The Geomycology of Elemental Cycling and Transformations in the Environment

Metal-Binding Protein TaGlo1 Improves Fungal Resistance to Arsenite (AsIII) and Methylarsenite (MAsIII) in Paddy Soil

Trivalent arsenicals such as arsenite (AsIII) and methylarsenite (MAsIII) are thought to be ubiquitous in flooded paddy soils and have higher toxicity than pentavalent forms. Fungi are widely prevalent in the rice rhizosphere, and the latter is considered a hotspot for As uptake. However, few studies have focused on alleviating As toxicity in paddy soils using fungi. In this study, we investigated the mechanism by which the protein TaGlo1, derived from the As-resistant fungal strain Trichoderma asperellum SM-12F1, mitigates AsIII and MAsIII toxicity in paddy soils. Taglo1 gene expression in Escherichia coli BL21 conferred strong resistance to AsIII and MAsIII, while purified TaGlo1 showed a high affinity for AsIII and MAsIII. Three cysteine residues (Cys13, Cys18, and Cys71) play crucial roles in binding with AsIII, while only two (Cys13 and Cys18) play crucial roles for MAsIII binding. TaGlo1 had a stronger binding strength for MAsIII than AsIII. Importantly, up to 90.2% of the homologous TaGlo1 proteins originate from fungi by GenBank searching. In the rhizospheres of 14 Chinese paddy soils, Taglo1 was widely distributed and its gene abundance increased with porewater As. This study highlights the potential of fungi to mitigate As toxicity and availability in the soil-rice continuum and suggests future microbial strategies for bioremediation.

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

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

Translocation of elements and fractionation of Mg, Cu, Zn, and Cd stable isotopes in a penny bun mushroom (Boletus edulis) from western Czech Republic

Boletus edulis mushroom behaved as an accumulating biosystem with respect to Ag, Rb, Zn, and K. The mushroom was not an efficient accumulator of toxic As, Pb, and Cr, but Se and Cd displayed much higher concentrations in the mushroom than in the substrate samples. Other elements were bioexclusive. Different elements had different within-mushroom mobilities. The highest mobilities were displayed by Zn and Ag, and the lowest by Ti. The mushroom's fruiting body preferentially took up lighter Mg, Cu, and Cd isotopes (Δ26MgFB-soil =  -0.75‰; Δ65CuFB-soil =  -0.96‰; Δ114CdFB-soil =  -0.63‰), and the heavier 66Zn isotope (Δ66ZnFB-soil = 0.92‰). Positive within-mushroom Zn isotope fractionation resulted in accumulation of the heavier 66Zn (Δ66Zncap-stipe = 0.12‰) in the mushroom's upper parts. Cadmium displayed virtually no within-mushroom isotope fractionation. Different parts of the fruiting body fractionated Mg and Cu isotopes differently. The middle part of the stipe (3-6 cm) was strongly depleted in the heavier 26 Mg with respect to the 0-3 cm (Δ26Mgstipe(3-6)-stipe(0-3) =  -0.73‰) and 6-9 cm (Δ26Mgstipe(6-9)-stipe(3-6) = 0.28‰) sections. The same stipe part was strongly enriched in the heavier 65Cu with respect to the 0-3 cm (Δ65Custipe(3-6)-stipe(0-3) = 0.63‰) and 6-9 cm (Δ65Custipe(6-9)-stipe(3-6) =  -0.42‰) sections. An overall tendency for the upper mushroom's parts to accumulate heavier isotopes was noted for Mg (Δ26Mgcap-stipe = 0.20‰), Zn (Δ66Zncap-stipe = 0.12‰), and Cd (Δ114Cdcap-stipe = 0.04‰), whereas Cu showed the opposite trend (Δ65Cucap-stipe =  -0.08‰).

A Versatile in Vivo DNA Assembly Toolbox for Fungal Strain Engineering

Efficient homologous recombination in baker's yeast allows accurate fusion of DNA fragments via short identical sequence tags in vivo. Eliminating the need for an Escherichia coli cloning step speeds up genetic engineering of this yeast and sets the stage for large high-throughput projects depending on DNA construction. With the aim of developing similar tools for filamentous fungi, we first set out to determine the genetic- and sequence-length requirements needed for efficient fusion reactions, and demonstrated that in nonhomologous end-joining deficient strains of Aspergillus nidulans, efficient fusions can be achieved by 25 bp sequence overlaps. Based on these results, we developed a novel fungal in vivo DNA assembly toolbox for simple and flexible genetic engineering of filamentous fungi. Specifically, we have used this method for construction of AMA1-based vectors, complex gene-targeting substrates for gene deletion and gene insertion, and for marker-free CRISPR based gene editing. All reactions were done via single-step transformations involving fusions of up to six different DNA fragments. Moreover, we show that it can be applied in four different species of Aspergilli. We therefore envision that in vivo DNA assembly can be advantageously used for many more purposes and will develop into a popular tool for fungal genetic engineering.

