Mycoremediation of hydrocarbons with basidiomycetes-a review

Rare earth contamination of edible vegetation: Ce, La, and summed REE in fungi

The increasing and diversified use of rare earth elements (REE) is considered a potential source of pollution of environmental media including soils. This work documents critically overview data on the occurrence of REE in the fruiting bodies of wild and farmed species of edible and medicinal mushrooms, as this was identified as the largest published dataset of REE occurrence in foodstuff. Most of the literature reported occurrences of cerium (Ce) and lanthanum (La), but a number of studies lacked data on all lanthanides. The Ce, La, and summed REE occurrences were assessed through the criteria of environmental geochemistry, analytical chemistry, food toxicology, mushroom systematics, and ecology. Ce and La accumulate similarly in fruiting bodies and are not fractionated during uptake, maintaining the occurrence patterns of their growing substrates. Similarly, there is no credible evidence of variable REE uptake because the evaluated species data show natural, unfractionated patterns in accordance with the Oddo-Harkins' order of environmental lanthanide occurrence. Thus, lithosphere occurrence patterns of Ce and La as the first and the third most abundant lanthanides are reflected in wild and farmed mushrooms regardless of substrate and show that Ce is around twice more abundant than La. The current state of knowledge provides no evidence that mushroom consumption at these REE occurrence levels poses a health risk either by themselves or when included with other dietary exposure. Macromycetes appear to bio-exclude lanthanides because independently reported bioconcentration factors for different species and collection sites, typically range from < 1 to 0.001. This is reflected in fruiting body concentrations which are four to two orders of magnitude lower than growing substrates. KEY POINTS: •Original REE occurrence patterns in soils/substrates are reflected in mushrooms •No evidence for the fractionation of REE during uptake by fungi •Mushrooms bio-exclude REE in fruiting bodies.

Integrating phytoremediation and mycoremediation with biosurfactant-producing fungi for hydrocarbon removal and the potential production of secondary resources

Treatment of petroleum-contaminated soil to a less toxic medium via physical and chemical treatment is too costly and requires posttreatment. This review focuses on the employment of phytoremediation and mycoremediation technologies in cleaning hydrocarbon-contaminated soil which is currently rare. It is considered environmentally beneficial and possibly cost-effective as it implements the synergistic interaction between plants and biosurfactant producing mycorrhiza to degrade hydrocarbon contaminants. This review also covers possible sources of hydrocarbon pollution in water and soil, toxicity effects, and current technologies for hydrocarbon removal and degradation. In addition to these problems, this review also discusses the challenges and opportunities of transforming the resultant treated sludge and treating plants into potential by-products for a higher quality of life for future generations.

A Review about the Mycoremediation of Soil Impacted by War-like Activities: Challenges and Gaps

(1) Background: The frequency and intensity of war-like activities (war, military training, and shooting ranges) worldwide cause soil pollution by metals, metalloids, explosives, radionuclides, and herbicides. Despite this environmentally worrying scenario, soil decontamination in former war zones almost always involves incineration. Nevertheless, this practice is expensive, and its efficiency is suitable only for organic pollutants. Therefore, treating soils polluted by wars requires efficient and economically viable alternatives. In this sense, this manuscript reviews the status and knowledge gaps of mycoremediation. (2) Methods: The literature review consisted of searches on ScienceDirect and Web of Science for articles (1980 to 2023) on the mycoremediation of soils containing pollutants derived from war-like activities. (3) Results: This review highlighted that mycoremediation has many successful applications for removing all pollutants of war-like activities. However, the mycoremediation of soils in former war zones and those impacted by military training and shooting ranges is still very incipient, with most applications emphasizing explosives. (4) Conclusion: The mycoremediation of soils from conflict zones is an entirely open field of research, and the main challenge is to optimize experimental conditions on a field scale.

Fungal biotechnology: From yesterday to tomorrow

Fungi have been used to better the lives of everyday people and unravel the mysteries of higher eukaryotic organisms for decades. However, comparing progress and development stemming from fungal research to that of human, plant, and bacterial research, fungi remain largely understudied and underutilized. Recent commercial ventures have begun to gain popularity in society, providing a new surge of interest in fungi, mycelia, and potential new applications of these organisms to various aspects of research. Biotechnological advancements in fungal research cannot occur without intensive amounts of time, investments, and research tool development. In this review, we highlight past breakthroughs in fungal biotechnology, discuss requirements to advance fungal biotechnology even further, and touch on the horizon of new breakthroughs with the highest potential to positively impact both research and society.

