Biodegradation of pyrene by sediment fungi

Function of chitinase in Penicillium ochrochloron Q-3-1 and its insecticidal and antifungal mechanism and biological control against citrus pests and diseases

The biocontrol potential strain of Penicillium ochrochloron Q-3-1 was isolated from Hepialus armoricanus larvae. However, the insecticidal and antifungal mechanisms of Q-3-1 are still unclear. Eleven chitinase genes (Poch1-Poch11) were isolated for functional identification. During Q-3-1 infection, Poch1, Poch2, and Poch11 were upregulated in Galleria mellonella, whereas Poch4, Poch6, and Poch11 were upregulated in Diaphorina citri. Chitinase activity was determined based on the expression of the chitinase genes in an in vitro prokaryotic expression system and an analysis of the p-nitrophenol (pNP) degradation ability of recombinant chitinase. They exhibit excellent degradation activities for chitin, citrus pectin, D-cellobiose, and G. mellonella epidermis. The exonuclease activity of Poch1 can effectively degrade insect chitin and pectin. The insect chitin utilization rate of Poch11 is higher than that of pectin, and it can randomly degrade different pNP substrates. In addition, the present study found that exogenous chitinase proteins showed significant antagonistic ability against citrus pathogens. The special antifungal and insecticidal character of Q-3-1 may lead to its potential application in agriculture as a biological control agent.

Three strategy rules of filamentous fungi in hydrocarbon remediation: an overview

Remediation of hydrocarbon contaminations requires much attention nowadays since it causes detrimental effects on land and even worse impacts on aquatic environments. Tools of bioremediation especially filamentous fungi permissible for cleaning up as much as conceivable, at least they turn into non-toxic residues with less consumed periods. Inorganic chemicals, CO2, H2O, and cell biomass are produced as a result of the breakdown and mineralization of petroleum hydrocarbon pollutants. This paper presents a detailed overview of three strategic rules of filamentous fungi in remediating the various aliphatic, and aromatic hydrocarbon compounds: utilizing carbons from hydrocarbons as sole energy, Co-metabolism manners (Enzymatic and Non-enzymatic theories), and Biosorption approaches. Upliftment in the degradation rate of complex hydrocarbon by the Filamentous Fungi in consortia scenario we can say, "Fungal Talk", which includes a variety of cellular mechanisms, including biosurfactant production, biomineralization, and precipitation, etc., This review not only displays its efficiency but showcases the field applications - cost-effective, reliable, eco-friendly, easy to culture as biomass, applicable in both land and any water bodies in operational environment cleanups. Nevertheless, the potentiality of fungi-human interaction has not been fully understood, henceforth further studies are highly endorsed with spore pathogenicity of the fungal species capable of high remediation rate, and the gene knockout study, if the specific peptides cause toxicity to any living matters via Genomics and Proteomics approaches, before application of any in situ or ex situ environments.

Potential biodegradation of polycyclic aromatic hydrocarbons (PAHs) and petroleum hydrocarbons by indigenous fungi recovered from crude oil-contaminated soil in Iran

A total of 265 fungal individuals were isolated from soils exposed to heavy oil spills in the Yadavaran oil field in Iran to discover indigenous fungal species with a high potential to biodegrade petroleum hydrocarbon pollutants. Morphological and molecular identification of obtained fungal species led to their assignment into 16 genera and 25 species. Alternaria spp. (78%), Fusarium spp. (5%), and Cladosporium spp. (4%) were the most common genera, along with Penicillium spp., Neocamarosporium spp., Epicoccum sp., Kotlabaea sp., Aspergillus sp., Mortierella sp., and Pleurotus sp. A preliminary screening using the DCPIP indicator revealed that approximately 35% of isolates from Alternaria, Epicoccum, Neocamarosporium, Cladosporium, Fusarium, Stachybotrys, Penicillium, and Stemphylium demonstrated promising tolerance to crude oil. The best-performing isolates (12 fungal individuals) were further investigated for their capacity to mineralize a mixture of four polycyclic aromatic hydrocarbons (PAH) for 47 days, quantified by GC-MS. Eventually, two top-performing isolates, namely 5c-12 (Alternaria tenuissima) and 3b-1 (Epicoccum nigrum), were applied to petroleum-contaminated soil. The GC-MS analysis showed that 60 days after inoculation, these isolates successfully degraded more than 70% of the long-chain hydrocarbons in the soil, including C8-C16 n-alkanes, C36 n-alkane, and Pristane. This study introduces two fungal species (5c-12 and 3b-1) with high potential for biodegrading petroleum compounds and PAHs, offering promising prospects for the decontamination of oil-contaminated soil.

Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons

This review presents a comprehensive summary of the latest research in the field of bioremediation with filamentous fungi. The main focus is on the issue of recent progress in remediation of pharmaceutical compounds, heavy metal treatment and oil hydrocarbons mycoremediation that are usually insufficiently represented in other reviews. It encompasses a variety of cellular mechanisms involved in bioremediation used by filamentous fungi, including bio-adsorption, bio-surfactant production, bio-mineralization, bio-precipitation, as well as extracellular and intracellular enzymatic processes. Processes for wastewater treatment accomplished through physical, biological, and chemical processes are briefly described. The species diversity of filamentous fungi used in pollutant removal, including widely studied species of Aspergillus, Penicillium, Fusarium, Verticillium, Phanerochaete and other species of Basidiomycota and Zygomycota are summarized. The removal efficiency of filamentous fungi and time of elimination of a wide variety of pollutant compounds and their easy handling make them excellent tools for the bioremediation of emerging contaminants. Various types of beneficial byproducts made by filamentous fungi, such as raw material for feed and food production, chitosan, ethanol, lignocellulolytic enzymes, organic acids, as well as nanoparticles, are discussed. Finally, challenges faced, future prospects, and how innovative technologies can be used to further exploit and enhance the abilities of fungi in wastewater remediation, are mentioned.