Fungi, P-Solubilization, and Plant Nutrition

The application of plant beneficial microorganisms is widely accepted as an efficient alternative to chemical fertilizers and pesticides. It was shown that annually, mycorrhizal fungi and nitrogen-fixing bacteria are responsible for 5 to 80% of all nitrogen, and up to 75% of P plant acquisition. However, while bacteria are the most studied soil microorganisms and most frequently reported in the scientific literature, the role of fungi is relatively understudied, although they are the primary organic matter decomposers and govern soil carbon and other elements, including P-cycling. Many fungi can solubilize insoluble phosphates or facilitate P-acquisition by plants and, therefore, form an important part of the commercial microbial products, with Aspergillus, Penicillium and Trichoderma being the most efficient. In this paper, the role of fungi in P-solubilization and plant nutrition will be presented with a special emphasis on their production and application. Although this topic has been repeatedly reviewed, some recent views questioned the efficacy of the microbial P-solubilizers in soil. Here, we will try to summarize the proven facts but also discuss further lines of research that may clarify our doubts in this field or open new perspectives on using the microbial and particularly fungal P-solubilizing potential in accordance with the principles of the sustainability and circular economy.

Occurrence, distribution, and associations of essential and non-essential elements in the medicinal and edible fungus "Fuling" from southern China

In Asian countries, the sclerotia of the wild-grown fungus Pachyma hoelen ("Fuling"), have been used as food and as medicinal products for centuries. To close the knowledge gaps about the value and possible environmental impacts, the occurrence, distribution, and associations of a range of elements (Ag, Al, As, Ba, Cd, Co, Cr, Cs, Cu, Li, Mg, Mn, Ni, Pb, Rb, Sb, Sr, Tl, U, V, and Zn) were studied in the inner (core) and outer (shell) morphological parts of the sclerotia from a diverse collection in Southern China. Quality of forest and agricultural soil in terms of a geogenic element source and composition can be considered as the main factor determining the occurrence of minerals in sclerotia through the host wood, largely of Pinus yunnanensis, while the anthropogenic impact (basically at remote rural areas of cultivation) in Southern China was negligible. In general, the mean concentration of each element in the outer part was significantly higher than that in the inner part (t-test, p < 0.01), except for Ag. The concentration of a given element in the outer part tended to have a positive relationship with that in the inner part, except for Cu, Se, Ag, and Zn. The elements in different morphological parts of sclerotia present different relation patterns. Compared to the outer part, there were stronger associations of elements in the inner part, suggesting homeostatic regulation of multiple elements in the inner parts. Further study on the sclerotia, infected wood substrate, and surrounding soil from a range of wild sample collections and intentional cultivation should provide a more complex view and allow assessment of the relationship between minerals and bioactive organic compounds produced by P. hoelen.

Cell Wall Integrity and Its Industrial Applications in Filamentous Fungi

Signal transduction pathways regulating cell wall integrity (CWI) in filamentous fungi have been studied taking into account findings in budding yeast, and much knowledge has been accumulated in recent years. Given that the cell wall is essential for viability in fungi, its architecture has been analyzed in relation to virulence, especially in filamentous fungal pathogens of plants and humans. Although research on CWI signaling in individual fungal species has progressed, an integrated understanding of CWI signaling in diverse fungi has not yet been achieved. For example, the variety of sensor proteins and their functional differences among different fungal species have been described, but the understanding of their general and species-specific biological functions is limited. Our long-term research interest is CWI signaling in filamentous fungi. Here, we outline CWI signaling in these fungi, from sensor proteins required for the recognition of environmental changes to the regulation of cell wall polysaccharide synthesis genes. We discuss the similarities and differences between the functions of CWI signaling factors in filamentous fungi and in budding yeast. We also describe the latest findings on industrial applications, including those derived from studies on CWI signaling: the development of antifungal agents and the development of highly productive strains of filamentous fungi with modified cell surface characteristics by controlling cell wall biogenesis.