Emerging bio-dispersant and bioremediation technologies as environmentally friendly management responses toward marine oil spill: A comprehensive review

Marine oil spills emanating from wells, pipelines, freighters, tankers, and storage facilities draw public attention and necessitate quick and environmentally friendly response measures. It is sometimes feasible to contain the oil with booms and collect it with skimmers or burn it, but this is impracticable in many circumstances, and all that can be done without causing further environmental damage is adopting natural attenuation, particularly through microbial biodegradation. Biodegradation can be aided by carefully supplying biologically accessible nitrogen and phosphorus to alleviate some of the microbial growth constraints at the shoreline. This review discussed the characteristics of oil spills, origin, ecotoxicology, health impact of marine oils spills, and responses, including the variety of remedies and responses to oil spills using biological techniques. The different bioremediation and bio-dispersant treatment technologies are then described, with a focus on the use of green surfactants and their advances, benefits/drawbacks. These technologies were thoroughly explained, with a timeline of research and recent studies. Finally, the hurdles that persist as a result of spills are explored, as well as the measures that must be taken and the potential for the development of existing treatment technologies, all of which must be linked to the application of integrated procedures.

Assessment of Different Spent Mushroom Substrates to Bioremediate Soils Contaminated with Petroleum Hydrocarbons

Bioremediation techniques are being developed as substitutes for physical–chemical methodologies that are expensive and not sustainable. For example, using the agricultural waste spent mushroom substrate (SMS) which contains valuable microbiota for soil bioremediation. In this work, SMSs of four cultivated fungal species, Pleurotus eryngii, Lentinula edodes, Pleurotus ostreatus, and Agaricus bisporus were evaluated for the bioremediation of soils contaminated by petroleum hydrocarbons (TPHs). The bioremediation test was carried out by mixing the four different SMSs with the TPH-contaminated soil in comparison with an unamended soil control to assess its natural attenuation. To determine the most efficient bioremediation strategy, hydrolase, dehydrogenase, and ligninolytic activities, ergosterol content, and percentage of TPHs degradation (total and by chains) were determined at the end of the assay at 40 days. The application of SMS significantly improved the degradation of TPHs with respect to the control. The most effective spent mushroom substrate to degrade TPHs was A. bisporus, followed by L. edodes and P. ostreatus. Similar results were obtained for the removal of aliphatic and aromatic hydrocarbons. The results showed the effectiveness of SMS to remove aliphatic and aromatic hydrocarbons from C10 to C35. This work demonstrates an alternative to valorizing an abundant agricultural waste as SMS to bioremediate contaminated soils.

Effects of Biodegradation of Corn-Starch-Sodium-Alginate-Based Liquid Mulch Film on Soil Microbial Functions

In response to the problems of the poor degradability and mechanical properties of liquid mulch, natural non-toxic polymer compound corn starch and sodium alginate were used to prepare fully biodegradable liquid mulch. The preparation conditions of the mulch were optimized, and the mechanical properties of the mulch and the changes in the microbial community in soil with the mulch degradation were analyzed. The corn-starch–sodium-alginate-based liquid mulch film had an optimum performance at a tensile strength of 0.145 MPa and an elongation at a break of 16.05%, which was attained by adding 33.33% sodium alginate, 50% glycerol 22 and 4% citric acid to corn starch after moist heat modification. Fourier transform infrared spectroscopy analysis showed that the -COOH in sodium alginate could interact with the -OH in starch and glycerol through hydrogen bonding, thus, resulting in a denser structure and better mechanical properties of the liquid mulch as a non-crystalline material. The soil burial degradation study of mulch revealed that corn-starch–sodium-alginate-based liquid mulch degraded completely at 25 days macroscopically, and mulch degradation increased soil organic matter content. Microbial kinetic analysis showed that the abundance and diversity of the bacterial community decreased with the degradation of the mulch, which was conducive to the optimization of the bacterial community structure and function. Arthrobacter of the class Actinomycetes became the dominant microorganism, and its abundance increased by 16.48-times at 14 days of mulch degradation compared with that before degradation, and Acidophilus phylum (14 days) decreased by 99.33%. The abundance of fungal communities was elevated in relation to the main functional microorganisms involved in liquid mulch degradation, with Alternaria and Cladosporium of the Ascomycete phylum Zygomycetes being the most active at the early stage of mulch degradation (7 days), and the relative abundance of Blastocystis was significantly elevated at the late stage of mulch degradation (14 days), which increased by 13.32%. This study provides important support for the green and sustainable development of modern agriculture.

Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps

Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.

Widespread Ability of Ligninolytic Fungi to Degrade Hazardous Organic Pollutants as the Basis for the Self-Purification Ability of Natural Ecosystems and for Mycoremediation Technologies

The ability of sixteen wood- and soil-inhabiting basidiomycete strains and four ascomycete strains to degrade the most hazardous, widespread, and persistent pollutants (polycyclic aromatic hydrocarbons, oxyethylated nonylphenol, alkylphenol, anthraquinone-type synthetic dyes, and oil) was found. The disappearance of the pollutants, their main metabolites, and some adaptive properties (activities of ligninolytic enzymes, the production of emulsifying compounds and exopolysaccharides) were evaluated. The toxicity of polycyclic aromatic hydrocarbons decreased during degradation. New data were obtained regarding (1) the dependence of the completeness of polycyclic aromatic hydrocarbon degradation on the composition of the ligninolytic enzyme complex; (2) the degradation of neonol AF9-12 by higher fungi (different accessibilities of the oxyethyl chain and the aromatic ring of the molecules to different fungal genera); and (3) the production of an emulsifying agent in response to the presence in the cultivation medium of hydrophobic pollutants as the common property of wood- and soil-inhabiting basidiomycetes and ascomycetes. Promise for use in mycoremediation was shown in the wood-inhabiting basidiomycetes Pleurotus ostreatus f. Florida, Schizophyllum commune, Trametes versicolor MUT 3403, and Trametes versicolor DSM11372; the litter-decomposing basidiomycete Stropharia rugosoannulata; and the ascomycete Cladosporium herbarum. These fungi degrade a wide range of pollutants without accumulation of toxic metabolites and produce ligninolytic enzymes and emulsifying compounds.

The Effectiveness of Biostimulation, Bioaugmentation and Sorption-Biological Treatment of Soil Contaminated with Petroleum Products in the Russian Subarctic

The effectiveness of different bioremediation methods (biostimulation, bioaugmentation, the sorption-biological method) for the restoration of soil contaminated with petroleum products in the Russian Subarctic has been studied. The object of the study includes soil contaminated for 20 years with petroleum products. By laboratory experiment, we established five types of microfungi that most intensively decompose petroleum hydrocarbons: Penicillium canescens st. 1, Penicillium simplicissimum st. 1, Penicillum commune, Penicillium ochrochloron, and Penicillium restrictum. One day after the start of the experiment, 6 to 18% of the hydrocarbons decomposed: at 3 days, this was 16 to 49%; at 7 days, 40 to 73%; and at 10 days, 71 to 87%. Penicillium commune exhibited the greatest degrading activity throughout the experiment. For soils of light granulometric composition with a low content of organic matter, a more effective method of bioremediation is sorption-biological treatment using peat or granulated activated carbon: the content of hydrocarbons decreased by an average of 65%, which is 2.5 times more effective than without treatment. The sorbent not only binds hydrocarbons and their toxic metabolites but is also a carrier for hydrocarbon-oxidizing microorganisms and prevents nutrient leaching from the soil. High efficiency was noted due to the biostimulation of the native hydrocarbon-oxidizing microfungi and bacteria by mineral fertilizers and liming. An increase in the number of microfungi, bacteria and dehydrogenase activity indicate the presence of a certain microbial potential of the soil and the ability of the hydrocarbons to produce biochemical oxidation. The use of the considered methods of bioremediation will improve the ecological state of the contaminated area and further the gradual restoration of biodiversity.

Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil

A deep-sea fungus Aspergillus sydowii BOBA1 isolated from marine sediment at a depth of 3000 m was capable of degrading spent engine (SE) oil. The response of immobilized fungi towards degradation at elevated pressure was studied in customized high pressure reactors without any deviation in simulating in situ deep-sea conditions. The growth rate of A. sydowii BOBA1 in 0.1 MPa was significantly different from the growth at 10 MPa pressure. The degradation percentage reached 71.2 and 82.5% at atmospheric and high pressure conditions, respectively, within a retention period of 21 days. The complete genome sequence of BOBA1 consists of 38,795,664 bp in size, comprises 2582 scaffolds with predicted total coding genes of 18,932. A total of 16,247 genes were assigned with known functions and many families found to have a potential role in PAHs and xenobiotic compound metabolism. Functional genes controlling the pathways of hydrocarbon and xenobiotics compound degrading enzymes such as dioxygenase, decarboxylase, hydrolase, reductase and peroxidase were identified. The spectroscopic and genomic analysis revealed the presence of combined catechol, gentisate and phthalic acid degradation pathway. These results of degradation and genomic studies evidenced that this deep-sea fungus could be employed to develop an eco-friendly mycoremediation technology to combat the oil polluted marine environment. This study expands our knowledge on piezophilic fungi and offer insight into possibilities about the fate of SE oil in deep-sea.

