 °C, pH 9.0, and 50 mg L^-1. Futhermore, 8 different PAHs were biodegraded and metabolites were identified. Then, experiments with anthracene in soil ex situ were performed and bioaugmentation with Didymellaceae sp. LaBioMMi 155 presented better results than natural attenuation by the native microbiome and biostimulation by the addition of liquid nutrient medium into soil. Therefore, an expanded knowledge about PAHs biodegradation processes was achieved with emphasis to the action of Didymellaceae sp. LaBioMMi 155, which can be further employed for in situ biodegradation (after strain security test), or for enzyme identification and isolation aiming at oxygenases with optimal activity under alkaline conditions.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

PUF-Immobilized Bjerkandera adusta DSM 3375 as a Tool for Bioremediation of Creosote Oil Contaminated Soil

Creosote oil, a byproduct of coal distillation, is primarily composed of aromatic compounds that are difficult to degrade, such as polycyclic aromatic hydrocarbons, phenolic compounds, and N-, S-, and O-heterocyclic compounds. Despite its toxicity and carcinogenicity, it is still often used to impregnate wood, which has a particularly negative impact on the condition of the soil in plants that impregnate wooden materials. Therefore, a rapid, effective, and eco-friendly technique for eliminating the creosote in this soil must be developed. The research focused on obtaining a preparation of Bjerkandera adusta DSM 3375 mycelium immobilized in polyurethane foam (PUF). It contained mold cells in the amount of 1.10 ± 0.09 g (DW)/g of the carrier. The obtained enzyme preparation was used in the bioremediation of soil contaminated with creosote (2% w/w). The results showed that applying the PUF-immobilized mycelium of B. adusta DSM 3375 over 5, 10, and 15 weeks of bioremediation, respectively, removed 19, 30, and 35% of creosote from the soil. After 15 weeks, a 73, 79, and 72% level of degradation of fluoranthene, pyrene, and fluorene, respectively, had occurred. The immobilized cells have the potential for large-scale study, since they can degrade creosote oil in soil.

Microbial communities in petroleum-contaminated sites: Structure and metabolisms

Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad

Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.

Toxicity evaluation and biodegradation of phenanthrene by laccase from Trametes polyzona PBURU 12

The newly isolated Trametes polyzona PBURU 12 demonstrated a high tolerance and potential for the degradation of phenanthrene. The fungal isolate was able to tolerate 100 ppm of phenanthrene with 45% relative growth. The crude laccase produced by Trametes polyzona PBURU 12 was able to degrade phenanthrene by up to 98% within 24 h. The degradation metabolites showed the absence of toxic compounds. Microbial viability tests using E. coli and B. subtilis revealed that the treated phenanthrene was less toxic than untreated phenanthrene. Phytotoxicity and genotoxicity tests, using Vigna radiata and Allium cepa, indicated that the treated phenanthrene was less toxic to the plants. No mutagenic activity was found in the Ames test. The crude laccase from Trametes polyzona PBURU 12 was demonstrated as a potential tool for the biodegradation of PAHs (phenanthrene), with low toxic effects after the degradation.

Ligninolytic Enzyme Production and Decolorization Capacity of Synthetic Dyes by Saprotrophic White Rot, Brown Rot, and Litter Decomposing Basidiomycetes

An extensive screening of saprotrophic Basidiomycetes causing white rot (WR), brown rot (BR), or litter decomposition (LD) for the production of laccase and Mn-peroxidase (MnP) and decolorization of the synthetic dyes Orange G and Remazol Brilliant Blue R (RBBR) was performed. The study considered in total 150 strains belonging to 77 species. The aim of this work was to compare the decolorization and ligninolytic capacity among different ecophysiological and taxonomic groups of Basidiomycetes. WR strains decolorized both dyes most efficiently; high decolorization capacity was also found in some LD fungi. The enzyme production was recorded in all three ecophysiology groups, but to a different extent. All WR and LD fungi produced laccase, and the majority of them also produced MnP. The strains belonging to BR lacked decolorization capabilities. None of them produced MnP and the production of laccase was either very low or absent. The most efficient decolorization of both dyes and the highest laccase production was found among the members of the orders Polyporales and Agaricales. The strains with high MnP activity occurred across almost all fungal orders (Polyporales, Agaricales, Hymenochaetales, and Russulales). Synthetic dye decolorization by fungal strains was clearly related to their production of ligninolytic enzymes and both properties were determined by the interaction of their ecophysiology and taxonomy, with a more relevant role of ecophysiology. Our screening revealed 12 strains with high decolorization capacity (9 WR and 3 LD), which could be promising for further biotechnological utilization.

White rot fungi can be a promising tool for removal of bisphenol A, bisphenol S, and nonylphenol from wastewater

Endocrine-disrupting chemicals (EDC) are a wide group of chemicals that interfere with the endocrine system. Their similarity to natural steroid hormones makes them able to attach to hormone receptors, thereby causing unfavorable health effects. Among EDC, bisphenol A (BPA), bisphenol S (BPS), and nonylphenol (NP) seem to be particularly harmful. As the industry is experiencing rapid expansion, BPA, BPS, and NP are being produced in growing amounts, generating considerable environmental pollution. White rot fungi (WRF) are an economical, ecologically friendly, and socially acceptable way to remove EDC contamination from ecosystems. WRF secrete extracellular ligninolytic enzymes such as laccase, manganese peroxidase, lignin peroxidase, and versatile peroxidase, involved in lignin deterioration. Owing to the broad substrate specificity of these enzymes, they are able to remove numerous xenobiotics, including EDC. Therefore, WRF seem to be a promising tool in the abovementioned EDC elimination during wastewater treatment processes. Here, we review WRF application for this EDC removal from wastewater and indicate several strengths and limitations of such methods.