Downscaling the in vitro test of fungal bioremediation of polycyclic aromatic hydrocarbons: methodological approach

Searching for Chemical Agents Suppressing Substrate Microbiota in White-Rot Fungi Large-Scale Cultivation

Edible fungi are a valuable resource in the search for sustainable solutions to environmental pollution. Their ability to degrade organic pollutants, extract heavy metals, and restore ecological balance has a huge potential for bioremediation. They are also sustainable food resources. Edible fungi (basidiomycetes or fungi from other divisions) represent an underutilized resource in the field of bioremediation. By maximizing their unique capabilities, it is possible to develop innovative approaches for addressing environmental contamination. The aim of the present study was to find selective chemical agents suppressing the growth of microfungi and bacteria, but not suppressing white-rot fungi, in order to perform large-scale cultivation of white-rot fungi in natural unsterile substrates and use it for different purposes. One application could be the preparation of a matrix composed of wooden sleeper (contaminated with PAHs) and soil for further hazardous waste bioremediation using white-rot fungi. In vitro microbiological methods were applied, such as, firstly, compatibility tests between bacteria and white-rot fungi or microfungi, allowing us to evaluate the interaction between different organisms, and secondly, the addition of chemicals on the surface of a Petri dish with a test strain of microorganisms of white-rot fungi, allowing us to determine the impact of chemicals on the growth of organisms. This study shows that white-rot fungi are not compatible to grow with several rhizobacteria or bacteria isolated from soil and bioremediated waste. Therefore, the impact of several inorganic materials, such as lime (hydrated form), charcoal, dolomite powder, ash, gypsum, phosphogypsum, hydrogen peroxide, potassium permanganate, and sodium hydroxide, was evaluated on the growth of microfungi (sixteen strains), white-rot fungi (three strains), and bacteria (nine strains) in vitro. Charcoal, dolomite powder, gypsum, and phosphogypsum did not suppress the growth either of microfungi or of bacteria in the tested substrate, and even acted as promoters of their growth. The effects of the other agents tested were strain dependent. Potassium permanganate could be used for bacteria and Candida spp. growth suppression, but not for other microfungi. Lime showed promising results by suppressing the growth of microfungi and bacteria, but it also suppressed the growth of white-rot fungi. Hydrogen peroxide showed strong suppression of microfungi, and even had a bactericidal effect on some bacteria, but did not have an impact on white-rot fungi. The study highlights the practical utility of using hydrogen peroxide up to 3% as an effective biota-suppressing chemical agent prior to inoculating white-rot fungi in the large-scale bioremediation of polluted substrates, or in the large-scale cultivation for mushroom production as a foodstuff.

Implementation of Genetic Engineering and Novel Omics Approaches to Enhance Bioremediation: A Focused Review

Bioremediation itself is considered to be a cost effective soil clean-up technique and preferred over invasive physical and chemical treatments. Besides increasing efficiency, application of genetic engineering has led to reduction in the time duration required to achieve remediation, overcoming the so called 'Achilles heel' of Bioremediation. Omics technologies, namely genomics, transcriptomics, proteomics, and metabolomics, are being employed extensively to gain insights at genetic level. A wise synchronised application of these approaches can help scrutinize complex metabolic pathways, and molecular changes in response to heavy metal stress, and also its fate i.e., uptake, transport, sequestration and detoxification. In the present review, an account of some latest achievements made in the field is presented.

Ligninolytic enzymes in Basidiomycetes and their application in xenobiotics degradation

Variety of microorganisms have already proven their capabilities for degradation of wide range of wastes with anthropogenic nature. These pollutants, both liquid and solids, also include so called xenobiotics like phenol and its derivatives, PAHs, dyes, pesticides, pharmaceuticals, etc. Xenobiotics as bisphenol A (BPA), chlorhexidine (CHX), octenidine (OCT), other disinfectants and antiseptics have high ecotoxicological impact. Moreover, they can also impair our quality of life and our health interfering different metabolic and hormone receptors pathways in human body. Chemical treatment of such wastes is not a viable option because of its poor socio-economics and environmental merits. Therefore, applying effective, ecofriendly and cheap treatment methods is of great importance. Basidiomycetes are extensively investigated for their abilities to degrade numerous pollutants and xenobiotics. Through their extracellular ligninolytic enzymes they are capable of reducing or completely removing wide range of hazardous compounds. These enzymes can be categorized in two groups: oxidases (laccase) and peroxidases (manganese peroxidase, lignin peroxidase, versatile peroxidase). Due to the broad substrate specificity of the secreted enzymes Basidiomycetes can be applied as a powerful tool for bioremediation of diverse xenobiotics and recalcitrant compounds.