The simultaneous removal of co-contaminants pyrene and Cu (II) from aqueous solutions by Fe/Mn bimetallic functionalized mesoporous silica

In recent years, the co-contamination of heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) has attracted more and more attention, and finding efficient and coordinated removal method has been the hot focus. In this study, Fe/Mn-SBA15 bimetallic mesoporous silica adsorbent (Fe/Mn-SBA15) was prepared by hydrothermal method with the functional groups Fe and Mn simultaneously doped into the framework structure of SBA15. Fe/Mn-SBA15 was systematically characterized by XRD, TEM, and BET and used in removal of typical PAHs-pyrene and heavy metal-Cu (II) from aqueous solutions simultaneously. The single and binary adsorption behaviors were studied by kinetics, isotherm, pH, and ionic strength. The results showed that the functional groups of Fe and Mn were successfully loaded into the structure of SBA15 and the prepared adsorbent was still a typical mesoporous adsorbent. The adsorption of pyrene and Cu (II) onto Fe/Mn-SBA15 was fast and the adsorption equilibrium was achieved in 100 min. The Langmuir model fitted the adsorption isotherm better and the maximum adsorption capacities for pyrene and Cu (II) were 120 mg/g and 10.52 mg/g, respectively. The increase of ionic strength could enhance and decrease the adsorption capacity of pyrene and Cu (II), which may be attributed to salting-out effect and potassium competitive. With the increase of pH values, the negative charge on the surface of the adsorbent increased, resulting in the decrease and increase of adsorption capacity of pyrene and Cu (II) onto Fe/Mn-SBA15. In addition, Fe/Mn-SBA15 was found to have a synergistic effect on the adsorption of pyrene and Cu (II). This result is mainly due to the formation of hydration complex by pyrene-Cu (II) through cation-π interaction, which increases the adsorption capacity by occupying each other's adsorption sites of adsorbent. This study provides a new method for the synergistic removal of PAHs and HMs from aqueous solutions.

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.

Microbial Hydrocarbon Degradation in Guaymas Basin-Exploring the Roles and Potential Interactions of Fungi and Sulfate-Reducing Bacteria

Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.

Kinetics and equilibrium study for the biosorption of lanthanum by Penicillium simplicissimum INCQS 40,211

Lanthanum (La) is a light rare-earth element that plays an essential role in manufacturing technological products, clean technologies, medical products, electron cathodes, scintillators, fluorescent lamps, and fertilizers. This study is the first investigation of La³⁺ biosorption using inactive lyophilized biomass from Penicillium simplicissimum INCQS 40,211. The maximum sorption capacity (q_max) for P. simplicissimum was 7.81 mg g^-1. La ³⁺ biosorption followed the Freundlich model, where the biosorption system possibly multilayer coverage of P. simplicissimum by lanthanum ions. The kinetic data for the adsorption process obeyed a pseudo-second-order (R ² > 0.92), indicating chemical sorption. The results indicated that inactive lyophilized biomass from Penicillium simplicissimum INCQS 40211are an excellent candidate for removing light rare-earth elements from aquatic environments.

Aerobic and Anaerobic Bacterial and Fungal Degradation of Pyrene: Mechanism Pathway Including Biochemical Reaction and Catabolic Genes

Microbial biodegradation is one of the acceptable technologies to remediate and control the pollution by polycyclic aromatic hydrocarbon (PAH). Several bacteria, fungi, and cyanobacteria strains have been isolated and used for bioremediation purpose. This review paper is intended to provide key information on the various steps and actors involved in the bacterial and fungal aerobic and anaerobic degradation of pyrene, a high molecular weight PAH, including catabolic genes and enzymes, in order to expand our understanding on pyrene degradation. The aerobic degradation pathway by Mycobacterium vanbaalenii PRY-1 and Mycobactetrium sp. KMS and the anaerobic one, by the facultative bacteria anaerobe Pseudomonas sp. JP1 and Klebsiella sp. LZ6 are reviewed and presented, to describe the complete and integrated degradation mechanism pathway of pyrene. The different microbial strains with the ability to degrade pyrene are listed, and the degradation of pyrene by consortium is also discussed. The future studies on the anaerobic degradation of pyrene would be a great initiative to understand and address the degradation mechanism pathway, since, although some strains are identified to degrade pyrene in reduced or total absence of oxygen, the degradation pathway of more than 90% remains unclear and incomplete. Additionally, the present review recommends the use of the combination of various strains of anaerobic fungi and a fungi consortium and anaerobic bacteria to achieve maximum efficiency of the pyrene biodegradation mechanism.

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.

