Untapped potential: exploiting fungi in bioremediation of hazardous chemicals

Synergistic Effects of Surfactant Biostimulation and Indigenous Fungal Bioaugmentation for Enhanced Bioremediation of PAH-Contaminated Soils

Surfactant biostimulation and autochthonous fungal bioaugmentation have emerged as promising strategies for the bioremediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs). However, the mechanisms driving their combined effects remain poorly understood. This study investigates the degradation mechanisms associated with bioaugmentation using the indigenous fungus Aspergillus fumigatus LJD-29 and surfactant Tween 80. By employing stable-isotope probing and high-throughput sequencing, we comprehensively assessed these processes. In our study, the results demonstrate that both Aspergillus fumigatus LJD-29 and Tween 80 significantly enhanced the degradation efficiency of phenanthrene and modified the microbial community composition, particularly among active degraders. Extracellular enzymes were identified as key players in the phenanthrene transformation process. Tween 80 improved the bioavailability of phenanthrene, stimulating the growth of native PAH degraders, with Pseudonocardia emerging as a prominent genus. Although the combined surfactant-fungal treatment did not substantially increase terminal degradation efficiency due to limitations in phenanthrene bioavailability, it accelerated the degradation rate. Additionally, Tween 80 helped restore the microbial community structure disrupted by fungal bioaugmentation. These findings provide valuable insights into the mechanisms of surfactant biostimulation and indigenous fungal bioaugmentation, highlighting the potential of this integrated bioremediation strategy for managing PAH-contaminated soils.

Advancing bioremediation: biosurfactants as catalysts for sustainable remediation

Emerging contaminants such as persistent organic pollutants, perfluorinated compounds, and microplastics pose unparallel challenges to environmental health and current remediation techniques. Microbial biosurfactants, biodegradable compounds produced by microorganisms, have gained attention as eco-friendly alternatives for degrading recalcitrant pollutants. Unlike traditional chemical surfactants, biosurfactants offer the dual benefit of being derived from renewable resources while enhancing the solubility and bioavailability of hydrophobic contaminants. This review is novel in its comprehensive exploration of microbial biosurfactants as a one-step solution for tackling the most persistent environmental pollutants. It introduces recent advancements in metabolic engineering and alternative fermentation strategies that have significantly improved biosurfactant production. Furthermore, the review critically examines the current limitations, including high production costs and complex downstream processing, and proposes cutting-edge approaches to overcome these barriers, such as the use of low-cost feedstocks and integrated bioprocessing techniques. Beyond their established uses, this review also sheds light on their untapped potential in heavy metal removal and microplastic degradation areas that have received little attention. By emphasizing these novel applications and outlining pathways for large-scale production, this review offers valuable insights into how biosurfactants could play a transformative role in sustainable environmental remediation.

Microbial community dynamics and bioremediation strategies for petroleum contamination in an in-service oil Depot, middle-lower Yellow River Basin

This study investigated soil and groundwater contamination at an in-service oil transportation station in the middle-lower Yellow River Basin, China. Spatial analysis combined with 16S rRNA and ITS sequencing revealed localized heavy metal (Cu, Ni, Cd, Pb) and petroleum hydrocarbon (PHs: 15.0 mg/kg) contamination in the oily sewage treatment area, with vertical migration constrained by silty sand layers. Volatile organic compounds (VOCs) primarily originated from oil tank emissions. Groundwater exhibited hydraulic gradient-driven downstream migration of PHs (0.03-0.04 mg/L) and arsenic (1.1-1.5 μg/L). Indigenous microbial communities exhibited redox-stratified functional differentiation: unclassified Comamonadaceae (Proteobacteria) dominated aerobic zones (monitoring well D5), utilizing nitrate for PHs degradation, while Desulfosporosinus (Firmicutes) mediated sulfate-coupled anaerobic alkane degradation and metal immobilization in anoxic zones (D6). Fungal communities featured Trametes (Basidiomycota), facilitating ligninolytic PAH breakdown via peroxidase secretion. Functional prediction (FAPROTAX/FUNGuild) confirmed a synergistic "fungal preprocessing-bacterial mineralization" mechanism. Microbial metabolic plasticity (e.g., nitrogen respiration, photoautotrophy) enabled adaptation to redox fluctuations. Given the site's medium-low risk profile, we proposed a tiered management framework: (1) in situ bioremediation that prioritizes indigenous microbes, (2) hierarchical risk zoning, and (3) dynamic monitoring networks. These strategies align with China's Green Low-Carbon Remediation principles through low-energy microbial technologies. The findings provide a mechanistic basis for balancing industrial operations and ecological health in the Yellow River Basin.

Control of Fungal Spores on Surfaces with UV-C Exposure Necessitates Complete Inactivation to Prevent Mycorrhizal Network Establishment

Mold infestations on surfaces present significant challenges to public health. Germicidal UV-C irradiation effectively inactivates spores suspended in water, yet information on surface spore mitigation is surprisingly absent. We show the effectiveness of 265-275 nm UV-C light to mitigateAspergillus nigeron nutrient-rich surfaces. UV-C mitigation of surface molds differs from inactivating spores suspended in water due to the unique characteristics of mycelial structures. Complete preinactivation of all viable cells during UV-C exposure is crucial to prevent mycelia formation; otherwise, even a single spore can gradually spread, covering surfaces by producing a progressive mycelial structure. A UV-C dose of 144 mJ/cm2 from 265 nm LEDs achieved complete preinactivation at lower concentrations (100-1000 CFU/plate), while higher concentrations required increased UV-C doses. Intermittent duty cycling of light delivery (10 min ON then 50 min OFF) at 275 nm delivered from side-emitting optical fibers achieved comparable mitigation to continuous irradiation. Insufficient UV-C exposure induced more resistant mycelial structures that shielded live spores beneath. This study highlights complete preinactivation of viable molds, or sustained inhibition by UV-C light, is more effective than UV-C posttreatment. Mycelial alteration triggered by sublethal stress helps spores to persist in unfavorable environments, where microbial control is the goal.

In vitro chrysene degradation by purified cell free laccase (P-CFL) from Cochliobolus lunatus strain CHR4D in the presence of various redox mediator systems (RMSs) and computational evaluation of their laccase-ligand interactions

An immense progression in global industrialization in recent years has astonishingly elevated the contamination of marine, coastal, aquatic and terrestrial habitats with pervasive pollutants such as polycyclic aromatic hydrocarbons. Despite being discovered early and exploited for the years, laccases - a copper oxidase has a wide spectrum of applications in the fields of toxicological studies, bioremediation and restoration of impacted ecological matrices. The present study focuses on purification of mid-redox potential laccase from marine-derived fungus C. lunatus strain CHR4D, which has very high capacity to degrade chrysene - a four ringed hydrocarbon. The purified laccase (66 kDa) was further used for the in vitro chrysene degradation in non-growth conditions, in the presence of various redox mediator systems (RMSs) containing ABTS, HBT and VA. RMS including ABTS was found the most effective, resulting in 53.30% chrysene degradation in 24 h, followed by HBT (30.99%) and VA (28.98%), when compared to control conditions (27.78%). Laccase-ligand interactions were further explained by computational simulations and docking protocols. It revealed that laccase exhibited the highest binding energy towards chrysene. It also showed hydrophobic interactions with HBT and VA. The study would be helpful to further establish role of laccase in in vitro degradation of HMW PAHs.

Blusher mushroom (Amanita rubescens Pers.): A Study of Mercury Content in Substrate and Mushroom Samples from Slovakia with Respect to Locality and Developmental Stages

The edible mushroom Amanita rubescens Pers., regularly collected and consumed in Slovakia, was assessed for health risk due to the mercury content in its fruiting body parts. For this purpose, 364 both from the soil/substrate and mushroom samples from 40 localities in Slovakia were evaluated. At the same time, 21 samples of 7 developmental stages of the fruiting body of A. rubescens were taken in the Žakýlske pleso locality. The total mercury content in the soil and mushroom samples was determined using an AMA-254 analyzer. The contamination factor (Cf) and index of geoaccumulation (Igeo) were used to detect the level of soil pollution by mercury. The ability of A. rubescens to accumulate mercury from the soil environment was evaluated using the bioconcentration factor (BCF), and the distribution of mercury in the mushroom body was evaluated using the translocation quotient (Qc/s). To determine the health risks resulting from mushroom consumption, the percentages of provisional tolerable weekly intake (%PTWI) and target hazard quotient (THQ) were used. The obtained results have confirmed serious content of mercury soil pollution, especially in former mining areas, where the situation is alarming from a health risk point of view. Consumption of A. rubescens was found to be risky, not only in former mining areas, but higher values of mercury were also detected in other parts of Slovakia. Evaluation of the developmental stages of the fruiting body of A. rubescens showed that the highest bioconcentration factor was determined at developmental stage no. VI for caps with a value of 2.47 mg kg-1 and developmental stage VII for stipes with a value of 1.65 mg kg-1 DW.

