Occurrence and diversity of cultivable autochthonous microscopic fungi in substrates of old environmental loads from mining activities in Slovakia

Microbial-mediated metal(loid) immobilization in mulch-covered tailings

Mulch coverage of mining tailings can create anaerobic conditions and consequently establish an anoxic environment that promotes the metabolic processes of anaerobic microorganisms. This anoxic environment has the potential to decrease heavy metal mobility and bioavailability. While tailings exposed to sunlight have been extensively studied, research on the effects of microbial-mediated geochemical cycling of heavy metals in mulch-covered tailings is scarce. This study aimed to examine the effects of mulch coverage-induced alterations in the structures of tailing microbial communities on the biogeochemical processes associated with heavy metals. Mulch coverage significantly reduced the pH of the tailings and the tailings exhibited heavy metal bioavailability. Random forest analysis demonstrated that mulch coverage-induced changes in the As/Cd-contaminated fractions and nutrients (total organic carbon and total nitrogen) were the most crucial predictors of microbial diversity and ecological clusters in the tailings. Notably, different from direct metal(loid) immobilization, mulch coverage can facilitate heavy metal immobilization in tailings by promoting microbial-mediated Fe, S, and As reduction. Overall, this study demonstrated that mulch coverage of tailings contributed to a reduction in heavy metal mobilization, which can be attributed to shifts in microbial-mediated Fe, S, and As reduction processes.The study provides valuable insights into the potential of mulch coverage as a remediation strategy and underscores the importance of microbial-mediated processes in managing heavy metal pollution in tailing systems.

Characterization of an antimony-resistant fungus Sarocladium kiliense ZJ-1 and its potential as an antimony bio-remediator

Antimony (Sb) is a toxic metalloid widely distributed in the natural environments. Microorganisms, especially fungi, could serve as ideal biomaterials for bioremediation of Sb-polluted soils and waters. In this study, we isolated an antimony-resistant fungus, Sarocladium kiliense ZJ-1, from a slag sample collected in Xikuangshan Sb mine in P. R. China. ZJ-1 showed an extremely high resistance to Sb, with a MIC level of > 175 mM for arsenite [Sb(Ⅲ)] and 40 mM for arsenate [Sb(V)]. Whole genomic analysis identified multiple Sb (Ⅲ)- and/or As(Ⅲ)-resistant genes on ZJ-1's genome, which may partially explain its hyper-resistance to Sb. The potential of ZJ-1 in removing Sb from Sb(Ⅲ) or Sb(V) solutions was also quantified. The average biosorption capacity of ZJ-1 for Sb(Ⅲ) and Sb(V) is 635.14 mg/g and 149.65 mg/g, respectively, in Sb aqueous solutions with an initial concentration of 2000 mg/L (16.43 mM). Besides, almost 99% of Sb(Ⅲ) in the growing system was removed with an initial concentration of 500 mg/L (4.11 mM). Furthermore, Fourier transformation infrared spectroscopy (FT-IR) and X-ray photoelectron spectroscopy (XPS) were used to probe the Sb adsorption mechanism on ZJ-1, and -OH, -NH2, -COOH, C-O and C-O-C were found to be the main surface functional groups of ZJ-1 cells to adsorb Sb.

The microbiome of a brownfield highly polluted with mercury and arsenic

Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.

Evaluation of Pollution Level, Spatial Distribution, and Ecological Effects of Antimony in Soils of Mining Areas: A Review