Fungi in PAH-contaminated marine sediments: Cultivable diversity and tolerance capacity towards PAH

The cultivable fungal diversity from PAH-contaminated sediments was examined for the tolerance to polycyclic aromatic hydrocarbon (PAH). The 85 fungal strains, isolated in non-selective media, revealed a large diversity by ribosomal internal transcribed spacer (ITS) sequencing, even including possible new species. Most strains (64%) exhibited PAH-tolerance, indicating that sediments retain diverse cultivable PAH-tolerant fungi. The PAH-tolerance was linked neither to a specific taxon nor to the peroxidase genes (LiP, MnP and Lac). Examining the PAH-removal (degradation and/or sorption), Alternaria destruens F10.81 showed the best capacity with above 80% removal for phenanthrene, pyrene and fluoranthene, and around 65% for benzo[a]pyrene. A. destruens F10.81 internalized pyrene homogenously into the hyphae that contrasted with Fusarium pseudoygamai F5.76 in which PAH-vacuoles were observed but PAH removal was below 20%. Thus, our study paves the way for the exploitation of fungi in remediation strategies to mitigate the effect of PAH in coastal marine sediments.

Investigating the mycobiome of the Holcomb Creosote Superfund Site

Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.

Marine sediment toxicity: A focus on micro- and mesocosms towards remediation

Micro- and/or mesocosms are experimental tools bringing ecologically relevant components of the natural environment under controlled conditions closest to the real world, without losing the advantage of reliable reference conditions and replications, providing a link between laboratory studies and filed studies in natural environments. Here, for the first time, a formal comparison of different types of mesocosm applied to the study of marine contaminants is offered, considering that pollution of coastal areas represented a major concern in the last decades because of the abundance of discharged toxic substances. In particular, the structural characteristics of micro- and mesocosms (m-cosms) used to study marine contaminated sediments were reviewed, focusing on their advantages/disadvantages. Their potentiality to investigate sediment remediation have been discussed, offering new perspective on how the use of m-cosms can be useful for the development of practical application in the development of solutions for contaminated sediment management in the contaminated marine environment.

Differential responses in the biotransformation systems of the oyster Crassostrea gasar (Adanson, 1757) elicited by pyrene and fluorene: molecular, biochemical and histological approach - Part I

Polycyclic aromatic hydrocarbons (PAHs) are among the main contaminants in aquatic environments. PAHs can affect organisms due to their carcinogenic, mutagenic and/or teratogenic characteristics. Depending on the PAHs, concentration, and period of exposure, biological damage can occur leading to histopathologic alterations. This study aimed to evaluate the molecular, biochemical and histological responses of the oyster Crassostrea gasar exposed to pyrene (0.25 and 0.5 μM) and fluorene (0.6 and 1.2 μM), after exposure for 24 and 96 h. Concentrations of both PAHs were quantified in the water and in oyster tissues. Transcript levels of phase I (CYP3475C1, CYP2-like, CYP2AU1 and CYP356A) and phase II (GSTO-like, MGST-like and SULT-like) biotransformation-related genes and the activities of ethoxyresorufin-O-deethylase (EROD), total and microsomal glutathione S-transferase (GST and MGST) were evaluated in the gills. Also, histological changes and localization of mRNA transcripts CYP2AU1 in gills, mantle, and digestive diverticula were evaluated. Both PAHs accumulated in oyster tissues. Pyrene half-life in water was significantly lower than fluorene. Transcript levels of all genes were higher in oysters exposed to of pyrene 0.5 μM (24 h). Only CYP2AU1 gene was up-regulated by fluorene exposure. EROD and MGST activities were higher in oysters exposed to pyrene. Tubular atrophy in the digestive diverticula and an increased number of mucous cells in the mantle were observed in oysters exposed to pyrene. CYP2AU1 transcripts were observed in different tissues of pyrene-exposed oysters. A significant correlation was observed between tubular atrophy and the CYP2AU1 hybridization signal in oysters exposed to pyrene, suggesting the sensibility of the species to this PAH. These results suggest an important role of biotransformation-related genes and enzymes and tissue alterations associated to pyrene metabolism but not fluorene. In addition, it reinforces the role of CYP2AU1 gene in the biotransformation process of PAHs in the gills of C. gasar.

Biodegradation and detoxification of aliphatic and aromatic hydrocarbons by new yeast strains

Seeking new efficient hydrocarbon-degrading yeast stains was the main goal of this study. Because microorganisms are greatly affected by the environmental factors, the biodegradation potentiality of the microorganisms varies from climatic area to another. This induces research to develop and optimize the endemic organisms in bioremediation technology. In this study, 67 yeast strains were tested for their growth potentiality on both aliphatic and aromatic hydrocarbons. The most efficient six strains were identified using sequence analysis of the variable D1/D2 domain of the large subunit 26S ribosomal DNA. The identity of these strains was confirmed as Yamadazyma mexicana KKUY-0160, Rhodotorula taiwanensis KKUY-0162, Pichia kluyveri KKUY-0163, Rhodotorula ingeniosa KKUY-0170, Candida pseudointermedia KKUY-0192 and Meyerozyma guilliermondii KKUY-0214. These species are approved for their ability to degrade both aliphatic and aromatic hydrocarbons for the first time in this study. Although, all of them were able to utilize and grow on both hydrocarbons, Rhodotorula taiwanensis KKUY-0162 emerged as the best degrader of octane, and Rhodotorula ingeniosa KKUY-170 was the best degrader of pyrene. GC-MS analysis approved the presence of many chemical compounds that could be transitional or secondary metabolites during the utilization of the hydrocarbons. Our results recommend the application of these yeast species on large scale to approve their efficiency in bioremediation of oil-contamination of the environment. Using these yeasts, either individually or in consortia, could offer a practical solution for aquatic or soil contamination with the crude oil and its derivatives in situ.

Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics

Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.

Biofilm and Planktonic Bacterial and Fungal Communities Transforming High-Molecular-Weight Polycyclic Aromatic Hydrocarbons

High-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs) are natural components of fossil fuels that are carcinogenic and persistent in the environment, particularly in oil sands process-affected water (OSPW). Their hydrophobicity and tendency to adsorb to organic matter result in low bioavailability and high recalcitrance to degradation. Despite the importance of microbes for environmental remediation, little is known about those involved in HMW-PAH transformations. Here, we investigated the transformation of HMW-PAHs using samples of OSPW and compared the bacterial and fungal community compositions attached to hydrophobic filters and in suspension. It was anticipated that the hydrophobic filters with sorbed HMW-PAHs would select for microbes that specialize in adhesion. Over 33 days, more pyrene was removed (75% ± 11.7%) than the five-ring PAHs benzo[a]pyrene (44% ± 13.6%) and benzo[b]fluoranthene (41% ± 12.6%). For both bacteria and fungi, the addition of PAHs led to a shift in community composition, but thereafter the major factor determining the fungal community composition was whether it was in the planktonic phase or attached to filters. In contrast, the major determinant of the bacterial community composition was the nature of the PAH serving as the carbon source. The main bacteria enriched by HMW-PAHs were Pseudomonas, Bacillus, and Microbacterium species. This report demonstrates that OSPW harbors microbial communities with the capacity to transform HMW-PAHs. Furthermore, the provision of suitable surfaces that encourage PAH sorption and microbial adhesion select for different fungal and bacterial species with the potential for HMW-PAH degradation.

A New Perspective on Sustainable Soil Remediation-Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants

Deciding upon a cost effective and sustainable method to address soil pollution is a challenge for many remedial project managers. High pressure to quickly achieve cleanup goals pushes for energy-intensive remedies that rapidly address the contaminants of concern with established technologies, often leaving little room for research and development especially for slower treatment technologies, such as bioremediation, for the more heavily polluted sites. In the present case study, new genomic approaches have been leveraged to assess fungal biostimulation potential in soils polluted with particularly persistent hydrophobic contaminants. This new approach provides insights into the genetic functions available at a given site in a way never before possible. In particular, this article presents a case study where next generation sequencing (NGS) has been used to categorize fungi in soils from the Atlantic Wood Industries Superfund site in Portsmouth, Virginia. Data suggest that original attempts to harness fungi for bioremediation may have focused on fungal genera poorly suited to survive under heavily polluted site conditions, and that more targeted approaches relying on native indigenous fungi which are better equipped to survive under site specific conditions may be more appropriate.

Variations in the bioavailability of polycyclic aromatic hydrocarbons in industrial and agricultural soils after bioremediation

The aim of this study was to demonstrate the variations in bioavailability remaining in industrial and agricultural soils contaminated by polycyclic aromatic hydrocarbons (PAHs) after bioremediation. After inoculation of Mycobacterium sp. and Mucor sp., PAH biodegradation was tested on a manufactured gas plant (MGP) soil and an agricultural soil. PAH bioavailability was assessed before and after biodegradation using solid-phase extraction (Tenax-TA extraction) and solid-phase micro-extraction (SPME) to represent bioaccessibility and chemical activity of PAHs, respectively. Only 3- and 4-ring PAHs were noticeably biodegradable in the MGP soil. PAH biodegradation in the agricultural soil was different from that in the MGP soil. The rapidly desorbing fractions (F(rap)) extracted by Tenax-TA and the freely dissolved concentrations of 3- and 4-ring PAHs determined by SPME from the MGP soil decreased after 30 days biodegradation; those values of the 5- and 6-ring PAHs changed to a lesser degree. For the agricultural soil, the F(rap) values of the 3- and 4-ring PAHs also decreased after the biodegradation experiment. The Tenax-TA extraction and the SPME have the potential to assess variations in the bioavailability of PAHs and the degree of biodegradation in contaminated MGP soils. In addition, Tenax-TA extraction is more sensitive than SPME when used in the agricultural soil.