Elucidating fungal Rigidoporus species FMD21 lignin-modifying enzyme genes and 2,3,7,8-tetrachlorodibenzo-p-dioxin degradation by laccase isozymes

White-rot fungus Rigidoporus sp. FMD21 is a lignin-modifying enzyme producing fungus that can degrade dioxin. Extracellular enzymes from FMD21 include laccase and manganese peroxidase which are promising enzymes for myco-remediation because of their wide substrate specificity and mild catalysis conditions. The FMD21 genome was sequenced using Ion Torrent technology and consists of 38.98 Mbps with a GC content of 47.4 %. Gene prediction using Augustus with Basidiomycota reference setting resulted in 8245 genes. Functional gene annotations were carried out by using several programs and databases. We focused on laccase and ligninolytic peroxidase genes, which are most likely involved in the degradation of aromatic pollutants. The genome of FMD21 contains 12 predicted laccase genes (10 out of 12 predicted as full length) and 13 putative ligninolytic peroxidases which were annotated as MnP or versatile peroxidases. Four predicted laccases showed a higher than 65 % binding chance to 2,3,7,8-TCDD with the highest at 72 % in in silico docking analysis. Heterologous expressed laccases showed activity towards three tested substrates included ABTS, guaiacol and 2,6-DMP. ABTS displayed two-stage oxidation which differed from natural FMD21 laccases. 2,3,7,8-TCDD was degraded by 50 % after two weeks of enzymatic treatment by three out of five laccase isozymes which were natural laccases secreted by FMD21. In this study, we provide direct evidence for the 2,3,7,8-TCDD biodegradation capability of fungal laccases.

Characterization of 2,3,7,8-tetrachlorodibenzo-p-dioxin biodegradation by extracellular lignin-modifying enzymes from ligninolytic fungus

Ligninolytic fungi secrete extracellular lignin-modifying enzymes (LME) that degrade plant polymers for fungal nutrition but that are, because of their broad substrate specificity, also applicable for the degradation of many hazardous pollutants. Laccase is one of the most well characterized LME and is involved in the removal and degradation of recalcitrant aromatic compounds with or without the assistance of laccase-mediators. The Ligninolytic fungus Rigidoporus sp. FMD21 can degrade 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD) with a half-life of 6.2 days. Using Rigidoporus sp. FMD21 crude extracellular enzyme extract (ExE) that mainly consisted of laccase, 77.4% of 2,3,7,8-TCDD was degraded within 36 days. The degradation rate did not depend on the 2,3,7,8-TCDD concentration in the tested range between 0.005 and 0.5 pgTEQ/μL. 2,3,7,8-TCDD was analysed by DR-CALUX® bioassay and the degradation was confirmed by GC-HRMS. In this study, we found evidence for cleavage of the diaryl ether bond in the 2,3,7,8-TCDD molecule and here we propose a new degradation mechanism in which 3,4-dichlorophenol is the main metabolite of 2,3,7,8-TCDD degradation by FMD21's ExE. Six laccase-mediators were tested. Three of them 1-hydroxybenzotriazole (HBT), syringaldehyde (Syr) and violuric acid (Vio) showed an equipotent added effect on 2,3,7,8-TCDD degradation by ExE, however only in case of Vio a level of significance was reached. The others showed no effect or negatively impacted degradation. In conclusion, we have shown that Rigidoporus sp. FMD21 produces extracellular enzymes, mainly laccases that apparently are able to degrade the highly recalcitrant and most toxic 2,3,7,8-congener of TCDD via diaryl bond cleavage into 3,4-dichlorophenol.

Stable and transient transformation, and a promoter assay in the selective lignin-degrading fungus, Ceriporiopsis subvermispora

A genetic transformation system was developed for the selective white rot basidiomycete Ceriporiopsis subvermispora using a modified protocol with polyethylene glycol and CaCl₂ treatment of the protoplasts and plasmids harboring recombinant hygromycin phosphotransferase (hph) driven by a homologous promoter. During repeated transfer on fresh potato dextrose agar plates containing 100 µg/ml hygromycin B, most transformants lost drug resistance, while the remaining isolates showed stable resistance over five transfers. No drug-resistant colonies appeared in control experiments without DNA or using a promoter-less derivative of the plasmid, indicating that a transient expression of the recombinant hph was driven by the promoter sequence in these unstable drug-resistant transformants. Southern blot analysis of the stable transformants revealed random integration of the plasmid DNA fragment in the chromosome at different copy numbers. This transformation system yielding mostly transient transformants was successfully used for promoter assay experiments, and only a 141-bp fragment was found to be essential for the basic promoter function of glyceraldehyde dehydrogenase gene (gpd) in this fungus. Subsequent mutational analyses suggested that a TATAA sequence is important for the basic promoter function of gpd gene. The promoter assay system will enable the functional analysis of gene expression control sequences quickly and easily, mostly in the absence of undesirable effects from differences in copy number and chromosomal position of an integrated reporter gene among stable transformants.

Accumulation of U, Th, Pb, V, Rb, and Ag in wild mushrooms Macrolepiota procera (Scop.) Singer from Goč, Serbia

In this study, the content of U, Th, Pb, V, Rb, and Ag in 19 soil samples from unpolluted Goč Mountain area (Serbia) was determined. The same elements were determined in 19 Macrolepiota procera samples, separately for caps and stipes. Soil samples were subjected to the BCR sequential extraction procedure. Element contents were determined by inductively coupled plasma mass spectrometry (ICP-MS). Obtained soil values for U were in the range from 0.30 to 0.86 mg/kg and for Th from 1.7 to 13.2 mg/kg. These values are the first for background levels at unpolluted Goč area, and they are lower than the corresponding values for European unpolluted soil. The mean values in soil for Pb, V, Rb, and Ag were 27.6, 57.4, 15.8, and 0.76 mg/kg, respectively. PCA was applied to establish criteria for translocation of the analyzed elements between two parts of the mushroom. Efficient translocation for all elements except Ag as the main amount of the elements was found in caps. The mean content in the caps for U and Th was 4.3 and 63 μg/kg, respectively. Bioconcentration factors were much higher than 1 only for Rb and Ag. M. procera only weakly accumulates U and Th from soil in unpolluted areas. These findings indicate limited role of M. procera in the mycoremediation of the mentioned actinides.

Removal of emerging contaminants using spent mushroom compost

Acetaminophen and sulfonamides are emerging contaminants. Conventional wastewater treatment systems fail to degrade these compounds properly. Mycoremediation, is a form of novel bioremediation that uses extracellular enzymes of white-rot fungi to degrade pollutants in the environment. In this study, spent mushroom compost (SMC), which contains fungal extracellular enzymes, was tested for acetaminophen and sulfonamides removal. Among the SMCs of nine mushrooms tested in batch experiments, the SMC of Pleurotus eryngii exhibited the highest removal rate for acetaminophen and sulfonamides. Several fungal extracellular enzymes that might be involved in removal of acetaminophen and sulfonamides were identified by metaproteomic analysis. The bacterial classes, Betaproteobacteria and Alphaproteobacteria, were revealed by metagenomic analysis and may be assisting with acetaminophen and sulfonamide removal, respectively, in the SMC of Pleurotus eryngii. Bioreactor experiments were used to simulate the capability of Pleurotus eryngii SMC for the removal of acetaminophen and sulfonamides from wastewater. The results of this study provide a feasible solution for acetaminophen and sulfonamide removal from wastewater using the SMC of Pleurotus eryngii.

[Yeasts from the CTG clade (Candida clade): Biology, impact in human health, and biotechnological applications]

Among the subdivision of Saccharomycotina (ascomycetes budding yeasts), the CTG clade (formerly the Candida clade) includes species that display a particular genetic code. In these yeasts, the CTG codon is predominantly translated as a serine instead of a leucine residue. It is now well-known that some CTG clade species have a major impact on human and its activities. Some of them are recognized as opportunistic agents of fungal infections termed candidiasis. In addition, another series of species belonging to the CTG clade draws the attention of some research groups because they exhibit a strong potential in various areas of biotechnology such as biological control, bioremediation, but also in the production of valuable biocompounds (biofuel, vitamins, sweeteners, industrial enzymes). Here we provide an overview of recent advances concerning the biology, clinical relevance, and currently tested biotechnological applications of species of the CTG clade. Future directions for scientific research on these particular yeasts are also discussed.