The first global-scale assessment of Sb contamination in soil that was related to mining/smelting activities was conducted based on 91 articles that were published between 1989 and 2021. The geographical variation, the pollution level, the speciation, the influencing factors, and the environmental effects of Sb that were associated with mining/smelting-affected soils were analyzed. The high Sb values mainly occurred in developed (Poland, Italy, Spain, Portugal, New Zealand, Australia) and developing (China, Algeria, Slovakia) countries. Sb concentrations of polluted soil from mining areas that were reported in most countries significantly exceeded the maximum permissible limit that is recommended by WHO, except in Turkey and Macedonia. The soil Sb concentrations decreased in the order of Oceania (29,151 mg/kg) > North Africa (13,022 mg/kg) > Asia (1527 mg/kg) > Europe (858 mg/kg) > South America (37.4 mg/kg). The existing extraction methods for Sb speciation have been classified according to the extractant, however, further research is needed in the standardization of these extraction methods. Modern analytical and characterization technologies, e.g., X-ray absorption spectroscopy, are effective at characterizing chemical speciation. Conditional inference tree (CIT) analysis has shown that the clay content was the major factor that influenced the soil Sb concentration. Non-carcinogenic risks to the public from soil Sb pollution were within the acceptable levels in most regions. An Sb smelter site at the Endeavour Inlet in New Zealand, an abandoned open-pit Sb mine in Djebel Hamimat, Algeria, an old Sb-mining area in Tuscany, Italy, and Hillgrove mine in Australia were selected as the priority control areas. Cynodon dactylon, Boehmeria, Pteris vittata, and Amaranthus paniculatus were found to be potential Sb accumulators. All of the values of bioaccumulation factors for the crops were less than one. However, ingestion of Sb through crop consumption posed potential non-carcinogenic health risks, which should not be neglected. The soil variables (pH, Eh, total sulfur, carbon nitrogen ratio, total organic carbon, and sulfate), the total Sb and the bioavailable Sb, and heavy metal(loid)s (As, Pb, and Fe) were the major parameters affecting the microbial community compositions.

Biocoagulation of Dried Algae Chlorella sp. and Pellets of Aspergillus Niger in Decontamination Process of Wastewater, as a Presumed Source of Biofuel

The removal of microalgae represents a problematic part of the water decontamination process, in which most techniques are expensive and non-ecological. In the paper, we focus on the synergistic relationship between microscopic filamentous fungi and algal culture. In the process of decontamination of a model sample containing ammonium ions, efficient biocoagulation, resp. co-pelletization of dried algae Chlorella sp. and Aspergillus niger sensu stricto are shown. The microscopic filamentous fungus species A. niger was added to a culture of an algal suspension of Chlorella sp., where the adhesion of the algal cells to the fungi subsequently occurred due to the electrostatic effect of the interaction, while the flocculation activity was approximately 70 to 80%. The algal cells adhered to the surface of the A. niger pellets, making them easily removable from the solution. The ability of filamentous fungi to capture organisms represents a great potential for the biological isolation of microalgae (biocoagulation) from production solutions because microalgae are considered to be a promising renewable source of oil and fermentables for bioenergy. This form of algae removal, or its harvesting, also represents a great low-cost method for collecting algae not only as a way of removing unnecessary material but also for the purpose of producing biofuels. Algae are a robust bioabsorbent for absorbing lipids from the environment, which after treatment can be used as a component of biodiesel. Chemical analyses also presented potential ecological innovation in the area of biofuel production. Energy-efficient and eco-friendly harvesting techniques are crucial to improving the economic viability of algal biofuel production.

Potential of bioaugmentation of heavy metal contaminated soils in the Zambian Copperbelt using autochthonous filamentous fungi

There is great potential to remediate heavy metal contaminated environments through bioaugmentation with filamentous fungi. However, these fungi have been poorly investigated in most developing countries, such as Zambia. Therefore, the present study aimed at isolating indigenous filamentous fungi from heavy metal contaminated soil and to explore their potential for use in bioaugmentation. The conventional streak plate method was used to isolate fungi from heavy metal-contaminated soil. Filamentous fungal isolates were identified using morphological and molecular techniques. The radial growth diameter technique was used to evaluate heavy metal tolerance of the fungi. The most abundant and highly tolerant fungi, identified as Aspergillus transmontanensis, Cladosporium cladosporioides, and Geotrichum candidum species, were used to bioremediate heavy metal contaminated soil samples with uncontaminated soil sample being employed as a control. A maximum tolerance index (TI) between 0.7 and 11.0 was observed for A. transmontanensis, and G. candidum while C. cladosporioides displayed the TI between 0.2 and 1.2 in the presence of 1,000 ppm of Cu, Co, Fe, Mn, and Zn. The interspecific interaction was analyzed to determine the compatibility among isolates. Our results showed mutual intermingling between the three evaluated fungal species, which confirms their common influence in biomineralization of heavy metals in contaminated soils. Maximum bio-removal capacities after 90 days were 72% for Cu, 99.8% for Co, 60.6% for Fe, 82.2% for Mn, and 100% for both Pb and Zn. This study has demonstrated the potential of highly resistant autochthonous fungal isolates to remediate the heavy metal contamination problem.