The poly-extreme tolerant black yeasts are prevalent under high ultraviolet light and climatic seasonality across soils of global biomes

Black yeasts are among the most stress‐tolerant organisms of the planet, thriving under all types of terrestrial habitats and extreme environments. Yet, their global patterns and ecology remain far less studied, limiting our capacity to identify the main environmental drivers of these important organisms across biomes. To fill this knowledge gap, we analysed topsoils from 235 terrestrial ecosystems across and within globally distributed climate groups (i.e. dry, temperate and continental). We found that soils are important repositories of black yeasts, and that ultraviolet light, fine soil texture, and precipitation seasonality are the most consistent environmental factors associated with their diversity across biomes. Finally, we identified Exophiala and Cladophialophora as the most dominant black yeasts genera in soils across the globe. These findings provide novel evidence of global distribution of black yeasts and their key environmental predictors, giving new insights for speculating the evolution and spreading of these extreme‐tolerant organisms throughout both natural and human associated extreme environments.

Glyphosate-Eating Fungi: Study on Fungal Saprotrophic Strains' Ability to Tolerate and Utilise Glyphosate as a Nutritional Source and on the Ability of Purpureocillium lilacinum to Degrade It

Glyphosate is the most commonly used herbicide worldwide. Its improper use during recent decades has resulted in glyphosate contamination of soils and waters. Fungal bioremediation is an environmentally friendly, cost effective, and feasible solution to glyphosate contamination in soils. In this study, several saprotrophic fungi isolated from agricultural environments were screened for their ability to tolerate and utilise Roundup in different cultural conditions as a nutritional source. Purpureocillium lilacinum was further screened to evaluate the ability to break down and utilise glyphosate as a P source in a liquid medium. The dose-response effect for Roundup, and the difference in toxicity between pure glyphosate and Roundup were also studied. This study reports the ability of several strains to tolerate 1 mM and 10 mM Roundup and to utilise it as nutritional source. P. lilacinum was reported for the first time for its ability to degrade glyphosate to a considerable extent (80%) and to utilise it as a P source, without showing dose-dependent negative effects on growth. Pure glyphosate was found to be more toxic than Roundup for P. lilacinum. Our results showed that pure glyphosate toxicity can be only partially addressed by the pH decrease determined in the culture medium. In conclusion, our study emphasises the noteworthy potential of P. lilacinum in glyphosate degradation.

Growth Enhancement of Arabidopsis (Arabidopsis thaliana) and Onion (Allium cepa) With Inoculation of Three Newly Identified Mineral-Solubilizing Fungi in the Genus Aspergillus Section Nigri

Some soil fungi play an important role in supplying elements to plants by the solubilizing of insoluble minerals in the soil. The present study was conducted to isolate the mineral-solubilizing fungi from rhizosphere soil in some agricultural areas in northern Thailand. Seven fungal strains were obtained and identified using a polyphasic taxonomic approach with multilocus phylogenetic and phenotypic (morphology and extrolite profile) analyses. All obtained fungal strains were newly identified in the genus Aspergillus section Nigri, Aspergillus chiangmaiensis (SDBR-CMUI4 and SDBR-CMU15), Aspergillus pseudopiperis (SDBR-CMUI1 and SDBR-CMUI7), and Aspergillus pseudotubingensis (SDBR-CMUO2, SDBR-CMUO8, and SDBR-CMU20). All fungal strains were able to solubilize the insoluble mineral form of calcium, copper, cobalt, iron, manganese, magnesium, zinc, phosphorus, feldspar, and kaolin in the agar plate assay. Consequently, the highest phosphate solubilization strains (SDBR-CMUI1, SDBR-CMUI4, and SDBR-CMUO2) of each fungal species were selected for evaluation of their plant growth enhancement ability on Arabidopsis and onion in laboratory and greenhouse experiments, respectively. Plant disease symptoms were not found in any treatment of fungal inoculation and control. All selected fungal strains significantly increased the leaf number, leaf length, dried biomass of shoot and root, chlorophyll content, and cellular inorganic phosphate content in both Arabidopsis and onion plants under supplementation with insoluble mineral phosphate. Additionally, the inoculation of selected fungal strains also improved the yield and quercetin content of onion bulb. Thus, the selected strains reveal the potential in plant growth promotion agents that can be applied as a biofertilizer in the future.

Resistance of Wood Treated with Iron Compounds against Wood-Destroying Decay and Mould Fungi

Treatment of wood with various physical and chemical factors can change the number of wood parameters, which can also lead to changes in resistance to wood-destroying fungi. This study evaluates the effects of hydrothermal treatments (additives Fe2O3 or FeCl3 with and without commercial tannins, also without additives and fresh wood) on decay and mould fungi resistance of modified wood of Scots pine (Pinus sylvestris), Norway spruce (Picea abies), Douglas fir (Pseudotsuga menziesii), walnut (Juglans regia), and Norway maple (Acer platanoides). For wood samples, the resistance against wood decay fungi Trametes versicolor (white rot) and Coniophora puteana (brown rot) and the resistance against mould fungi Aspergillus niger and Penicillium sp. were assessed. The study findings showed that wood modified with iron compounds could cause a higher resistance to wood-destroying fungi. The weight losses of the modified and control wood, caused by T. versicolor and C. puteana, differed for coniferous and deciduous: the average weight loss of treated pine, spruce, and fir wood caused by C. puteana was higher than that caused by T. versicolor, while these differences on maple and walnut wood were not significant. The wood hydrothermal treatment with Fe2Cl3 with and without tannins significantly reduced the weight loss caused by T. versicolor and C. puteana, and the treatment with Fe2O3 slightly improved the decay resistance. For the wood, hydrothermally modified with FeCl3 and FeCl3 + tannins, the mould area for both tested Aspergillus niger and Penicillium sp. was smallest for the wood of all tested tree species compared to other treatments. A different response was obtained for coniferous and deciduous tree species wood. The spruce wood, followed by fir wood, treated with FeCl3 with and without tannins, was the most resistant against the mould fungi. Relatively low resistance against the mould fungi was fixed for the maple wood treated by various iron compounds, except the treatment with Fe2O3 + tannins, which gave a very positive response against the Penicillium sp.

Rock phosphate solubilization by abiotic and fungal-produced oxalic acid: reaction parameters and bioleaching potential

Oxalic acid-producing fungi play an important role in biogeochemical transformations of rocks and minerals and possess biotechnological potential for extraction of valuable elements from primary or waste ores and other solid matrices. This research investigates the extraction of phosphate from rock phosphate (RP) by oxalic acid. Reaction parameters were derived using pure oxalic acid solutions to solubilize RP. It was found that the oxalic acid concentration was the main factor driving reaction kinetics. Excess oxalic acid could retard the reaction due to calcium oxalate encrustation on RP surfaces. However, complete P extraction was reached at stoichiometric proportions of apatite and oxalic acid. This reaction reached completion after 168 h, although most of the P (up to 75%) was released in less than 1 h. Most of the Ca released from the apatite formed sparingly soluble calcium oxalate minerals, with a predominance of whewellite over weddellite. Bioleaching of RP employing biomass-free spent culture filtrates containing oxalic acid (100 mM) produced by Aspergillus niger extracted ~ 74% of the P contained in the RP. These findings contribute to a better understanding of the reaction between apatite and oxalic acid and provide insights for potential applications of this process for biotechnological production of phosphate fertilizer.

Influences of phosphate addition on fungal weathering of carbonate in the red soil from karst region

Carbonate in soil from karst region is a substantial carbon sink on Earth. Many karst regions are covered by P-deficient soil. This study evaluated the influences of phosphate addition on fungal weathering (by typical phosphate-solubilizing fungus Aspergillus niger) of carbonate in the soil with red color from karst region. Two weathering pathways were recognized, i.e., biochemical and biomechanical deterioration. The biochemical pathway was performed by dissolving carbonate via secreting organic acids. Meanwhile, the dominant organic acid, i.e., oxalic acid, induced the formation of calcium oxalate, which prevented the loss of Ca²⁺ cations. It was estimated that the ideal carbonate solubilization driven by geological fluorapatite and fungal weathering is up to 3.3% per year, based on the equation of 12 × (R_Base + R_PSF) × m × (A_real/A_PSF). Moreover, fungal weathering of carbonate is very sensitive to the solubility of phosphates. Phosphates supply essential P source for the fungal growth and subsequently raise water-soluble P content in the soil. The addition of bioapatite (a variety of natural apatite with relatively high solubility) elevated the value to 4.6% (a ~ 40% enhancement compared with FAp). This research hence elucidated the tight correlation between carbonate weathering and P supply. Inorganic C release driven by P availability and microbial weathering should be addressed in karst region.

Terrestrial eutrophication of building materials and buildings: An emerging topic in environmental studies

Eutrophication has been analyzed mostly in aquatic or soil environments to date. Direct terrestrial eutrophication of building materials and buildings, contrary e.g. to their biodeterioration or biodegradation, was studied so rarely that even its exact definition does not exist yet. In this paper, eutrophication of building materials and buildings as an emerging topic in environmental studies is analyzed in detail and future developments in the field are contemplated. The analysis includes a survey of directly and indirectly related research studies, identification of basic mechanisms and principal factors, and a critical assessment of current methodologies potentially applicable for recognition and classification of eutrophication of building materials and buildings. A definition of direct terrestrial eutrophication of building materials and buildings is proposed afterwards and an alternative method for the calculation of their eutrophication potential is suggested. Finally, recommendations for solving the most urgent problems in future research are formulated.