Spatial and Temporal Characteristics of Riverine Fungal Communities and Their Responses to Environmental Factors in China's Largest Jiang-Flavor Baijiu-Producing Region

The Chishui River is the prime production area for Jiang-flavor Baijiu in China, with 85% of the country's production capacity. To understand the spatial and temporal characteristics of fungal communities in the water column of the Maotai reach of the Chishui River and the relationship between fungal communities and environmental factors as well as the brewing of Jiang-flavor Baijiu, we analyzed the fungal species richness and diversity, structural changes, community composition, and correlation with environmental factors in different seasons and river reaches of the Chishui River Maotai reach. It was found that species richness and diversity followed the following seasonal pattern: summer > autumn > winter ≈ spring. Fungal species richness and diversity were significantly higher in polluted tributary river water than in main stream. The composition and structure of the fungal community varied in all seasons and in different river reaches. Ascomycota (76.5%), Basidiomycota (13.53%), and Chytridiomycota (9.37%) are the relatively dominant phyla, and a number of genera such as Trichosporon, Aspergillus, and Thermomyces have been reported to be associated with the brewing of Jiang-flavor Baijiu. In addition, total nitrogen (TN), chemical oxygen demand (COD), water temperature (WT), dissolved oxygen (DO), sulfate (SO42-), and manganese (Mn) affected the fungal community structure of the Chishui River water body to different degrees (p < 0.05), and they were significantly correlated with Millerozyma and Candida, the genera related to Jiang-flavor Baijiu brewing, respectively. Our findings provide scientific basis and reference for further understanding the water ecological environment of Chishui River and its relationship with the brewing of Jiang-flavor Baijiu.

Microbial Community Composition of Explosive-Contaminated Soils: A Metataxonomic Analysis

Munition disposal practices have significant effects on microbial composition and overall soil health. Explosive soil contamination can disrupt microbial communities, leading to microbial abundance and richness changes. This study investigates the microbial diversity of soils and roots from sites with a history of ammunition disposal, aiming to identify organisms that may play a role in bioremediation. Soil and root samples were collected from two types of ammunition disposal (through open burning and open detonation) and unpolluted sites in Machachi, Ecuador, over two years (2022 and 2023). High-throughput sequencing of the 16S rRNA gene (for bacteria) and the ITS region (for fungi and plants) was conducted to obtain taxonomic profiles. There were significant variations in the composition of bacteria, fungi, and plant communities between polluted and unpolluted sites. Bacterial genera such as Pseudarthrobacter, Pseudomonas, and Rhizobium were more abundant in roots, while Candidatus Udaeobacter dominated unpolluted soils. Fungal classes Dothideomycetes and Sordariomycetes were prevalent across most samples, while Leotiomycetes and Agaricomycetes were also highly abundant in unpolluted samples. Plant-associated reads showed a higher abundance of Poa and Trifolium in root samples, particularly at contaminated sites, and Alchemilla, Vaccinium, and Hypericum were abundant in unpolluted sites. Alpha diversity analysis indicated that bacterial diversity was significantly higher in unpolluted root and soil samples, whereas fungal diversity was not significantly different among sites. Redundancy analysis of beta diversity showed that site, year, and sample type significantly influenced microbial community structure, with the site being the most influential factor. Differentially abundant microbial taxa, including bacteria such as Pseudarthrobacter and fungi such as Paraleptosphaeria and Talaromyces, may contribute to natural attenuation processes in explosive-contaminated soils. This research highlights the potential of certain microbial taxa to restore environments contaminated by explosives.

Enhancing Se(IV) bioremediation efficiency via immobilization of filamentous fungi and yeasts in eco-friendly alginate bead hydrogels

The immobilization of microorganisms in polymeric hydrogel has gained attention as a potential method for applications in various fields, offering several advantages over traditional cell free-living technologies. The present study aims to compare the efficiency of selenium (Se) bioremediation and biorecovery by two different fungal types, both in their free and immobilized forms using alginate hydrogels. Our results demonstrated an improvement in the amount of Se(IV) removed from the hydrogels of Aspergillus ochraceus (∼97%) and Rhodotorula mucilaginosa (∼43%) compared to that of the planktonic cultures (∼57% and ∼9-17%). In both cases, most of the Se(IV) is enzymatically reduced by the cells to amorphous Se(0) nanospheres, which are retained throughout the alginate hydrogels. The extensive growth, colonization and distribution of the cells throughout the highly porous hydrogel, along with their ability to maintain viability over long periods and the preservation of the structural integrity of the hydrogel, demonstrated the enormous biotechnological potential of the studied system for practical applications. The results reported show that the immobilization of fungi in alginate hydrogels is an efficient and environmentally friendly alternative for bioremediation and biorecovery of Se nanoparticles, which are of significant industrial and medical interest within the framework of a circular economy.

Fungal impacts on Earth's ecosystems

Over the past billion years, the fungal kingdom has diversified to more than two million species, with over 95% still undescribed. Beyond the well-known macroscopic mushrooms and microscopic yeast, fungi are heterotrophs that feed on almost any organic carbon, recycling nutrients through the decay of dead plants and animals and sequestering carbon into Earth's ecosystems. Human-directed applications of fungi extend from leavened bread, alcoholic beverages and biofuels to pharmaceuticals, including antibiotics and psychoactive compounds. Conversely, fungal infections pose risks to ecosystems ranging from crops to wildlife to humans; these risks are driven, in part, by human and animal movement, and might be accelerating with climate change. Genomic surveys are expanding our knowledge of the true biodiversity of the fungal kingdom, and genome-editing tools make it possible to imagine harnessing these organisms to fuel the bioeconomy. Here, we examine the fungal threats facing civilization and investigate opportunities to use fungi to combat these threats.

Ganoderma lucidum Immobilized on Wood Demonstrates High Persistence During the Removal of OPFRs in a Trickle-Bed Bioreactor

Emerging pollutants such as organophosphate flame retardants (OPFRs) pose a critical threat to environmental and human health, while conventional wastewater treatments often fail to remove them. This study addresses this issue by evaluating the bioremediation potential of white-rot fungi for the removal of two OPFRs: tris(2-chloroethyl) phosphate (TCEP) and tributyl phosphate (TBP). Three fungal species-Ganoderma lucidum, Trametes versicolor, and Phanerochaete velutina-were screened for their degradation capabilities. Among these, G. lucidum and T. versicolor demonstrated removal efficiencies exceeding 99% for TBP, while removal rates for TCEP were significantly lower, with a maximum of 30%. The exploration of the enzyme role showed that cytochrome P450 is involved in the degradation while the extracellular laccase is not involved. Continuous batch experiments were performed using a trickle-bed reactor (TBR) operating under non-sterile conditions, a setting that closely resembles real-world wastewater treatment environments. G. lucidum was immobilized on oak wood chips, and the removal efficiencies were measured to be 85.3% and 54.8% for TBP and TCEP, respectively, over 10 cycles. Microbial community analysis showed that G. lucidum remained the dominant species in the reactor. These findings demonstrate the efficacy of fungal-based trickle-bed bioreactors, offering a sustainable and efficient alternative for addressing environmental pollution caused by highly recalcitrant pollutants.

New insights into autochthonous fungal bioaugmentation mechanisms for recalcitrant petroleum hydrocarbon components using stable isotope probing

Autochthonous fungal bioaugmentation (AFB) is a promising strategy for the microbial remediation of petroleum hydrocarbon (PH)-contaminated soils. However, the mechanisms underlying AFB, particularly for degrading recalcitrant PH components, are not fully understood. This study employed stable isotope probing (SIP) and high-throughput sequencing to investigate the AFB mechanisms of two hydrocarbon-degrading fungi, Fusarium solani LJD-11 and Aspergillus fumigatus LJD-29, focusing on three challenging PH components: n-Hexadecane (n-Hex), Benzo[a]pyrene (BaP), and Dibenzothiophene (DBT). Our findings indicate that both fungal strains significantly enhanced pollutant removal rates, with combined application yielding optimal results. AFB treatment reduced the microbial diversity index and altered the soil microbial community, especially affecting fungal populations. A significant correlation between the microbial diversity index and degradation efficiency suggests that greater diversity enhances pollutant removal. SIP analysis showed that LJD-11 and LJD-29 could directly assimilate n-Hex and DBT, but not BaP. Correlation analyses between functional microorganisms and other biological indicators suggest that the removal of pollutants is also attributable to indigenous functional bacteria. Additionally, non-inoculated functional fungi present in the soil play a crucial role in BaP degradation. These findings reveal distinct degradation pathways for the three pollutants. The addition of carrier substrate reduced the complexity of the network, while AFB treatment restored it. In addition, the combined fungal treatment resulted in higher network parameters, leading to a more complex and stable network structure. These results provide insights into the mechanisms of AFB for degrading recalcitrant PH components, underscoring its potential for in situ bioremediation of petroleum-contaminated soils.

A comprehensive review on advanced trends in treatment technologies for removal of Bisphenol A from aquatic media

Toxic environmental pollutants are considered to be posed a major threat to human and aquatic systems. The fast advancement of the petrochemical and chemical industries has woken up rising worries concerning the pollution of water by contaminants including phenolic Bisphenol A (BPA), an endocrine-disrupting chemical (EDC). The intermediate BPA used in synthesis of certain plastics, polycarbonate polymers, polysulfone, and epoxy resins of various polyesters. Due to potential health risks, severe toxicity, and widespread distribution, there is an urgent need to develop efficient techniques for the removal of BPA. Therefore, advance management for the active elimination of BPA prior to its release into the water sources is of serious concern. Degradation, membrane separation, adsorption, and biological treatments have been extensively examined as they are easy to operate and cost-effective for effective BPA removal. In this review, we summarized the mechanism and performance for removal of BPA by several sorbents, including natural polymers, natural inorganic minerals, porous and carbon-based materials. Comparative results revealed that composite materials and modified adsorbents have good performances for removal of BPA. Furthermore, kinetic study investigating adsorption mechanisms was also discussed. Hazardous quantities of such types of chemicals in various samples have thus been the subject of increasing concern of investigation. This review clarified the extensive literature regarding the major health effects of BPA and its advanced treatment technologies including biological treatment by natural and synthetic materials have been discussed briefly. It delivers regulation for future development and research from the aspects of materials functionalization, development of methods, and mechanism investigation that directing to stimulate developments for removal of emerging contaminants.

Dynamic response of soil microbial communities and network to hymexazol exposure

Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60 days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.

Unappreciated role of secondary metabolism-derived small mediators in degrading bisphenol A and antibiotics by a laccase-expressing fungus

Fungal laccase producers can effectively address bisphenol A (BPA) and antibiotic-contaminated water. However, the role of small mediators produced by fungal secondary metabolism in enhancing the removal of refractory contaminants is often overlooked. In this work, an efficient laccase-producing strain, Trametes hirsuta La-7, was activated to simultaneously treat BPA and antibiotics. Coexisting tetracycline, ciprofloxacin, sulfadiazine, or roxithromycin inhibited fungal cell growth, reducing laccase biosynthesis but largely increasing the formation of syringaldehyde (SYR), 4-hydroxybenzoic acid (HBA), and vanillin (VAN) through a complex regulatory network. These specialized metabolites (i.e., small mediators) acted as diffusible electron carriers for laccase, enabling the oxidative decomposition of the four antibiotics with high redox potentials. According to laccase-mediator-regulated radical random polymerization and decomposition, the identified intermediates of copollutants were parallelly concentrated in oligomeric coupling products and oxidative cleavage species. By inoculating logarithmic phase cell pellets in conjunction with an artificially added small mediator (SYR, HBA, or VAN), the removal efficiencies of BPA and the four antibiotics within 5 d reached 100% and 69-100% in artificial wastewater, respectively. The low and ultimately non-biotoxic intermediate products generated in the fungus-mediator systems mitigated the eco-environmental risks of the parent compounds. This work highlights the previously underappreciated role of secondary metabolism-derived small mediators in enhancing the degradation of BPA and antibiotics by a laccase-expressing fungus and is beneficial to the rational design of a robust fungus-mediator system for environmental bioremediation.

Unlocking the biodegradative potential of native white-rot fungi: a comparative study of fiberbank organic pollutant mycoremediation

Fiberbanks refer to a type of fibrous sediment originated by the forestry and wood pulping industry in Sweden. These anthropogenic sediments are significantly contaminated with potentially toxic elements, and a diverse array of organic pollutants. Additionally, these sediments are of environmental concern due to their potential role in greenhouse gas emissions. Given the environmental risks posed by these sediments, the development of effective remediation strategies is of critical importance. However, no specialized methods have been established yet for the cleanup of this specific type of contaminated sediments. To identify effective fungal species for the mycoremediation of the fiberbank substrate, we performed a detailed screening experiment. In this research, we primarily aimed at assessing both the growth capacity and the proficiency in degrading organic pollutants of 26 native white-rot fungi (WRF) species. These species were sourced from natural forest environments in northern Sweden. The experimental setup involved evaluating the WRF on plates containing fiberbank material with a central Hagem-agar disc to closely monitor the interaction of these species with fiberbank substrates. Among the fungi tested, Laetiporus sulphureus exhibited the highest growth area percentage at 72%, followed by Hymenochaete tabacina at 68% and Diplomitoporus crustulinus at 67%. For the removal of 2-3 ring polycyclic aromatic hydrocarbons (PAHs), Phellinus punctatus led with 68%, with Cystostereum muraii at 57% and Diplomitoporus crustulinus at 49%. Regarding the removal percentage of 4-6 ring PAHs, Diplomitoporus crustulinus showed the highest efficiency at 44%, followed by Phlebia tremellosa at 40% and Phlebiopsis gigantea at 28%.

Whispers in the mangroves: Unveiling the silent impact of potential toxic metals (PTMs) on Indian Sundarbans fungi

This study investigates sediment samples from the Indian Sundarbans' mangrove habitat, where most samples were alkaline and hypersaline, except for one acidic sample. Elemental analysis revealed poor sediment quality, with elevated Enrichment Factors (2.20-9.7), Geo-accumulation indices (-2.19-1.19), Contamination Factors (0.61-3.18), and Pollution Load Indices (1.04-1.32). Toxic metal ions, including Pb, Cu, Ni, Cd, Zn, and Cr, were identified as key contributors to compromised sediment quality. These metals inhibit crucial sediment enzymes, such as CMC-cellulase, β-glucosidase, aryl sulfatase, urease, and phosphatases, essential for nutrient cycling and organic matter decomposition. A negative correlation was found between heavy metals and biodiversity, as indicated by the Shannon index, and a similar trend was observed with fungal load. The study highlights the adverse effects of persistent trace metals on the fungal community, potentially disrupting the mangrove ecosystem and suggests using manglicolous fungi as biological indicators of environmental health.

The diversity of ignorance and the ignorance of diversity: origins and implications of "shadow diversity" for conservation biology and extinction

Biodiversity shortfalls and taxonomic bias can lead to inaccurate assessment of conservation priorities. Previous literature has begun to explore practical reasons why some species are discovered sooner or are better researched than others. However, the deeper socio-cultural causes for undiscovered and neglected biodiversity, and the value of collectively analysing species at risk of unrecorded, or "dark", extinction, are yet to be fully examined. Here, we argue that a new label (we propose "shadow diversity") is needed to shift our perspective from biodiversity shortfalls to living, albeit unknown, species. We suggest this linguistic shift imparts intrinsic value to these species, beyond scientific gaze and cultural systems. We review research on undiscovered, undetected and hidden biodiversity in the fields of conservation biology, macroecology and genetics. Drawing on philosophy, geography, history and sociology, we demonstrate that a range of socio-cultural factors (funding, education and historical bias) combine with traditional, practical impediments to limit species discovery and detection. We propose using a spectrum of shadow diversity which enables a complex, non-binary and comprehensive approach to biodiversity unknowns. Shadow diversity holds exciting potential as a tool to increase awareness, appreciation and support for the conservation of traditionally less studied wildlife species and sites, from soil microbes to less charismatic habitat fragments. We advocate for a shift in how the conservation community and wider public see biodiversity and an increase in popular support for conserving a wider range of life forms. Most importantly, shadow diversity provides appropriate language and conceptual frameworks to discuss species absent from conservation assessment and at potential risk of dark extinction.

Fungal community dynamics in a hyper-arid ecosystem after 7 and 47 years of petroleum contamination

This study investigates the impact of crude oil contamination on the fungal community dynamics in the Evrona Nature Reserve, situated in Israel's hyper-arid Arava Valley. The reserve experienced petroleum-hydrocarbon-spill pollution at two neighboring sites in 1975 and 2014. The initial contamination was left untreated, providing a unique opportunity to compare its effects to those of the second contamination event. In 2022, soil samples were collected from both contaminated areas and nearby clean (control) sites, 47 and 7 years after the spills. The taxonomic diversity of fungal community and functional guilds, as well as various properties of the soil, were analyzed. We focused on three functional groups within fungal communities: saprotrophs, symbiotrophs, and pathotrophs. The results revealed a significant decrease in number of fungal species in the contaminated samples over time. Consequently, prolonged effect of crude oil-contaminated soils can facilitate the development of a distinct fungal community, which has adapted to the conditions of oil contamination. This study aims to elucidate the dynamics of fungal communities in oil-contaminated soils, contributing to a better understanding of their behavior and adaptation in such environments.

Clay-polymer hybrid hydrogels in the vanguard of technological innovations for bioremediation, metal biorecovery, and diverse applications

Polymeric hydrogels are among the most studied materials due to their exceptional properties for many applications. In addition to organic and inorganic-based hydrogels, "hybrid hydrogels" have been gaining significant relevance in recent years due to their enhanced mechanical properties and a broader range of functionalities while maintaining good biocompatibility. In this sense, the addition of micro- and nanoscale clay particles seems promising for improving the physical, chemical, and biological properties of hydrogels. Nanoclays can contribute to the physical cross-linking of polymers, enhancing their mechanical strength and their swelling and biocompatibility properties. Nowadays, they are being investigated for their potential use in a wide range of applications, including medicine, industry, and environmental decontamination. The use of microorganisms for the decontamination of environments impacted by toxic compounds, known as bioremediation, represents one of the most promising approaches to address global pollution. The immobilization of microorganisms in polymeric hydrogel matrices is an attractive procedure that can offer several advantages, such as improving the preservation of cellular integrity, and facilitating cell separation, recovery, and transport. Cell immobilization also facilitates the biorecovery of critical materials from wastes within the framework of the circular economy. The present work aims to present an up-to-date overview on the different "hybrid hydrogels" used to date for bioremediation of toxic metals and recovery of critical materials, among other applications, highlighting possible drawbacks and gaps in research. This will provide the latest trends and advancements in the field and contribute to search for effective bioremediation strategies and critical materials recovery technologies.

Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils

Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.

Revolutionizing Mushroom processing: Innovative techniques and technologies

In recent years, the global mushroom industry has seen remarkable growth due to its nutritional benefits, increasing market value, and rising consumer demand. Mushrooms are valued for their unique flavor, low sugar and salt, and rich Vitamin D content. In India as well as across the globe, mushroom cultivation is becoming increasingly popular among new entrepreneurs, leveraging the diverse agro-climatic conditions and substantial agricultural waste. Various government policies are also fostering research and development in this sector. To extend shelf life and preserve quality, various preservation techniques are employed, including drying, freezing, canning, high-pressure processing and modified atmosphere packaging. Furthermore, cutting-edge technologies such as nuclear magnetic resonance and spectroscopy are improving post-harvest processing, helping to maintain sensory properties and nutritional content. Automation is also transforming mushroom processing by enhancing efficiency and scalability. This review examines the innovative methods and technologies driving advancements in mushroom production and quality worldwide.

Strain selection and adaptation of a fungal-yeast-microalgae consortium for sustainable bioethanol production and wastewater treatment from livestock wastewater

This study explores the potential of strain selection and adaptation for developing a fungi-yeast-microalgae consortium capable of integrated bioethanol production and livestock wastewater treatment. We employed a multi-stage approach involving isolation and strain selection/adaptation of these consortiums. The study started with screening some isolated fungi to grow on the cellulosic biomass of the livestock wastewater (saccharification) followed by a fermentation process using yeast for bioethanol production. The results revealed that Penicillium chrysogenum (Cla) and Saccharomyces cerevisiae (Sc) produced a remarkable 99.32 ppm of bioethanol and a concentration of glucose measuring 0.56 mg ml- 1. Following the impact of fungi and yeast, we diluted the livestock wastewater using distilled water and subsequently inoculated Nile River microalgae into the wastewater. The findings demonstrated that Chlorella vulgaris emerged as the dominant species in the microalgal community. Particularly, the growth rate reached its peak at a 5% organic load (0.105385), indicating that this concentration provided the most favorable conditions for the flourishing of microalgae. The results demonstrated the effectiveness of the microalgal treatment in removing the remaining nutrients and organic load, achieving a 92.5% reduction in ammonia, a 94.1% reduction in nitrate, and complete removal of phosphate (100%). The algal treatment also showed remarkable reductions in COD (96.5%) and BOD (96.1%). These findings underscore the potential of fungi, yeast, and Nile River microalgae in the growth and impact on livestock wastewater, with the additional benefit of bioethanol production.

Unveiling fungal strategies: Mycoremediation in multi-metal pesticide environment using proteomics

Micropollutants, such as heavy metals and pesticides, inhibit microbial growth, threatening ecosystems. Yet, the mechanism behind mycoremediation of the pesticide lindane and multiple metals (Cd, Total Cr, Cu, Ni, Pb, Zn) remains poorly understood. In our study, we investigated cellular responses in Aspergillus fumigatus PD-18 using LC-MS/MS, identifying 2190 proteins, 1147 of which were consistently present under both stress conditions. Specifically, Cu-Zn superoxide dismutase and heat shock proteins were up-regulated to counter oxidative stress and protein misfolding. Proteins involved in intracellular trafficking, secretion, and vesicular transport; RNA processing and modification showed enhanced abundance and regulating stress response pathways. Additionally, haloalkane dehalogenase and homogentisate 1,2-dioxygenase played pivotal roles in lindane mineralization. Bioinformatics analysis highlighted enriched pathways such as Glyoxylate and dicarboxylate metabolism and Purine metabolism, that are crucial for combating adverse environments. We identified the hub protein 26 S proteasome regulatory subunit complex as potential biomarker and remedial targets for mycoremediation of wastewater, suggesting practical applications for environmental remediation.

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.

Bioremediation of Contaminated Soil by Fungi: A Call for Research

Soil contamination represents a global environmental challenge, posing a threat to soil ecosystems, agricultural production, and human health [...].

Biodegradation of low-density polyethylene by mixed fungi composed of Alternaria sp. and Trametes sp. isolated from landfill sites

With the development of industry and modern manufacturing, nondegradable low-density polyethylene (LDPE) has been widely used, posing a rising environmental hazard to natural ecosystems and public health. In this study, we isolated a series of LDPE-degrading fungi from landfill sites and carried out LDPE degradation experiments by combining highly efficient degrading fungi in pairs. The results showed that the mixed microorganisms composed of Alternaria sp. CPEF-1 and Trametes sp. PE2F-4 (H-3 group) had a greater degradation effect on heat-treated LDPE (T-LDPE). After 30 days of inoculation with combination strain H-3, the weight loss rate of the T-LDPE film was approximately 154% higher than that of the untreated LDPE (U-LDPE) film, and the weight loss rate reached 0.66 ± 0.06%. Environmental scanning electron microscopy (ESEM) and Fourier transform infrared spectroscopy (FTIR) were used to further investigate the biodegradation impacts of T-LDPE, including the changes on the surface and depolymerization of the LDPE films during the fungal degradation process. Our findings revealed that the combined fungal treatment is more effective at degrading T-LDPE than the single strain treatment, and it is expected that properly altering the composition of the microbial community can help lessen the detrimental impact of plastics on the environment.

Visualizing liquid distribution across hyphal networks with cellular resolution

Filamentous fungi and fungal-like organisms contribute to a wide range of important ecosystem functions. Evidence has shown the movement of liquid across mycelial networks in unsaturated environments, such as soil. However, tools to investigate liquid movement along hyphae at the level of the single cell are still lacking. Microfluidic devices permit the study of fungal and fungal-like organisms with cellular resolution as they can confine hyphae to a single optical plane, which is compatible with microscopy imaging over longer timescales and allows for precise control of the microchannel environment. The aim of this study was to develop a method that enables the visualization and quantification of liquid movement on hyphae of fungal and fungal-like microorganisms. For this, the fungal-fungal interaction microfluidic device was modified to allow for the maintenance of unsaturated microchannel conditions. Fluorescein-containing growth medium solidified with agar was used to track liquid transported by hyphae via fluorescence microscopy. Our key findings highlight the suitability of this novel methodology for the visualization of liquid movement by hyphae over varying time scales and the ability to quantify the movement of liquid along hyphae. Furthermore, we showed that at the cellular level, extracellular movement of liquid along hyphae can be bidirectional and highly dynamic, uncovering a possible link between liquid movement and hyphal growth characteristics. We envisage that this method can be applied to facilitate future research probing the parameters contributing to hyphal liquid movement and is an essential step for studying the phenomenon of fungal highways.

Biosensors for detection of airborne pathogenic fungal spores: a review

The excessive presence of airborne fungal spores presents major concerns with potential adverse impacts on public health and food safety. These spores are recognized as pathogens and allergens prevalent in both outdoor and indoor environments, particularly in public spaces such as hospitals, schools, offices and hotels. Indoor environments pose a heightened risk of pulmonary diseases due to continuous exposure to airborne fungal spore particles through constant inhalation, especially in those individuals with weakened immunity and immunocompromised conditions. Detection methods for airborne fungal spores are often expensive, time-consuming, and lack sensitivity, making them unsuitable for indoor/outdoor monitoring. However, the emergence of micro-nano biosensor systems offers promising solutions with miniaturized designs, nanomaterial integration, and microfluidic systems. This review provides a comprehensive overview of recent advancements in bio-nano-sensor system technology for detecting airborne fungal spores, while also discussing future trends in biosensor device development aimed at achieving rapid and selective identification of pathogenic airborne fungi.

Laccase Immobilized on Arginine-Functionalized Boron Nitride Nanosheets for Enhanced Atrazine Degradation

Enzyme-mediated systems have been widely employed for the biotransformation of environmental contaminants. However, the catalytic performance of free enzymes is restricted by the rapid loss of their catalytic activity, stability, and reusability. In this work, we developed an enzyme immobilization platform by elaborately anchoring fungal laccase onto arginine-functionalized boron nitride nanosheets (BNNS-Arg@Lac). BNNS-Arg@Lac showcased ∼75% immobilization yield and enhanced stability against fluctuating pH values and temperatures, along with remarkable reusability across six consecutive cycles, outperforming free natural laccase (nlaccase). A model pollutant, atrazine, was selected for a proof-of-concept demonstration, given the substantial environmental and public health concerns in agriculture runoff. BNNS-Arg@Lac-catalyzed atrazine degradation rate was nearly twice that of nlaccase. Moreover, BNNS-Arg@Lac consistently demonstrated superior atrazine degradation in synthetic agricultural wastewater and various mediator systems compared to nlaccase. Comprehensive product analysis unraveled distinct degradation pathways for BNNS-Arg@Lac and nlaccase. Overall, this research provides a foundation for the future development of enzyme-nanomaterial hybrids for degrading environmental chemicals and may unlock new potential for green and efficient resource recovery and waste management strategies.

Two Zn2Cys6-type transcription factors respond to aromatic compounds and regulate the expression of laccases in the white-rot fungus Trametes hirsuta

White-rot fungi differentially express laccases when they encounter aromatic compounds. However, the underlying mechanisms are still being explored. Here, proteomics analysis revealed that in addition to increased laccase activity, proteins involved in sphingolipid metabolism and toluene degradation as well as some cytochrome P450s (CYP450s) were differentially expressed and significantly enriched during 48 h of o-toluidine exposure, in Trametes hirsuta AH28-2. Two Zn2Cys6-type transcription factors (TFs), TH8421 and TH4300, were upregulated. Bioinformatics docking and isothermal titration calorimetry assays showed that each of them could bind directly to o-toluidine and another aromatic monomer, guaiacol. Binding to aromatic compounds promoted the formation of TH8421/TH4300 heterodimers. TH8421 and TH4300 silencing in T. hirsuta AH28-2 led to decreased transcriptional levels and activities of LacA and LacB upon o-toluidine and guaiacol exposure. EMSA and ChIP-qPCR analysis further showed that TH8421 and TH4300 bound directly with the promoter regions of lacA and lacB containing CGG or CCG motifs. Furthermore, the two TFs were involved in direct and positive regulation of the transcription of some CYP450s. Together, TH8421 and TH4300, two key regulators found in T. hirsuta AH28-2, function as heterodimers to simultaneously trigger the expression of downstream laccases and intracellular enzymes. Monomeric aromatic compounds act as ligands to promote heterodimer formation and enhance the transcriptional activities of the two TFs.IMPORTANCEWhite-rot fungi differentially express laccase isoenzymes when exposed to aromatic compounds. Clarification of the molecular mechanisms underlying differential laccase expression is essential to elucidate how white-rot fungi respond to the environment. Our study shows that two Zn2Cys6-type transcription factors form heterodimers, interact with the promoters of laccase genes, and positively regulate laccase transcription in Trametes hirsuta AH28-2. Aromatic monomer addition induces faster heterodimer formation and rate of activity. These findings not only identify two new transcription factors involved in fungal laccase transcription but also deepen our understanding of the mechanisms underlying the response to aromatics exposure in white-rot fungi.

Bioremediation of petroleum hydrocarbons polluted soil by spent mushroom substrates: Microbiological structure and functionality

Spent mushroom substrate (SMS) holds valuable microbiota that can be useful in remediating polluted soils with hydrocarbons. However, the microorganisms behind the bioremediation process remain uncertain. In this work, a bioremediation assay of total petroleum hydrocarbons (TPHs) polluted soil by SMS application was performed to elucidate the microorganisms and consortia involved in biodegradation by a metabarcoding analysis. Untreated polluted soil was compared to seven bioremediation treatments by adding SMS of Agaricus bisporus, Pleurotus eryngii, Pleurotus ostreatus, and combinations. Soil microbial activity, TPH biodegradation, taxonomic classification, and predictive functional analysis were evaluated in the microbiopiles at 60 days. Different metagenomics approaches were performed to understand the impact of each SMS on native soil microbiota and TPHs biodegradation. All SMSs enhanced the degradation of aliphatic and aromatic hydrocarbons, being A. bisporus the most effective, promoting an efficient consortium constituted by the bacterial families Alcanivoraceae, Alcaligenaceae, and Dietziaceae along with the fungal genera Scedosporium and Aspergillus. The predictive 16 S rRNA gene study partially explained the decontamination efficacy by observing changes in the taxonomic structure of bacteria and fungi, and changes in the potential profiles of estimated degradative genes across the different treatments. This work provides new insights into TPHs bioremediation.

Biodegradation of polyethylene by the marine fungus Parengyodontium album

Plastic pollution in the marine realm is a severe environmental problem. Nevertheless, plastic may also serve as a potential carbon and energy source for microbes, yet the contribution of marine microbes, especially marine fungi to plastic degradation is not well constrained. We isolated the fungus Parengyodontium album from floating plastic debris in the North Pacific Subtropical Gyre and measured fungal-mediated mineralization rates (conversion to CO2) of polyethylene (PE) by applying stable isotope probing assays with 13C-PE over 9 days of incubation. When the PE was pretreated with UV light, the biodegradation rate of the initially added PE was 0.044 %/day. Furthermore, we traced the incorporation of PE-derived 13C carbon into P. album biomass using nanoSIMS and fatty acid analysis. Despite the high mineralization rate of the UV-treated 13C-PE, incorporation of PE-derived 13C into fungal cells was minor, and 13C incorporation was not detectable for the non-treated PE. Together, our results reveal the potential of P. album to degrade PE in the marine environment and to mineralize it to CO2. However, the initial photodegradation of PE is crucial for P. album to metabolize the PE-derived carbon.

Tapping into fungal potential: Biodegradation of plastic and rubber by potent Fungi

Plastic polymers are present in most aspects of routine daily life. Their increasing leakage into the environment poses a threat to environmental, animal, and human health. These polymers are often resistant to microbial degradation and are predicted to remain in the environment for tens to hundreds of years. Fungi have been shown to degrade complex polymers and are considered good candidates for bioremediation (biological pollutant reduction) of plastics. Therefore, we screened 18 selected fungal strains for their ability to degrade polyurethane (PU), polyethylene (PE), and tire rubber. As a proxy for plastic polymer mineralization, we quantified O2 consumption and CO2 production in an enclosed biodegradation system providing plastic as the sole carbon source. In contrast to most studies we demonstrated that the tested fungi attach to, and colonize the different plastic polymers without any pretreatment of the plastics and in the absence of sugars, which were suggested essential for priming the degradation process. Functional polymer groups identified by Fourier-transform infrared spectroscopy (FTIR), and changes in fungal morphology as seen in light and scanning electron microscopy (SEM) were used as indicators of fungal adaptation to growth on PU as a substrate. Thereby, SEM analysis revealed new morphological structures and deformation of the cell wall of several fungal strains when colonizing PU and utilizing this plastic polymer for cell growth. Strains of Fusarium, Penicillium, Botryotinia cinerea EN41, and Trichoderma demonstrated a high potential to degrade PU, rubber, and PE. Growing on PU, over 90 % of the O2 was consumed in <14 days with 300-500 ppm of CO2 generated in parallel. Our study highlights a high bioremediation potential of some fungal strains to efficiently degrade plastic polymers, largely dependent on plastic type.

Hybrid constructed wetlands and filamentous fungi for treatment of mixed sewage and industrial effluents

Developing countries face multifaceted problems of water pollution and futile measures to combat water pollution. This study was conducted to explore the potential application of sustainable nature-based solutions, hybrid constructed wetlands, and the application of filamentous fungi to treat polluted river water that receives sewage and industrial wastewater. A pilot-scale hybrid constructed wetland design comprising two types of floating plants in distinct tanks along with a floating wetland and a free-water surface wetland connected in series was commissioned and tested. The system successfully removed organic pollution (BOD 94% and COD 90%), nutrients (NH4-N and NO3-N 67% and PO4-P 81%), and heavy metals (Cr 75%, Ni 56%, and Fe 79%) in 40 h and showed a high buffering capacity to cope with the varying pollutant loads. Metagenomics analysis of treated and untreated samples of river water revealed a diversified spatial bacterial community with ~ 25% sequences related to sulfur-metabolizing bacteria, genus Sulfuricurvum. The application of an immobilized strain of A. niger as a mycoremediation technique was also tested. It successfully removed pollutants in the combined sewage and industrial wastewater present in river water: COD (96%), TSS (97%), NH4-N (65%), NO3-N (67%), and PO4-P (78%). This study demonstrated that hybrid constructed wetlands and mycoremediation can be used as sustainable wastewater treatment options in the local context and also in developing countries where most of the conventional wastewater treatment plants do not operate.

Determination of soil phenanthrene degradation through a fungal-bacterial consortium

Fungal-bacterial consortia enhance organic pollutant removal, but the underlying mechanisms are unclear. We used stable isotope probing (SIP) to explore the mechanism of bioaugmentation involved in polycyclic aromatic hydrocarbon (PAH) biodegradation in petroleum-contaminated soil by introducing the indigenous fungal strain Aspergillus sp. LJD-29 and the bacterial strain Pseudomonas XH-1. While each strain alone increased phenanthrene (PHE) degradation, the simultaneous addition of both strains showed no significant enhancement compared to treatment with XH-1 alone. Nonetheless, the assimilation effect of microorganisms on PHE was significantly enhanced. SIP revealed a role of XH-1 in PHE degradation, while the absence of LJD-29 in 13C-DNA indicated a supporting role. The correlations between fungal abundance, degradation efficiency, and soil extracellular enzyme activity indicated that LJD-29, while not directly involved in PHE assimilation, played a crucial role in the breakdown of PHE through extracellular enzymes, facilitating the assimilation of metabolites by bacteria. This observation was substantiated by the results of metabolite analysis. Furthermore, the combination of fungus and bacterium significantly influenced the diversity of PHE degraders. Taken together, this study highlighted the synergistic effects of fungi and bacteria in PAH degradation, revealed a new fungal-bacterial bioaugmentation mechanism and diversity of PAH-degrading microorganisms, and provided insights for in situ bioremediation of PAH-contaminated soil.IMPORTANCEThis study was performed to explore the mechanism of bioaugmentation by a fungal-bacterial consortium for phenanthrene (PHE) degradation in petroleum-contaminated soil. Using the indigenous fungal strain Aspergillus sp. LJD-29 and bacterial strain Pseudomonas XH-1, we performed stable isotope probing (SIP) to trace active PHE-degrading microorganisms. While inoculation of either organism alone significantly enhanced PHE degradation, the simultaneous addition of both strains revealed complex interactions. The efficiency plateaued, highlighting the nuanced microbial interactions. SIP identified XH-1 as the primary contributor to in situ PHE degradation, in contrast to the limited role of LJD-29. Correlations between fungal abundance, degradation efficiency, and extracellular enzyme activity underscored the pivotal role of LJD-29 in enzymatically facilitating PHE breakdown and enriching bacterial assimilation. Metabolite analysis validated this synergy, unveiling distinct biodegradation mechanisms. Furthermore, this fungal-bacterial alliance significantly impacted PHE-degrading microorganism diversity. These findings advance our understanding of fungal-bacterial bioaugmentation and microorganism diversity in polycyclic aromatic hydrocarbon (PAH) degradation as well as providing insights for theoretical guidance in the in situ bioremediation of PAH-contaminated soil.

A comparison of the performance of bacterial biofilters and fungal-bacterial coupled biofilters in BTEp-X removal

Background

Conventional biofilters, which rely on bacterial activity, face challenges in eliminating hydrophobic compounds, such as aromatic compounds. This is due to the low solubility of these compounds in water, which makes them difficult to absorb by bacterial biofilms. Furthermore, biofilter operational stability is often hampered by acidification and drying out of the filter bed.

Methods

Two bioreactors, a bacterial biofilter (B-BF) and a fungal-bacterial coupled biofilter (F&B-BF) were inoculated with activated sludge from the secondary sedimentation tank of the Sinopec Yangzi Petrochemical Company wastewater treatment plant located in Nanjing, China. For approximately 6 months of operation, a F&B-BF was more effective than a B-BF in eliminating a gas-phase mixture containing benzene, toluene, ethylbenzene, and para-xylene (BTEp-X).

Results

After operating for four months, the F&B-BF showed higher removal efficiencies for toluene (T), ethylbenzene (E), benzene (B), and para-X (p-Xylene), at 96.9%, 92.6%, 83.9%, and 83.8%, respectively, compared to those of the B-BF (90.1%, 78.7%, 64.8%, and 59.3%). The degradation activity order for B-BF and F&B-BF was T > E > B > p-X. Similarly, the rates of mineralization for BTEp-X in the F&B-BF were 74.9%, 66.5%, 55.3%, and 45.1%, respectively, which were higher than those in the B-BF (56.5%, 50.8%, 43.8%, and 30.5%). Additionally, the F&B-BF (2 days) exhibited faster recovery rates than the B-BF (5 days).

Conclusions

It was found that a starvation protocol was beneficial for the stable operation of both the B-BF and F&B-BF. Community structure analysis showed that the bacterial genus Pseudomonas and the fungal genus Phialophora were both important in the degradation of BTEp-X. The fungal-bacterial consortia can enhance the biofiltration removal of BTEp-X vapors.

Biodegradable plastics in Mediterranean coastal environments feature contrasting microbial succession

Plastic pollution of the ocean is a top environmental concern. Biodegradable plastics present a potential "solution" in combating the accumulation of plastic pollution, and their production is currently increasing. While these polymers will contribute to the future plastic marine debris budget, very little is known still about the behavior of biodegradable plastics in different natural environments. In this study, we molecularly profiled entire microbial communities on laboratory confirmed biodegradable polybutylene sebacate-co-terephthalate (PBSeT) and polyhydroxybutyrate (PHB) films, and non-biodegradable conventional low-density polyethylene (LDPE) films that were incubated in situ in three different coastal environments in the Mediterranean Sea. Samples from a pelagic, benthic, and eulittoral habitat were taken at five timepoints during an incubation period of 22 months. We assessed the presence of potential biodegrading bacterial and fungal taxa and contrasted them against previously published in situ disintegration data of these polymers. Scanning electron microscopy imaging complemented our molecular data. Putative plastic degraders occurred in all environments, but there was no obvious "core" of shared plastic-specific microbes. While communities varied between polymers, the habitat predominantly selected for the underlying communities. Observed disintegration patterns did not necessarily match community patterns of putative plastic degraders.

Landfill leachate treatment using fungi and fungal enzymes: a review

Landfill leachate raises a huge risk to human health and the environment as it contains a high concentration of organic and inorganic contaminants, heavy metals, ammonia, and refractory substances. Among leachate treatment techniques, the biological methods are more environmentally benign and less expensive than the physical-chemical treatment methods. Over the last few years, fungal-based treatment processes have become popular due to their ability to produce powerful oxidative enzymes like peroxidases and laccases. Fungi have shown better removal efficiency in terms of color, ammonia, and COD. However, their use in the treatment of leachate is relatively recent and still needs to be investigated. This review article assesses the potential of fungi and fungal-derived enzymes in treating landfill leachate. The review also compares different enzymes involved in the fungal catabolism of organic pollutants and the enzyme degradation mechanisms. The effect of parameters like pH, temperature, contact time, dosage variation, heavy metals and ammonia are discussed. The paper also explores the reactor configuration used in the fungal treatment and the techniques used to improve leachate treatment efficacy, like pretreatment and fungi immobilisation. Finally, the review summarises the limitations and the future direction of work required to adapt the fungal application for leachate treatment on a large scale.

Identification and recombinant expression of a cutinase from Papiliotrema laurentii that hydrolyzes natural and synthetic polyesters

Given the multitude of extracellular enzymes at their disposal, many of which are designed to degrade nature's polymers (lignin, cutin, cellulose, etc.), fungi are adept at targeting synthetic polyesters with similar chemical composition. Microbial-influenced deterioration of xenobiotic polymeric surfaces is an area of interest for material scientists as these are important for the conservation of the underlying structural materials. Here, we describe the isolation and characterization of the Papiliotrema laurentii 5307AH (P. laurentii) cutinase, Plcut1. P. laurentii is basidiomycete yeast with the ability to disperse Impranil-DLN (Impranil), a colloidal polyester polyurethane, in agar plates. To test whether the fungal factor involved in this clearing was a secreted enzyme, we screened the ability of P. laurentii culture supernatants to disperse Impranil. Using size exclusion chromatography (SEC), we isolated fractions that contained Impranil-clearing activity. These fractions harbored a single ~22 kD band, which was excised and subjected to peptide sequencing. Homology searches using the peptide sequences identified, revealed that the protein Papla1 543643 (Plcut1) displays similarities to serine esterase and cutinase family of proteins. Biochemical assays using recombinant Plcut1 confirmed that this enzyme has the capability to hydrolyze Impranil, soluble esterase substrates, and apple cutin. Finally, we confirmed the presence of the Plcut1 in culture supernatants using a custom antibody that specifically recognizes this protein. The work shown here supports a major role for the Plcut1 in the fungal degradation of natural polyesters and xenobiotic polymer surfaces.IMPORTANCEFungi play a vital role in the execution of a broad range of biological processes that drive ecosystem function through production of a diverse arsenal of enzymes. However, the universal reactivity of these enzymes is a current problem for the built environment and the undesired degradation of polymeric materials in protective coatings. Here, we report the identification and characterization of a hydrolase from Papiliotrema laurentii 5307AH, an aircraft-derived fungal isolate found colonizing a biodeteriorated polymer-coated surface. We show that P. laurentii secretes a cutinase capable of hydrolyzing soluble esters as well as ester-based compounds forming solid surface coatings. These findings indicate that this fungus plays a significant role in biodeterioration through the production of a cutinase adept at degrading ester-based polymers, some of which form the backbone of protective surface coatings. The work shown here provides insights into the mechanisms employed by fungi to degrade xenobiotic polymers.

Nitro-PAHs: Occurrences, ecological consequences, and remediation strategies for environmental restoration

Nitrated polycyclic aromatic hydrocarbons (nitro-PAHs) are persistent pollutants that have been introduced into the environment as a result of human activities. They are produced when PAHs undergo oxidation and are highly resistant to degradation, resulting in prolonged exposure and significant health risks for wildlife and humans. Nitro-PAHs' potential to induce cancer and mutations has raised concerns about their harmful effects. Furthermore, their ability to accumulate in the food chain seriously threatens the ecosystem and human health. Moreover, nitro-PAHs can disrupt the normal functioning of the endocrine system, leading to reproductive and developmental problems in humans and other organisms. Reducing nitro-PAHs in the environment through source management, physical removal, and chemical treatment is essential to mitigate the associated environmental and human health risks. Recent studies have focused on improving nitro-PAHs' phytoremediation by incorporating microorganisms and biostimulants. Microbes can break down nitro-PAHs into less harmful substances, while biostimulants can enhance plant growth and metabolic activity. By combining these elements, the effectiveness of phytoremediation for nitro-PAHs can be increased. This study aimed to investigate the impact of introducing microbial and biostimulant agents on the phytoremediation process for nitro-PAHs and identify potential solutions for addressing the environmental risks associated with these pollutants.

NmrB (AN9181) expression is activated under oxidative stress conditions acting as a metabolic repressor of Aspergillus nidulans

Aspergilli comprise a diversity of species that have been extensively studied due to their catabolic diversity, biotechnological and ecological value, and pathogenicity. An impressive level of structural and functional conservation has been shown for aspergilli, regardless of many (yet) cryptic genomic elements. We have hypothesized the existence of conserved genes responsive to stress in aspergilli. To test the hypothesis of such conserved stress regulators in aspergilli, a straightforward computational strategy integrating well-established bioinformatic tools was used as the starting point. Specifically, five transcriptome-based datasets on exposure to organic compounds were used, covering three distinct Aspergillus species. Among the identified up-regulated genes, only one gene showed the same response in all conditions, AN9181. This gene encodes a protein containing a phenylcoumaran benzylic ether reductase-like domain and a Nitrogen metabolite repressor regulator domain (NmrA). Deletion of this gene caused significant phenotypic alterations compared to that of the parental strain across diverse conditions. Specifically, the deletion of AN9181 raised the mutant's metabolic activity in different nitrogen sources. The acquired data supports that AN9181 acts by repressing (slowing down) A. nidulans growth when exposed to aromatic compounds in a concentration dependent manner. The same phenotype was observed for amphotericin B. Finally, AN9181 underwent differential upregulation under oxidative stress conditions. Collectively, the data suggest that AN9181, herein assigned as NmrB (Nitrogen Metabolite Repression Regulator B), builds up the genetic machinery of perception of oxidative stress by negatively regulating growth under such conditions.

Pure lignin induces overexpression of cytochrome P450 (CYP) encoding genes and brings insights into the lignocellulose depolymerization by Trametes villosa

Trametes villosa is a remarkable white-rot fungus (WRF) with the potential to be applied in lignocellulose conversion to obtain chemical compounds and biofuels. Lignocellulose breakdown by WRF is carried out through the secretion of oxidative and hydrolytic enzymes. Despite the existing knowledge about this process, the complete molecular mechanisms involved in the regulation of this metabolic system have not yet been elucidated. Therefore, in order to understand the genes and metabolic pathways regulated during lignocellulose degradation, the strain T. villosa CCMB561 was cultured in media with different carbon sources (lignin, sugarcane bagasse, and malt extract). Subsequently, biochemical assays and differential gene expression analysis by qPCR and high-throughput RNA sequencing were carried out. Our results revealed the ability of T. villosa CCMB561 to grow on lignin (AL medium) as the unique carbon source. An overexpression of Cytochrome P450 was detected in this medium, which may be associated with the lignin O-demethylation pathway. Clusters of up-regulated CAZymes-encoding genes were identified in lignin and sugarcane bagasse, revealing that T. villosa CCMB561 acts simultaneously in the depolymerization of lignin, cellulose, hemicellulose, and pectin. Furthermore, genes encoding nitroreductases and homogentisate-1,2-dioxygenase that act in the degradation of organic pollutants were up-regulated in the lignin medium. Altogether, these findings provide new insights into the mechanisms of lignocellulose degradation by T. villosa and confirm the ability of this fungal species to be applied in biorefineries and in the bioremediation of organic pollutants.