Biodegradation of polycyclic aromatic hydrocarbons by Trichoderma species: a mini review

Fungi belonging to Trichoderma genus are ascomycetes found in soils worldwide. Trichoderma has been studied in relation to diverse biotechnological applications and are known as successful colonizers of their common habitats. Members of this genus have been well described as effective biocontrol organisms through the production of secondary metabolites with potential applications as new antibiotics. Even though members of Trichoderma are commonly used for the commercial production of lytic enzymes, as a biological control agent, and also in the food industry, their use in xenobiotic biodegradation is limited. Trichoderma stands out as a genus with a great range of substrate utilization, a high production of antimicrobial compounds, and its ability for environmental opportunism. In this review, we focused on the recent advances in the research of Trichoderma species as potent and efficient aromatic hydrocarbon-degrading organisms, as well as aimed to provide insight into its potential role in the bioremediation of soils contaminated with heavy hydrocarbons. Several Trichoderma species are associated with the ability to metabolize a variety of both high and low molecular weight polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, chrysene, pyrene, and benzo[a]pyrene. PAH-degrading species include Trichoderma hamatum, Trichoderma harzianum, Trichoderma reesei, Trichoderma koningii, Trichoderma viride, Trichoderma virens, and Trichoderma asperellum using alternate enzyme systems commonly seen in other organisms, such as multicooper laccases, peroxidases, and ring-cleavage dioxygenases. Within these species, T. asperellum stands out as a versatile organism with remarkable degrading abilities, high tolerance, and a remarkable potential to be used as a remediation agent in polluted soils.

Characterization and tissue distribution of conjugated metabolites of pyrene in the rat

Pyrene (PY) is a polycyclic aromatic hydrocarbon (PAH) that is often used as a biomarker for human and wildlife exposure to PAHs. As the metabolites of PAHs, similar to their parent compounds, pose public health risks, it is necessary to study their characteristics and tissue-specific distribution. The present study was performed to experimentally characterize PY metabolites and analyze the tissue-specific distribution of the conjugated metabolites after oral administration of PY to rats. PY metabolites, such as pyrenediol-disulfate (PYdiol-diS), pyrenediol-sulfate (PYdiol-S), pyrene-1-sufate (PYOS), pyrene-1-glucuronide (PYOG) and 1-hydroxypyrene (PYOH), were detected in rat urine. Although glucuronide conjugate was the predominant metabolite, the metabolite composition varied among tissues. Interestingly, the proportion of PYOH was high in the large intestine. Furthermore, PYOH was the only PY metabolite detected in feces.

Degradation of polycyclic aromatic hydrocarbons in soil by a tolerant strain of Trichoderma asperellum

Trichoderma asperellum H15, a previously isolated strain characterized by its high tolerance to low (LMW) and high molecular weight (HMW) PAHs, was tested for its ability to degrade 3-5 ring PAHs (phenanthrene, pyrene, and benzo[a]pyrene) in soil microcosms along with a biostimulation treatment with sugarcane bagasse. T. asperellum H15 rapidly adapted to PAH-contaminated soils, producing more CO2 than uncontaminated microcosms and achieving up to 78 % of phenanthrene degradation in soils contaminated with 1,000 mg Kg(-1) after 14 days. In soils contaminated with 1,000 mg Kg(-1) of a three-PAH mixture, strain H15 was shown to degrade 74 % phenanthrene, 63 % pyrene, and 81 % of benzo[a]pyrene. Fungal catechol 1,2 dioxygenase, laccase, and peroxidase enzyme activities were found to be involved in the degradation of PAHs by T. asperellum. The results demonstrated the potential of T. asperellum H15 to be used in a bioremediation process. This is the first report describing the involvement of T. asperellum in LMW and HMW-PAH degradation in soils. These findings, along with the ability to remove large amounts of PAHs in soil found in the present work provide enough evidence to consider T. asperellum as a promising and efficient PAH-degrading microorganism.

Tolerance and growth of 11 Trichoderma strains to crude oil, naphthalene, phenanthrene and benzo[a]pyrene

Petroleum hydrocarbons (PHs) are major organic contaminants in soils, whose degradation process is mediated by microorganisms such as the filamentous fungi Cunninghamella elegans and Phanerochaete chrysosporium. However, little is known about the tolerance and the degradation capability of Trichoderma species when exposed to PH. This research evaluated the tolerance and growth of 11 Trichoderma strains to crude oil (COil), naphthalene (NAPH), phenanthrene (PHE) and benzo[a]pyrene (B[a]P) by using in vitro systems. Petri dishes containing solid mineral minimum medium were separately contaminated with COil, with seven doses of either NAPH or PHE (250, 500, 750, 1000, 2000, and 3000 mg L(-1)), and with six doses of B[a]P (10, 25, 50, 75, and 100 mg L(-1)). Non-contaminated plates were used as controls. Trichoderma strains were exposed to all the contaminants by triplicate, and the growth of each fungal colony was daily recorded. No significant differences were observed among Trichoderma strains when they were exposed to COil in which the maximum fungal growth was reached at 96 h. In contrast, Trichoderma strains showed variations to tolerate and grow under different doses of either NAPH, PHE or B[a]P. Increasing NAPH doses resulted on significant greater fungal growth inhibition than PHE doses. The exposure to B[a]P did not inhibited growth of some Trichoderma strains.

Pyrene degradation by Pseudomonas sp. and Burkholderia sp. enriched from coking wastewater sludge

A pyrene-degrading consortium was enriched from sludge of coking wastewater treatment plant which included a combination of aerobic and anaerobic reactors. Biodegradation of pyrene by the consortium follows first-order kinetics. Addition of a co-substrate (glucose or anthraquinone) facilitated pyrene degrading. The highest degradation rate was achieved at 35°C and pH 7.0, as glucose was added. In this case, pyrene (100 mg L(-1)) was degraded by 93.1 % within 36 h. An intermediate, 1-naphthol was detected via GC-MS analysis, indicating that pyrene degradation by the consortium proceeded with a pathway different from that associated with Mycobacterium sp. By comparisons of 16S rRNA gene sequences, two strains in this consortium were identified as Pseudomonas sp. and Burkholderia sp. The enriched pyrene-degrading consortium from coking wastewater treatment system shows highest pyrene-degrading activity compared with the reported pyrene degraders.