Apophysomycesthailandensis (Mucorales, Mucoromycota), a new species isolated from soil in northern Thailand and its solubilization of non-soluble minerals

A new species of soil fungi, described herein as Apophysomycesthailandensis, was isolated from soil in Chiang Mai Province, Thailand. Morphologically, this species was distinguished from previously described Apophysomyces species by its narrower trapezoidal sporangiospores. A physiological determination showed that A.thailandensis differs from other Apophysomyces species by its assimilation of D-turanose, D-tagatose, D-fucose, L-fucose, and nitrite. A phylogenetic analysis, performed using combined internal transcribed spacers (ITS), the large subunit (LSU) of ribosomal DNA (rDNA) regions, and a part of the histone 3 (H3) gene, lends support to our the finding that A.thailandensis is distinct from other Apophysomyces species. The genetic distance analysis of the ITS sequence supports A.thailandensis as a new fungal species. A full description, illustrations, phylogenetic tree, and taxonomic key to the new species are provided. Its metal minerals solubilization ability is reported.

Weathering of granitic gneiss: A geochemical and microbiological study in the polluted sub-tropical city of Rio de Janeiro

Chemical and biological weathering were studied on two historic churches in the city of Rio de Janeiro, Brazil. The churches exhibited contour scaling, granular disintegration and black crust development. High levels of SO₄ were found in façade stones of one church, São José, with significant levels of lead and copper. This suggests that vehicle emissions were important in stonework decay. Both gypsum and halite were detected, typical of buildings influenced by marine atmosphere and fuel-polluted environment. There was little bioweathering on this church, although the filamentous cyanobacterium Scytonema detected could be involved in black crust production. The other church (Nossa Senhora da Gloria) showed strong granular disintegration, with a green coloration on internal surfaces of some flakes removed for study. This church showed lower levels of geochemically important weathering compounds but was more colonized by fungi and cyanobacteria. The latter were shown by scanning electron microscopy to grow within the granitic gneiss stone and were probably involved in dissolution and redeposition of minerals. This church is rather far from the intense traffic of the centre of Rio de Janeiro and from Guanabara Bay, source of marine aerosols; it is located upon a green hill, where plant-associated fungi and cyanobacteria can readily gain access to the façade. The results of this study show the importance of local environment on the relative proportions of chemical and biological weathering of stone.

Metabolic Activity of Micromycetes Affecting Urban Concrete Constructions

Concrete resistance to the destructive action of microorganisms is considered as a measure of its durability and is increasingly being raised as an important issue. We focused our study on the biodeterioration of concrete specimens widely used as a building material of urban houses by micromycetes isolated from the inner wall surface of the former military hospital in Kazan city, Tatarstan, Russia. Fungal community consists of 9 Penicillium isolates, 6 Aspergillus, 2 Trichoderma, and 1 isolate of Alternaria. First, we have identified two dominant isolates, Aspergillus fumigatus and Penicillium brevicompactum, and characterized their destructive properties according to the radial growth rate, antagonistic activity towards bacterial habitants of concrete, and production of organic acids. Then, we have demonstrated that five tested brands of high-strength concrete differ in bioreceptivity. The alterations in concrete resistances to compression and flexure after fungal attack were recorded at the trend level, mainly due to a short exposure time of concrete to fungal destructors in tests recommended by national Russian standard. Finally, using scanning electron microscopy we have shown that colonization of concrete by the dominant fungi includes their penetration into the thickness of concrete and germination in cracks. Elementary analysis revealed the decrease of calcium content on about 41% after fungal growth on the concrete in liquid phase and on 32% by superficial growth in comparison with the samples without fungal treatment.

Applications of Microbial Processes in Geotechnical Engineering

Over the last 10-15 years, a new field of "biogeotechnics" has emerged as geotechnical engineers seek to find ground improvement technologies which have the potential to be lower carbon, more ecologically friendly, and more cost-effective than existing practices. This review summarizes the developments which have occurred in this new field, outlining in particular the microbial processes which have been shown to be most promising for altering the hydraulic and mechanical responses of soils and rocks. Much of the research effort in this new field has been focused on microbially induced carbonate precipitation (MICP) via ureolysis, while a comprehensive review of MICP is presented here, the developments which have been made regarding other microbial processes, including MICP via denitrification and biogenic gas generation are also presented. Furthermore, this review outlines a new area of study: the potential deployment of fungi in geotechnical applications which has until now been unexplored.