Soil microbiota associated with immune-mediated disease was influenced by heavy metal stress in roadside soils of Shanghai

Heavy metals (HMs) and total petroleum hydrocarbons (TPHs) in soils can be detrimental to both soil microorganisms and public health. However, the effects of HMs and TPHs on microbes as well as the consequent microbial-derived health risk remains unclear in soils by local roads where citizens are clearly accessible to traffic-derived pollutants. Herein, we sampled 84 roadside soils throughout Shanghai. We measured the levels of soil edaphic factors, 6 HMs, and alkane TPHs. We further focused on the responses of bacterial and fungal communities assessed via sequencing and network analysis. Results showed that all soil HMs exceeded background levels of Shanghai soil, while the levels of TPHs are comparable to unpolluted sites. Bacterial network nodes and links decreased sharply under HM stress whereas that of fungal networks remained unchanged. The differential pattern was attributed to the asynchronous response of key classes that fungal key classes were more resistant to HMs than bacteria. In addition, 66.8 % of fungal genera associated with immune-mediated disease increased with increased HM stress for its HM tolerance. Together our findings indicate that despite the relatively stable fungal community in response to environmental stresses, the elevation of harmful fungi likely pose threats to health of urban dwellers.

Characterization of siderophore-producing microorganisms associated to plants from high-Andean heavy metal polluted soil from Callejón de Huaylas (Ancash, Perú)

Endophytic and rhizospheric microorganisms associated with six native plants adapted to heavy metal polluted soil from Punta Olímpica and Chahuapampa, located in Callejón de Huaylas mountains, were evaluated as potential candidates for technologies to clean polluted ecosystems. It was selected 14 bacteria and 9 fungi strains by their iron and/or aluminum siderophore production trait, where BEP17-Dm showed higher production. According to the 16S rDNA analysis, bacteria belong to Pseudomonas, Bacillus, and Achromobacter genera, whereas by ITS analysis fungi belong to Talaromyces, Hypoxylon, Tolypocladium, and Penicillium. All bacteria strains tolerated lead (2-8 mM) and eigth tolerated cadmium (1-6 mM); also all fungi tolerated lead (9-70 mM) and cadmium (3-10 mM). Two bacteria and six fungi solubilized cadmium carbonate, while eleven bacteria and two fungi solubilized tricalcium phosphate, where P. japonica BEP18-Dm and B. subtilis BRU16-Sr exhibited higher solubilization index. None strains solubilized lead carbonate. BEP18-Dm produced higher concentration of IAA (53.42 μgml^-1); while six bacteria and all fungi strains produced a low concentration of auxins. Medicago sativa seedlings inoculated with BEP17-Dm, BEP18-Dm, or BRU16-Sr showed more surviving percentage under in vitro culture in presence of Cd, Pb (0.5-1.0 mM), or Al (2.5-5.0 mM). Finally, it is the first report of siderophore-producing microorganisms from polluted soil of Callejón de Huaylas highlands, interestedly they displayed metabolic properties useful to enhance phytoremediation and biotechnology application.

Aspergillus niger Environmental Isolates and Their Specific Diversity Through Metabolite Profiling

We present a biological profile of 16 Aspergillus niger environmental isolates from different types of soils and solid substrates across a pH range, from an ultra-acidic (<3.5) to a very strongly alkaline (>9.0) environment. The soils and solid substrates also differ in varying degrees of anthropic pollution, which in most cases is caused by several centuries of mining activity at old mining sites, sludge beds, ore deposits, stream sediments, and coal dust. The values of toxic elements (As, Sb, Zn, Cu, Pb) very often exceed the limit values. The isolates possess different macro- and micromorphological features. All the identifications of Aspergillus niger isolates were confirmed by molecular PCR analysis and their similarity was expressed by RAMP analysis. The biochemical profile of isolates based on FF-MicroPlate tests from the Biolog system showed identical biochemical reactions in 50 tests, while in 46 tests the utilisation reactions differed. The highest similarity of strains isolated from substrates with the same pH, as well as the most suitable biochemical tests for analysis of the phenotypic similarity of isolated strains, were confirmed when evaluating the biochemical profile using multicriterial analysis in the Canoco program. The isolates were screened for mycotoxin production by thin-layer chromatography (TLC), as well. Two of them were able to synthesise ochratoxin A, while none produced fumonisins under experimental conditions. Presence of toxic compounds in contaminated sites may affect environmental microscopic fungi and cause the genome alteration, which may result in changes of their physiology, including the production of different (secondary) metabolites, such as mycotoxins.