Biotechnology of marine fungi

Filamentous fungi are the most widely used eukaryotes in industrial and pharmaceutical applications. Their biotechnological uses include the production of enzymes, vitamins, polysaccharides, pigments, lipids and others. Marine fungi are a still relatively unexplored group in biotechnology. Taxonomic and habitat diversity form the basis for exploration of marine fungal biotechnology. This review covers what is known of the potential applications of obligate and marine-derived fungi obtained from coastal to the oceanic and shallow water to the deep-sea habitats. Recent studies indicate that marine fungi are potential candidates for novel enzymes, bioremediation, biosurfactants, polysaccharides, polyunsaturated fatty acids and secondary metabolites. Future studies that focus on culturing rare and novel marine fungi, combined with knowledge of their physiology and biochemistry will provide a firm basis for marine mycotechnology.

Degradation pathway of pentachlorophenol by Mucor plumbeus involves phase II conjugation and oxidation-reduction reactions

Environmental pollution by pentachlorophenol (PCP) is a critical concern worldwide and fungal bioremediation constitutes an elegant and environment-friendly solution. Mucorales from the Zygomycota phylum are often observed to be competitive in field conditions and Mucor plumbeus, in particular, can efficiently deplete PCP from media. The pathway for PCP degradation used by this fungus has not been investigated. In this study, PCP-derived metabolites were identified by liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, including tetra- and tri-chlorohydroquinones and phase II-conjugated metabolites. Amongst the latter are the previously reported glucose, sulfate and ribose conjugates, and identified for the first time in fungi sulfate-glucose conjugates. A PCP transformation pathway for M. plumbeus is proposed, which excludes the involvement of cytochrome P-450 and extracellular ligninolytic enzymes.

Marine-derived filamentous fungi and their potential application for polycyclic aromatic hydrocarbon bioremediation

Eight marine-derived fungi that were previously selected for their abilities to decolorize RBBR dye were subjected to pyrene and benzo[a]pyrene degradation. The fungus Aspergillus sclerotiorum CBMAI 849 showed the best performance with regard to pyrene (99.7%) and benzo[a]pyrene (76.6%) depletion after 8 and 16 days, respectively. Substantial amounts of benzo[a]pyrene (>50.0%) depletion were also achieved by Mucor racemosus CBMAI 847. Therefore, these two fungal strains were subjected to metabolism evaluation using the HPLC-DAD-MS technique. The results showed that A. sclerotiorum CBMAI 849 and M. racemosus CBMAI 847 were able to metabolize pyrene to the corresponding pyrenylsulfate and were able to metabolize benzo[a]pyrene to benzo[a]pyrenylsulfate, suggesting that the mechanism of hydroxylation is mediated by a cytochrome P-450 monooxygenase, followed by conjugation with sulfate ions. Because these fungi were adapted to the marine environment, the strains that were used in the present study are considered to be attractive targets for the bioremediation of saline environments, such as ocean and marine sediments that are contaminated by PAHs.

Diversity of fungi in creosote-treated crosstie wastes and their resistance to polycyclic aromatic hydrocarbons

This study was conducted to generate information regarding the diversity of fungi inhabiting creosote-treated wood in a storage yard for crosstie wastes in Gwangmyeong, Korea. Additionally, the resistance to polycyclic aromatic hydrocarbons (PAHs) of indigenous fungi that mainly occupy creosote-treated wood was evaluated. We isolated fungi from the surface and inner area of crosstie wastes and identified them using a combination of traditional methods and molecular techniques. Overall, 179 isolates including 47 different species were isolated from 240 sampling sites. The identified fungal species included 23 ascomycetes, 19 basidiomycetes, and 5 zygomycetes. Three species, Alternaria alternata, Irpex lacteus, and Rhizomucor variabilis, were the most frequently isolated ascomycetes, basidiomycetes, and zygomycetes, respectively. The results of this study showed that there was a large difference in the fungal diversity between the surface and the inner area. Additionally, zygomycetes and ascomycetes were found to have a greater tolerance to PAHs than basidiomycetes. However, two basidiomycetes, Heterobasidion annosum and Schizophyllum commune, showed very high resistance to PAHs, even in response to the highest concentration (1,000 ppm), which indicates that these species may play a role in the degradation of PAHs.

Potential of Penicillium species in the bioremediation field

The effects on the environment of pollution, particularly that caused by various industrial activities, have been responsible for the accelerated fluxes of organic and inorganic matter in the ecosphere. Xenobiotics such as phenol, phenolic compounds, polycyclic aromatic hydrocarbons (PAHs), and heavy metals, even at low concentrations, can be toxic to humans and other forms of life. Many of the remediation technologies currently being used for contaminated soil and water involve not only physical and chemical treatment, but also biological processes, where microbial activity is the responsible for pollutant removal and/or recovery. Fungi are present in aquatic sediments, terrestrial habitats and water surfaces and play a significant part in natural remediation of metal and aromatic compounds. Fungi also have advantages over bacteria since fungal hyphae can penetrate contaminated soil, reaching not only heavy metals but also xenobiotic compounds. Despite of the abundance of such fungi in wastes, penicillia in particular have received little attention in bioremediation and biodegradation studies. Additionally, several studies conducted with different strains of imperfecti fungi, Penicillium spp. have demonstrated their ability to degrade different xenobiotic compounds with low co-substrate requirements, and could be potentially interesting for the development of economically feasible processes for pollutant transformation.