Emergence of per- and poly-fluoroalkyl substances (PFAS) and advances in the remediation strategies

A group of fluorinated organic molecules known as per- and poly-fluoroalkyl substances (PFAS) have been commonly produced and circulated in the environment. PFAS, owing to multiple strong CF bonds, exhibit exceptional stability and possess a high level of resistance against biological or chemical degradation. Recently, PFAS have been identified to cause numerous hazardous effects on the biotic ecosystem. As a result, extensive efforts have been made in recent years to develop effective methods to remove PFAS. Adsorption, filtration, heat treatment, chemical oxidation/reduction, and soil washing are a few of the physicochemical techniques that have shown their ability to remove PFAS from contaminated matrixes. However these methods also carry significant drawbacks, including the fact that they are expensive, energy-intensive, unsuitable for in-situ treatment, and requirement to be carried under dormant conditions. The metabolic products released upon PFAS degradation are largely unknown, despite the fact that thermal disintegration methods are widely used. In contrast to physical and chemical methods, biological degradation of PFAS has been regarded as efficient method. However, PFAS are difficult to instantly and completely metabolize through biological methods due to the limitations of biocatalytic mechanisms. Nevertheless, cost, easy-to-operate and environmentally safe are some of the advantages over its counterpart. The present review comprehensively discusses the occurrence of PFAS, the state-of-the science of remediation technologies and approaches applied, and the remediation challenges. The article also focuses on the future research directions toward the development of effective methods for PFAS-contaminated site in-situ treatment.

Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

Low uptake of pharmaceuticals in edible mushrooms grown in polluted biogas digestate

The uptake dynamics of two sulfonamide antibiotics, two fluoroquinolone antibiotics, and the anticonvulsant carbamazepine during the cultivation of two species of edible mushrooms (Agaricus subrufescens and A. bisporus) was investigated. None of the antibiotics were accumulated by the mushrooms, while carbamazepine and its transformation product carbamazepine-10,11-epoxide were taken up by A. bisporus fruiting body but only in small amounts (up to 0.76 and 1.85 μg kg-1 dry weight, respectively). The sulfonamides were quickly removed from the mushroom growth substrate, while the recalcitrant fluoroquinolones and carbamazepine were only partially removed. Dissipation half-lives were generally lower for A. subrufescens than A. bisporus, but A. subrufescens was also grown at a slightly higher culture temperature. A. subrufescens also showed a lower uptake of contaminants. Comparison of maximum dietary intake with other common exposure sources showed that these mushrooms can safely be eaten although produced on a polluted substrate, with respect to the investigated compounds.

Asynchronous application of modified biochar and exogenous fungus Scedosporium sp. ZYY for enhanced degradation of oil-contaminated intertidal mudflat sediment

Intertidal mudflats are susceptible to oil pollution due to their proximity to discharges from industries, accidental spills from marine shipping activities, oil drilling, pipeline seepages, and river outflows. The experimental study was divided into two periods. In the first period, microcosm trials were carried out to examine the effect of chemically modified biochar on biological hydrocarbon removal from sediments. The modified biochar's surface area increased from 2.544 to 25.378 m2/g, followed by a corresponding increase in the hydrogen-carbon and oxygen-carbon ratio, indicating improved stability and polarity. In the second period, the effect of exogenous fungus - Scedoporium sp. ZYY on the bacterial community structure was examined in relation to total petroleum hydrocarbon (TPH) removal. The maximum TPH removal efficiency of 82.4% was achieved in treatments with the modified biochar, followed by a corresponding increase in Fluorescein diacetate hydrolysis activity. Furthermore, high-throughput 16S RNA gene sequencing employed to identify changes in the bacterial community of the original sediment and treatments before and after fungal inoculation revealed Proteobacteria as the dominant phylum. In addition, it was observed that Scedoporium sp. ZYY promoted the proliferation of specific TPH-degraders, particularly, Hyphomonas adhaerens which accounted for 77% of the total degrading populations in treatments where TPH removal was highest. Findings in this study provide valuable insights into the effect of modified biochar and the fundamental role of exogenous fungus towards the effective degradation of oil-contaminated intertidal mudflat sediments.

Isolation of Diaphorobacter sp. LW2 capable of degrading Phenanthrene and its migration mediated by Pythium ultimum

Phenanthrene, one of the polycyclic aromatic hydrocarbons, is stubborn and persistent and exists widely in petroleum-contaminated soil. Filamentous fungi are good assistants to bacterial transport, by hyphae passing through soil pores and reaching further positions. An isolated bacterial strain, from the contaminated soil of the coking plant, was identified as Diaphorobacter and named LW2, which could use phenanthrene as the only carbon source and energy for its growth. LW2 could degrade phenanthrene in a wide range of pH, temperature and initial concentration. When pH was 6 and 10, the removal rate of phenanthrene was 38.59% and 76.44%, respectively, and the removal rate of phenanthrene was 68.25% at 15 ℃. And LW2 could degrade 86.64% phenanthrene when the initial concentration was 100 mg L-1. The detection of DI-N-octyl phthalate, phthalic acid and p-hydroxybenzoic acid revealed that the strain LW2 metabolised phenanthrene through the phthalic acid pathway. Meanwhile, swimming and swarming test results suggested that LW2 was motile. The auxiliary effect of Pythium ultimum on LW2 migration was assessed. In the presence of Pythium ultimum, LW2 could migrate within the range of centimters by its mycelium, which was also observed by fluorescence microscopy. Meanwhile, the degradation ability of LW2 after the migration was also explored. The results proved that the migration process had no significant effect on its degradation ability, and LW2 still showed good phenanthrene metabolism ability. This study provides more possibilities for the bioremediation of phenanthrene-contaminated soil by screening the degradation bacteria and testing the effect of fungi on its migration.

White Rot Fungi as Tools for the Bioremediation of Xenobiotics: A Review

Industrial development has enhanced the release into the environment of large quantities of chemical compounds with high toxicity and limited prospects of degradation. The pollution of soil and water with xenobiotic chemicals has become a major ecological issue; therefore, innovative treatment technologies need to be explored. Fungal bioremediation is a promising technology exploiting their metabolic potential to remove or lower the concentrations of xenobiotics. In particular, white rot fungi (WRF) are unique microorganisms that show high capacities to degrade a wide range of toxic xenobiotic compounds such as synthetic dyes, chlorophenols, polychlorinated biphenyls, organophosphate pesticides, explosives and polycyclic aromatic hydrocarbons (PAHs). In this review, we address the main classes of enzymes involved in the fungal degradation of organic pollutants, the main mechanisms used by fungi to degrade these chemicals and the suitability of fungal biomass or extracellular enzymes for bioremediation. We also exemplify the role of several fungi in degrading pollutants such as synthetic dyes, PAHs and emerging pollutants such as pharmaceuticals and perfluoroalkyl/polyfluoroalkyl substances (PFASs). Finally, we discuss the existing current limitations of using WRF for the bioremediation of polluted environments and future strategies to improve biodegradation processes.

Combining fungal bioremediation and ozonation for rinse wastewater treatment

In this work, agricultural rinse wastewater, which is produced during the cleaning of agricultural equipment and constitutes a major source of pesticides, was treated by fungal bioremediation and ozonation, both individually and combined in a two-stage treatment train. Three major pesticides (thiacloprid, chlortoluron, and pyrimethanil) were detected in rinse wastewater, with a total concentration of 38.47 mg C L-1. Comparing both technologies, ozonation in a stirred reactor achieved complete removal of these pesticides (720 min) while proving to be a more effective approach for reducing colour, organic matter, and bacteria. However, this technique produced transformation products and increased toxicity. In contrast, fungal bioremediation in a rotating drum bioreactor attenuated toxicity levels and did not produce such metabolites, but only removed approximately 50 % of target pesticide - hydraulic retention time (HRT) of 5 days - and obtained worse results for most of the general quality parameters studied. This work also includes a preliminary economic assessment of both technologies, revealing that fungal bioremediation was 2 times more cost-effective than ozonation. The treatment train, consisting of a first stage of fungal bioremediation followed by ozonation, was found to be a promising approach as it synergistically combines the advantages of both treatments, achieving high removals of pesticides (up to 100 %) and transformation products, while reducing operating costs and producing a biodegradable effluent. This is the first time that fungal bioremediation and ozonation technologies have been compared and combined in a treatment train to deal with pesticides in agricultural rinse wastewater.