Mycoremediation potential of Aspergillus ochraceus NRRL 3174

Mycoremediation is an important process that targets the removal of petroleum hydrocarbons by fungi. Fungi have advantages with their extensive enzymatic systems, rapid adaptation to toxic organic pollutants, and to adverse environmental conditions. In this study, the colorimetric method was used for the preliminary investigation of petroleum degradation with ten fungal strains. Petroleum degradation ability of spore suspension, live biomass (fungal pellet and disc) and cell-free culture supernatant of the potent A. ochraceus strain were investigated by gravimetric analysis. It was found that the fungal disc (94%) was more successful than the spore suspension (87%) in petroleum degradation under physiological conditions determined as pH:5.0, 1% of petroleum concentration, 5% (v/v) of inoculum concentration (with spore suspension) and 1 g/100 mL of inoculum amount (with fungal disc) and 7 days of the incubation period. The degradation rate constant and half-life period of spore suspension were calculated as 0.291 day^-1 and t_1/2 = 0.340 and of the fungal disc were 0.401 day^-1 and t_1/2 = 0.247. Although, 7.5% and 10% (v/v) concentration of cell-free culture supernatant achieved more than 80% petroleum removal, it was not as effective as a fungal disc. According to gas chromatography/mass spectrometry analysis, the fungal disc of A. ochraceus strain degraded long-chain n-alkanes such as C₃₅ and C₃₆ more effectively than n-alkanes in the range of C₂₂-C₃₄. The fact that the A. ochraceus NRRL 3174 strain has a high petroleum degradation capacity as well as being a potent biosurfactant producer will provide a different perspective to advanced mycoremediation studies.

Mathematical Model Coupled to Neural Networks Calculates the Extraction Recovery of Polycyclic Aromatic Hydrocarbons in Problematic Matrix

Unknown extraction recovery from solid matrix samples leads to meaningless chemical analysis results. It cannot always be determined, and it depends on the complexity of the matrix and properties of the extracted substances. This paper combines a mathematical model with the machine learning method-neural networks that predict liquid extraction recovery from solid matrices. The prediction of the three-stage extraction recovery of polycyclic aromatic hydrocarbons from a wooden railway sleeper matrix is demonstrated. Calculation of the extraction recovery requires the extract's volume to be measured and the polycyclic aromatic hydrocarbons' concentration to be determined for each stage. These data are used to calculate the input values for a neural network model. Lowest mean-squared error (0.014) and smallest retraining relative standard deviation (20.7%) were achieved with the neural network setup 6:5:5:4:1 (six inputs, three hidden layers with five, five, and four neurons in a layer, and one output). To train such a neural network, it took less than 8000 steps-less than a second--using an average-performance laptop. The relative standard deviation of the extraction recovery predictions ranged between 1.13 and 5.15%. The three-stage recovery of the extracted dry sample showed 104% of three different polycyclic aromatic hydrocarbons. The extracted wet sample recovery was 71, 98, and 55% for phenanthrene, anthracene, and pyrene, respectively. This method is applicable in the environmental, food processing, pharmaceutical, biochemical, biotechnology, and space research areas where extraction should be performed autonomously without human interference.

Fungal bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals

Abstract

Much research has been carried out on the bacterial bioremediation of soil contaminated with petroleum hydrocarbons and toxic metals but much less is known about the potential of fungi in sites that are co-contaminated with both classes of pollutants. This article documents the roles of fungi in soil polluted with both petroleum hydrocarbons and toxic metals as well as the mechanisms involved in the biotransformation of such substances. Soil characteristics (e.g., structural components, pH, and temperature) and intracellular or excreted extracellular enzymes and metabolites are crucial factors which affect the efficiency of combined pollutant transformations. At present, bioremediation of soil co-contaminated with petroleum hydrocarbons and toxic metals is mostly focused on the removal, detoxification, or degradation efficiency of single or composite pollutants of each type. Little research has been carried out on the metabolism of fungi in response to complex pollutant stress. To overcome current bottlenecks in understanding fungal bioremediation, the potential of new approaches, e.g., gradient diffusion film technology (DGT) and metabolomics, is also discussed.

Key points

• Fungi play important roles in soil co-contaminated with TPH and toxic metals.

• Soil characteristics, enzymes, and metabolites are major factors in bioremediation.

• DGT and metabolomics can be applied to overcome current bottlenecks.

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.

Degradation of some representative polycyclic aromatic hydrocarbons by the water-soluble protein extracts from Zea mays L. cv PR32-B10

The ability of the water-soluble protein extracts from Zea mais L. cv. PR32-B10 to degrade some representative polycyclic aromatic hydrocarbons (PAHs), has been evaluated. Surface sterilized seeds of corn (Zea mais L. Pioneer cv. PR32-B10) were hydroponically cultivated in a growth chamber under no-stressful conditions. The water-soluble protein extracts isolated from maize tissues showed peroxidase, polyphenol oxidase and catalase activities. Incubation of the extracts with naphthalene, fluorene, phenanthrene and pyrene, led to formation of oxidized and/or degradation products. GC-MS and TLC monitoring of the processes showed that naphthalene, phenanthrene, fluorene and pyrene underwent 100%, 78%, 92% and 65% oxidative degradation, respectively, after 120 min. The chemical structure of the degradation products were determined by (1)H NMR and ESI-MS spectrometry.