Biodegradation of phenanthrene by fungi screened from nature

Microbial degradation of Phenanthrene with several fungi screened from nature was conducted to select fungi for the bioremediation ofPhenanthrene. Thrichoderma sp. S019, a fungus collected from soil, had the highest rate of degradation on the agar medium containing Phenanthrene. Maximal degradation (72%) was obtained when Trichoderma sp. S019 was incubated for 30 days after the addition of 0.1 mM of Phenanthrene to the liquid medium. Furthermore, the degradation of Phenanthrene was affected by the addition of a carbon source, the addition of a nitrogen source and agitation. Also, 1,2-Dioxygenase and 2,3-Dioxygenase were produced by Trichoderma sp. S019 in a liquid medium. These enzymes play an important role in the metabolism of substrates, revealing a high stereoselectivity for initial dioxygenase and enzymatic hydration since the K-region of phenanthrene was the major site of metabolism. Phenanthrene was indeed degraded by Trichoderma sp. S019 because 1-Hydroxy-2-naphthoic acid, Salicyaldehyde, Salicylic acid and Catechol, considered to be the intermediates in the bioremediation of Phenanthrene, were detected among the reaction products.

Biodegradation of polycyclic aromatic hydrocarbons in sediments from the Daliao River watershed, China

The Daliao River, as an important water system in Northeast China, was reported to be heavily polluted by polycyclic aromatic hydrocarbons (PAHs). Aerobic biodegradations of four selected PAHs (naphthalene, phenanthrene, fluorene and anthracene) alone or in their mixture in river sediments from the Daliao River water systems were studied in microcosm systems. Effects of additional carbon source, inorganic nitrogen and phosphorus, temperature variation on PAHs degradation were also investigated. Results showed that the degradation of phenanthrene in water alone system was faster than that in water-sediment combined system. Degradation of phenanthrene in sediment was enhanced by adding yeast extract and ammonium, but retarded by adding sodium acetate and not significantly influenced by adding phosphate. Although PAHs could also be biodegraded in sediment under low temperature (5 degrees C), much lower degradation rate was observed. Sediments from the three main streams of the Daliao River water system (the Hun River, the Taizi River and the Daliao River) demonstrated different degradation capacities and patterns to four PAHs. Average removal rates (15 or 19 d) of naphthalene, phenanthrene, fluorene and anthracene by sediment were in the range of 0.062-0.087, 0.005-0.066, 0.008-0.016 and 0-0.059 mg/(L x d), respectively. As a result, naphthalene was most easily degraded compound, anthracene was the hardest one. In multiple PAHs systems, the interactions between PAHs influenced each PAH biodegradation.

Mycelial pellet formation by Penicillium ochrochloron species due to exposure to pyrene

Five indigenous fungal strains with characteristics of the genus Penicillium capable of degrading and utilizing pyrene, as sole carbon source were isolated from soil of a former gas work site. Two strains were identified as Penicillium ochrochloron. One of the strains was able to degrade a maximum of 75% of 50 mg l(-1) pyrene at 22 degrees C during 28 days of incubation. The presence of pyrene in the medium resulted in an aggregation of hyphae into pellets by the two Penicillium ochrochloron strains. Formation of pellets was observed after 48 h of incubation with difference in size and texture between the two strains. This indicated the individual variation within the same genus of fungi. However, remaining strains did not show this behavior even though they were capable of utilizing pyrene as sole carbon source. The macro- and microscopic morphology of fungal pellets was studied using scanning electron microscopy. It was found that the addition of varying concentration of pyrene ranging from 10 to 50 mg l(-1) in the medium influenced shape and structure of the mycelial pellets. A two-fold increase in hyphal branching (with concomitant decrease in the average hyphal growth unit) was observed at a concentration of 10mg l(-1). The relevance of fungal growth and morphology for bioremediation of polycyclic aromatic hydrocarbons (PAHs) contaminated sites are discussed.

Transformation of Eutypa dieback and esca disease pathogen toxins by antagonistic fungal strains reveals a second detoxification pathway not present in Vitis vinifera

Eutypine, 4-hydroxybenzaldehyde, and 3-phenyllactic acid are some of the phytotoxins produced by the pathogens causing Eutypa dieback and esca disease, two trunk diseases of grapevine (Vitis vinifera). Known biocontrol agents such as Fusarium lateritium and Trichoderma sp. were screened for their ability to consume these toxins. Transformation time courses were performed, and an high-performance liquid chromatography-based method was developed to analyze toxin metabolism and to identify and quantify the converted products. The results show that the aldehyde function of eutypine was reduced to eutypinol, as by V. vinifera cv. Merlot, the cultivar tolerant to Eutypa dieback. We revealed a supplementary detoxification pathway, not known in Merlot, where the aldehyde function was oxidized to eutypinic acid. Moreover, some strains tested could further metabolize the transformation products. Every strain tested could transform 4-hydroxybenzaldehyde to the corresponding alcohol and acid, and these intermediates disappeared totally at the end of the time courses. When biological assays on cells of V. vinifera cv. Chasselas were carried out, the transformation products exhibited a lower toxicity than the toxins. The possibility of selecting new biocontrol agents against trunk diseases of grapevine based on microbial detoxification is discussed.