Arsenic Accumulation in Hydroponically Grown Schizachyrium scoparium (Little Bluestem) Amended with Root-Colonizing Endophytes

We integrated microscopy, spectroscopy, culturing and molecular biology, and aqueous chemistry techniques to evaluate arsenic (As) accumulation in hydroponically grown Schizachyrium scoparium inoculated with endophytic fungi. Schizachyrium scoparium grows in historically contaminated sediment in the Cheyenne River Watershed and was used for laboratory experiments with As(V) ranging from 0 to 2.5 mg L^-1 at circumneutral pH. Arsenic accumulation in regional plants has been a community concern for several decades, yet mechanisms affecting As accumulation in plants associated with endophytic fungi remain poorly understood. Colonization of roots by endophytic fungi supported better external and vascular cellular structure, increased biomass production, increased root lengths and increased P uptake, compared to noninoculated plants (p value <0.05). After exposure to As(V), an 80% decrease of As was detected in solution and accumulated mainly in the roots (0.82-13.44 mg kg^-1) of noninoculated plants. Endophytic fungi mediated intracellular uptake into root cells and translocation of As. Electron microprobe X-ray mapping analyses detected Ca-P and Mg-P minerals with As on the root surface of exposed plants, suggesting that these minerals could lead to As adsorption on the root surface through surface complexation or coprecipitation. Our findings provide new insights regarding biological and physical-chemical processes affecting As accumulation in plants for risk assessment applications and bioremediation strategies.

Heavy Metal-Resistant Filamentous Fungi as Potential Mercury Bioremediators

Filamentous fungi native to heavy metals (HMs) contaminated sites have great potential for bioremediation, yet are still often underexploited. This research aimed to assess the HMs resistance and Hg remediation capacity of fungi isolated from the rhizosphere of plants resident on highly Hg-contaminated substrate. Analysis of Hg, Pb, Cu, Zn, and Cd concentrations by X-ray spectrometry generated the ecological risk of the rhizosphere soil. A total of 32 HM-resistant fungal isolates were molecularly identified. Their resistance spectrum for the investigated elements was characterized by tolerance indices (TIs) and minimum inhibitory concentrations (MICs). Clustering analysis of TIs was coupled with isolates’ phylogeny to evaluate HMs resistance patterns. The bioremediation potential of five isolates’ live biomasses, in 100 mg/L Hg²⁺ aqueous solution over 48 h at 120 r/min, was quantified by atomic absorption spectrometry. New species or genera that were previously unrelated to Hg-contaminated substrates were identified. Ascomycota representatives were common, diverse, and exhibited varied HMs resistance spectra, especially towards the elements with ecological risk, in contrast to Mucoromycota-recovered isolates. HMs resistance patterns were similar within phylogenetically related clades, although isolate specific resistance occurred. Cladosporium sp., Didymella glomerata, Fusarium oxysporum, Phoma costaricensis, and Sarocladium kiliense isolates displayed very high MIC (mg/L) for Hg (140–200), in addition to Pb (1568), Cu (381), Zn (2092–2353), or Cd (337). The Hg biosorption capacity of these highly Hg-resistant species ranged from 33.8 to 54.9 mg/g dry weight, with a removal capacity from 47% to 97%. Thus, the fungi identified herein showed great potential as bioremediators for highly Hg-contaminated aqueous substrates.

Mobilisation of hazardous elements from arsenic-rich mine drainage ochres by three Aspergillus species

Natural ferric ochres that precipitate in streambeds at abandoned mining sites are natural scavengers of various metals and metalloids. Thus, their chemical and structural modification via microbial activity should be considered in evaluation of the risks emerging from probable spread of contamination at mining sites. Our results highlight the role of various aspergilli strains in this process via production of acidic metabolites that affect mobility and bioavailability of coprecipitated contaminants. The Mössbauer analysis revealed subtle structural changes of iron in ochres, while the elemental analysis of non-dissolved residues of ochres that were exposed to filamentous fungi suggest coinciding bioextraction of arsenic and antimony with extensive iron mobilisation. However, the zinc bioextraction by filamentous fungi is less likely dependent on iron leaching from ferric ochres. The strain specific bioextraction efficiency and subsequent bioaccumulation of mobilised metals resulted in distinct tolerance responses among the studied soil fungal strains. However, regardless the burden of bioextracted metal(loid)s on its activity, the Aspergillus niger strain has shown remarkable capability to decrease pH of its environment and, thus, bioextract significant and environmentally relevant amounts of potentially toxic elements from the natural ochres.

Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas.