Understanding fungal functional biodiversity during the mitigation of environmentally dispersed pentachlorophenol in cork oak forest soils

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.

Hydroquinone Ecotoxicity: Unveiling Risks in Soil and River Ecosystems with Insights into Microbial Resilience

Despite widespread industrial use, the environmental safety of hydroquinone (HQ), a benzene compound from plants used in processes like cosmetics, remains uncertain. This study evaluated the ecotoxicological impact of HQ on soil and river environments, utilizing non-target indicator organisms from diverse trophic levels: Daphnia magna, Aliivibrio fischeri, Allium cepa, and Eisenia fetida. For a more environmentally realistic assessment, microbial communities from a river and untreated soil underwent 16S rRNA gene sequencing, with growth and changes in community-level physiological profiling assessed using Biolog EcoPlate™ assays. The water indicator D. magna exhibited the highest sensitivity to HQ (EC50 = 0.142 µg/mL), followed by A. fischeri (EC50 = 1.446 µg/mL), and A. cepa (LC50 = 7.631 µg/mL), while E. fetida showed the highest resistance (EC50 = 234 mg/Kg). Remarkably, microbial communities mitigated HQ impact in both aquatic and terrestrial environments. River microorganisms displayed minimal inhibition, except for a significant reduction in polymer metabolism at the highest concentration (100 µg/mL). Soil communities demonstrated resilience up to 100 µg/mL, beyond which there was a significant decrease in population growth and the capacity to metabolize carbohydrates and polymers. Despite microbial mitigation, HQ remains highly toxic to various trophic levels, emphasizing the necessity for environmental regulations.

Drosophilin A methyl ether (DAME) and other chlorinated dimethoxybenzenes in fungi and forest litter from Sweden

Fungi and substrates undergoing fungal decomposition were collected from forests in northern and southern Sweden and analyzed for chlorinated dimethoxybenzenes (DMBs). Specimens were fungi fruiting bodies, rotting wood, forest litter and underlying humus. Targeted compounds were DAME (1,2,4,5-tetrachloro-3,6-DMB) and related fungal secondary metabolites. A screening procedure was developed which involved soaking the specimens in ethyl acetate followed by analysis by capillary gas chromatography - mass spectrometry with mass selective detection (GC-MSD). DAME was the most frequently found (62% of 47 specimens) and often the most abundant target compound, with range and mean ± SD concentrations of <0.0017-3.81 and 0.21 ± 0.63 mg kg-1 ww. Based on log-log correlations of partition coefficients of hydrophobic compounds between fungal biomass/water (KD) and octanol/water (KOW), five species of fungi are suggested to produce DAME de novo versus bioaccumulation from forest runoff water. Full-scan mass spectra of some high-concentration specimens indicated the presence of a Cl2DMB and a Cl3DMB, which could not be identified further due to lack of standards, and drosophilin A (DA = 2,3,5,6-tetrachloro-4-methoxyphenol), the precursor to DAME. Tetrachloroveratrole (TeCV = 1,2,3,4-tetrachloro-5,6-DMB) was found in only a few specimens. This study supports our hypothesis of fungi as a source of DAME in terrestrial runoff and indicates that other chlorinated secondary metabolites are present. DAME is widely distributed globally, and it would be good to have a better understanding of its sources and pathways as a marker of terrestrial organochlorines and their availability for bioaccumulation.

Increased Production of Pathogenic, Airborne Fungal Spores upon Exposure of a Soil Mycobiota to Chlorinated Aromatic Hydrocarbon Pollutants

Organic pollutants are omnipresent and can penetrate all environmental niches. We evaluated the hypothesis that short-term (acute) exposure to aromatic hydrocarbon pollutants could increase the potential for fungal virulence. Specifically, we analyzed whether pentachlorophenol and triclosan pollution results in the production of airborne fungal spores with greater virulence than those derived from an unpolluted (Control) condition. Each pollutant altered the composition of the community of airborne spores compared to the control, favoring an increase in strains with in vivo infection capacity (the wax moth Galleria mellonella was used as an infection model). Fungi subsisting inside larvae at 72 h postinjection with airborne spore inocula collected in polluted and unpolluted conditions exhibited comparable diversity (mainly within Aspergillus fumigatus). Several virulent Aspergillus strains were isolated from larvae infected with the airborne spores produced in a polluted environment. Meanwhile, strains isolated from larvae injected with spores from the control, including one A. fumigatus strain, showed no virulence. Potential pathogenicity increased when two Aspergillus virulent strains were assembled, suggesting the existence of synergisms that impact pathogenicity. None of the observed taxonomic or functional traits could separate the virulent from the avirulent strains. Our study emphasizes pollution stress as a possible driver of phenotypic adaptations that increase Aspergillus pathogenicity, as well as the need to better understand the interplay between pollution and fungal virulence. IMPORTANCE Fungi colonizing soil and organic pollutants often meet. The consequences of this encounter constitute an outstanding question. We scrutinized the potential for virulence of airborne fungal spores produced under unpolluted and polluted scenarios. The airborne spores showed increased diversity of strains with higher infection capacity in Galleria mellonella whenever pollution is present. Inside the larvae injected with either airborne spore community, the surviving fungi demonstrated a similar diversity, mainly within Aspergillus fumigatus. However, the isolated Aspergillus strains greatly differ since virulence was only observed for those associated with a polluted environment. The interplay between pollution and fungal virulence still hides many unresolved questions, but the encounter is costly: pollution stress promotes phenotypic adaptations that may increase Aspergillus pathogenicity.

Irrigation of soil with reclaimed wastewater acts as a buffer of microbial taxonomic and functional biodiversity

The usage of reclaimed wastewater (RWW) for irrigation of agricultural soils is increasingly being acknowledged for reducing water consumption by promoting reuse of treated wastewater, and for the delivery of extant nutrients in the soil. The downside is that RWW may be a vector for contamination of soils with contaminants of emerging concern (CECs), if left uncontrolled. Its usage is anticipated to alter the soil properties, consequently also the soil microbial community. In the present study, soil microcosms were set to monitor how short periods (up to fourteen days) of RWW irrigation influence the soil ecosystem, namely its physicochemical properties, functioning, and colonising microbiota (differentiating fungi from bacteria). Two scenarios were studied: clean soil and soil contaminated (spiked) with 9 CECs, at conditions that limit any abiotic decay processes, monitoring along time fluctuations in the taxonomic and functional microbiota diversity. As shortly as fourteen days, the irrigation of either soil with RWW did not significantly (p > 0.05) alter its physicochemical properties and scarcely impacted the bioremediation processes of the CECs that showed decay levels ranging from 24% to 100%. Bacillus spp. dominance was enhanced along time in all the soil microcosms (reaching over 70% of the total abundance on the 7th day) but the RWW help to preserve, to some extent, high bacterial diversity. Besides, irrigation with RWW acted as a buffer of the soil mycobiota, limiting alterations in its composition caused either along time (to a minor degree) or due to contamination with CECs (to a great degree). This includes limiting the rise of Rhizopus sp. relative abundance. Collectively, our data support the utility of short-term periods of RWW irrigation for preserving the soil microbial diversity and functioning, especially when fungi are considered.

Application of an indigenous microorganisms-based fixed-bed GAC-biofilm reactor for passive and sustainable treatment of oil sands process water through combined adsorption and biodegradation processes

In this study, a fixed-bed biofilm reactor (biofilter) was developed and applied for oil sands process water (OSPW) remediation by using granular activated carbon (GAC) as packing media. Using quantitative polymerase chain reaction (qPCR) detection, the total bacterial copy number (16S) in the GAC biofiltration system was found to reach a relatively stable level (1.3 ± 0.2 × 10⁹ copies/g GAC) after 62 days of operation, and the thickness of biofilm on GAC surface was 26.7 ± 4.3 μm based on the scan of confocal laser scanning microscopy (CLSM). The established GAC-biofilter showed 95.4% naphthenic acids (NAs) removal from raw OSPW after 2 months of operation. The GAC-biofilter also showed 88.3% NAs removal after a long operation time (2 years), indicating its sustainable bioremediation capacity for OSPW. 16S and 18S rRNA gene-targeted metagenomic sequencing showed that the microbial community in the GAC biofilter had higher diversity and richness than that found in the sand biofilter which was used for OSPW treatment previously. Comamonadaceae and Saccharomycotina were found to be the dominant bacterial and fungal families in the GAC biofilter, respectively. Xenobiotic metabolism function of the microbial community may contribute significantly to the biodegradation of NAs. The GAC biofiltration process is a promising passive OSPW treatment approach that can be used in-situ.

Decay Process Characteristics and Fungal Community Composition of Salix psammophila Sand Barriers in an Arid Area, Northern China

With the increase in setting years in deserts, Salix psammophila sand barriers with different degrees of lodging damage caused by decay are losing wind-prevention and sand-fixation properties. In this study, we focus on the change in chemical properties of soils, and physical and mechanical properties of plants along different setting years; meanwhile, the change in fungal communities has been analyzed using high-throughput sequencing technology. The results show that a change in physical and mechanical properties and the loss of primary chemical components led to the degradation of the protective properties of the barrier to different degrees. After five years of setting, the physical parameters of basic density and shrinkage rate decreased by 44.04% and 28.68%, respectively, and the loss of the modulus of rupture mechanical index declined by 62.72%. After seven years of setting, the mechanical indexes of the modulus of rupture decreased by 76.95%. Five and seven years represented important inflection points in the decay process. Sordariomycetes (53.75%) and Eurotiomycetes (19.78%) were the main fungal groups present during the decay of the sand barrier. The basic density, moisture content, cellulose, and lignin of the sand barrier were the main driving factors affecting the distribution of fungal communities. The mechanism on fungal community to the decay of sand barriers still needs further studies to keep the function of sand barriers in fragile desert ecosystems.

Multiple degrees of separation in the central pathways of the catabolism of aromatic compounds in fungi belonging to the Dikarya sub-Kingdom

The diversity and abundance of aromatic compounds in nature is crucial for proper metabolism in all biological systems, and also impacts greatly the development of many industrial processes. Naturally, understanding their catabolism becomes fundamental for many scientific fields of research, from clinical and environmental to technological. The genetic basis of the central pathways for the catabolism of aromatic compounds in fungi, particularly of benzene derivatives, remains however poorly understood largely overlooking their significance. In some Dikarya species the genes of the central pathways are clustered in the genome, often in an array with peripheral pathway genes, even if the existence of a specific pathway does not necessarily mean that the composing genes are clustered. The current availability of many annotated fungal genomes in the postgenomic era creates conditions to reach a more holistic view of these processes through target analysis of the central pathways gene clusters. Inspired by this, we have critically analyzed the established biochemical and genetic data on the catabolism of aromatic compounds in Dikarya after dissecting the presence and distribution of central catabolic gene clusters (at times including also details on gene diversity, order and orientation) and of peripheral genes. Our methodological approach illustrates the multiple degrees of separation in these central pathways gene clusters across Dikarya. Surprisingly, they show a great degree of similarity irrespectively of the Dikarya division, emphasizing that knowledge established on either phyla can guide the identification of clusters of comparable composition (in-cluster plus peripheral genes) in uncharacterized species.

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential

BACKGROUND

The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many organisms. We have previously demonstrated that the belowground mycobiota of forest soils acts as a buffer against the biocide pollutant pentachlorophenol. However, the trade-offs made by mycobiota to mitigate this pollutant remain cryptic.

RESULTS

Herein, we demonstrate using a culture-dependent approach that exposure to pentachlorophenol led to alterations in the composition and functioning of the metacommunity, many of which were not fully alleviated when most of the biocide was degraded. Proteomic and physiological analyses showed that the carbon and nitrogen metabolisms were particularly affected. This dysregulation is possibly linked to the higher pathogenic potential of the metacommunity following exposure to the biocide, supported by the secretion of proteins related to pathogenicity and reduced susceptibility to a fungicide. Our findings provide additional evidence for the silent risks of environmental pollution, particularly as it may favour the development of pathogenic trade-offs in fungi, which may impose serious threats to animals and plant hosts.

A three-act play: pentachlorophenol threats to the cork oak forest soils mycobiome

Atmospheric release of persistent organic pollutants (POPs) constitutes a silent threat through chronic contamination of soils at global scale; yet fundamental understanding of their occurrence, sources and fate is still largely lacking. Similar to a three act play, this review comprises Setup, Confrontation and Resolution. The first emphasises the eighty years of the history of pentachlorophenol (PCP) usage, only recently classified as POP. The second focus on active sources of PCP pollution, including inside cork oak forests in N.W. Tunisia; a threat partially neutralised by the soil microbial diversity, especially fungi. As Resolution, the need for improved knowledge on the global distribution and impacts of PCP in soil microbial diversity as means to preserve the multi-functionality of terrestrial ecosystem is emphasised.

Ionic Liquids as Unforeseen Assets to Fight Life-Threatening Mycotic Diseases

Ionic liquids discovery has celebrated 100 years. They consist solely of ions, one of which is typically organic and asymmetrical. Remarkable physical and chemical properties stirred their use as alternative solvents in many chemical processes. The recent demonstration of their occurrence in nature might boost their interest in biological sciences. In the search of mechanistic understandings of ionic liquids’ ecotoxicological impacts in fungi, we have analyzed the proteome, transcriptome, and metabolome responses to this chemical stress. Data illuminated new hypotheses that altered our research path – exploit ionic liquids as tools for the discovery of pathways and metabolites that may impact fungal development and pathogenicity. As we get closer to solve the primary effects of each ionic liquid family and their specific gene targets, the vision of developing antifungal ionic liquids and/or materials, by taking advantage of elegant progresses in this field, might become a reality. Task-designed formulations may improve the performance of conventional antifungal drugs, build functional coatings for reducing allergens production, or aid in the recovery of antifungal plant polymers. The frontier research in this cross-disciplinary field may provide us unforeseen means to address the global concern of mycotic diseases. Pathogenic and opportunistic fungi are responsible for numerous infections, killing annually nearly 1.5 million immunocompromised individuals worldwide, a similar rate to malaria or tuberculosis. This perspective will review our major findings and current hypotheses, contextualizing how they might bring us closer to efficient strategies to prevent and fight mycotic diseases.