Fungal biodegradation of naphthalene: microcosms studies

The present work is aimed to ascertain naphthalene biodegradation capability of P. chrysosporium and T. harzianum in soil microcosms. Considering the high naphthalene volatility, a suitable soil microcosm was set-up and used. Several degradation tests were conducted with different C/N ratio media for the two fungi in order to enquire the best range of working conditions. The kinetic studies were conducted at a maximal naphthalene concentration of 600 mg kg(-1). During experimental time course naphthalene concentration, CO2 evolution as well as phytotoxicity tests were performed as monitoring parameters. The results shown in the current paper, put in evidence that T. harzianum, differently than in liquid culture, is not able to biodegrade naphthalene directly in soil microcosm, while P. chrysosporium in the same conditions biodegrades the PAH till about 600 mg kg(-1). As concern the founded kinetics for P. chrysosporium, a saturation shape in presence of N-limited medium (high C/N ratio) was evaluated while a growing form more than linear in no-N limited medium (normal C/N ratio) was determined.

Fungal communities in PAH-impacted sediments of Genoa-Voltri Harbour (NW Mediterranean, Italy)

Organic matter (in terms of carbohydrates and proteins), polycyclic aromatic hydrocarbons (PAHs) and bacterial density were investigated in the sediments of three stations in Genoa-Voltri Harbour (NW Mediterranean), and related to the sedimentary fungal community. Sites were significantly different in all investigated parameters (ANOVA, p<0.05), and a sharp gradient of impact in the area was found. All the 81 strains of filamentous fungi isolated, belonging to 7 genera, appeared to be linked with PAHs (p<0.05; r=0.95), whereas bacterial density was positively correlated with organic matter content (p<0.05; r=0.98). Within the fungal community, strains with a high capability to degrade xenobiotics were found. Among the genera identified, Penicillium, Mucor and Cladosporium showed the highest frequency in the sites where the heaviest concentrations of PAHs were recorded. This study suggests that fungal communities are important for in situ degradation of xenobiotics in impacted sediments.

Novel method for determining pyrene biodegradation using synchronous fluorimetry

To study the biodegradation rate of pyrene dissolved in liquid medium supplemented with mineral salts, a synchronous fluorimetry (SF) method was established. The limit of detection for pyrene dissolved in mineral salts medium (MSM) was determined as 0.19 ng/ml with a relative standard deviation of less than 1.3% (n = 9). The pyrene degrading rates of four bacterial strains were investigated using this method under the same experimental conditions. The degradation rates of the three active strains ranged from 76% to 87% after a 14-h incubation. The results were confirmed by the gas chromatography with a flame ionized detector (GC/FID) method. This implies that pyrene degradation can be directly monitored by the SF method without the solvent extraction of samples. The advantages of SF are that it is less laborious, faster, and less expensive than the GC/FID determination method with solvent extraction. The SF method provides a new tool for studying the degradation of polynuclear aromatic hydrocarbons (PAHs) in the natural environment and under experimental conditions.

Oxidation of polycyclic aromatic hydrocarbons by fungal isolates from an oil contaminated refinery soil

BACKGROUND AND OBJECTIVE

Indigenous soil microorganisms are used for the biodegradation of petroleum hydrocarbons in oily waste residues from the petroleum refining industry. The objective of this investigation was to determine the potential of indigenous strains of fungi in soil contaminated with petroleum hydrocarbons to biodegrade polycyclic aromatic hydrocarbons (PAH).

MATERIALS AND METHODS

Twenty one fungal strains were isolated from a soil used for land-farming of oily waste residues from the petrochemical refining industry in Singapore and identified to genus level using laboratory culture and morphological techniques. Isolates were incubated in the presence of 30 mg/L of phenanthrene over a period of 28 days at 30 degrees C. The most effective strain was further evaluated to determine its ability to oxidise a wider range of PAH compounds of various molecular weight i.e acenaphthene, fluorene, fluoranthene, chrysene, benzo(a)pyrene and dibenz(ah)anthracene

RESULTS AND DISCUSSION

After 28 days of incubation, 18 of the 21 fungal cultures were capable of oxidising over 50% of the phenanthrene present in culture medium, relative to abiotic controls. Fungal isolate, Penicillium sp. 06, was able to oxidise 89% of the phenanthrene present. This isolate could also oxidise more than 75% of the acenaphthene, fluorene and fluoranthene after 30 days of incubation. However, the oxidation of high molecular weight PAH i.e. chrysene, benzo(a)pyrene and dibenz(ah)anthracene by the Penicillium sp. 06 isolate was limited, where the extent of oxidation was inversely proportional to PAH molecular weight.

CONCLUSIONS

Fungal isolate, Penicillium sp. 06, was effective at oxidising a range of PAH in petroleum contaminated soils, but higher molecular weight PAH were more recalcitrant.

RECOMMENDATIONS AND OUTLOOK

There is potential for the re-application of this fungal strain to soil for bioremediation purposes.