Fungal Community Structure and As-Resistant Fungi in a Decommissioned Gold Mine Site

Toxicity and bioremediation of the lead: a critical review

Lead is a naturally occurring, bluish-gray metal that is found in small quantities in the earth's crust. The existing literature demonstrates that non-biodegradable character and continuous use results in accumulation of lead concentration in the environment and causes various ill effects such as neurotoxicity, change in psychological and behavioral development of different organisms. Nowadays the most effective technique in the revival of the environment is bioremediation and it is environmentally friendly and cost-effective. Bacterial strains such as Oceanobacillus profundus and Lactobacillus acidophilus ATCC4356 have the ability to reduce lead 97% and 73.9%, respectively. Similarly some species of algae and fungal strains also showed lead removal efficiency as 74% (spirulina), 97.1% (Chlorella kessleri), 95.5% (Penicillium janthinillum) and 86% (Aspergillus flavus). Biodegradation of lead by various microbes would be the most efficient and sustainable approach. This review focuses on toxicity, fate of lead in the environment and its microbial degradation.

Interactions between bacteria and eukaryotic microorganisms and their response to soil properties and heavy metal exchangeability nearby a coal-fired power plant

Persistent heavy metal (HM) contaminated soil provides special habitat for microorganisms, HM stress and complex abiotic factors bring great uncertainty for the development of bacteria and eukaryotic microbes. Despite numerous studies about HMs' effect on soil microorganisms, the key factors affecting microbial communities in severe HM contaminated soil and their interactions are still not definite. In this study, the effect of HM fractions and soil properties on the interaction between bacterial communities and eukaryotic microorganisms was studied by high-throughput Illumina sequencing and simplified continuous extraction of HM in severe HM contaminated soil. Based on amplification and sequencing of the 18S rRNA gene, this study revealed that protists and algae were the most predominant eukaryotic microorganisms, and the dominant phyla were SAR, Opisthokonta and Archaeplastida in HM seriously polluted soil. These results also showed that exchangeable As was negatively correlated with bacterial Shannon and Simpson indexes, while exchangeable Zn was positively correlated with Shannon and Simpson indexes of eukaryotic microbes. Moreover, the structural equation model illustrated that pH, moisture content, available potassium and phosphorus, and exchangeable Cd, As and Zn were the dominant factors shaping bacterial communities, while total organic carbon and exchangeable Zn made the predominant contributions to variations in eukaryotic microbes. In addition, eukaryotic microbes were intensely affected by the bacterial communities, with a standardized regression weight of 0.53, which exceeded the influence of other abiotic factors. It was suggested that community-level adaptions through cooperative interactions under serious HM stress in soil.

Fire as a driver of fungal diversity - A synthesis of current knowledge

Fires occur in most terrestrial ecosystems where they drive changes in the traits, composition, and diversity of fungal communities. Fires range from rare, stand-replacing wildfires to frequent, prescribed fires used to mimic natural fire regimes. Fire regime factors, including burn severity, fire intensity, and timing, vary widely and likely determine how fungi respond to fires. Despite the importance of fungi to post-fire plant communities and ecosystem functioning, attempts to identify common fungal responses and their major drivers are lacking. This synthesis addresses this knowledge gap and ranges from fire adaptations of specific fungi to succession and assembly fungal communities as they respond to spatially heterogenous burning within the landscape. Fires impact fungi directly and indirectly through their effects on fungal survival, substrate and habitat modifications, changes in environmental conditions, and/or physiological responses of the hosts with which fungi interact. Some specific pyrophilous, or "fire-loving," fungi often appear after fire. Our synthesis explores whether such taxa can be considered cosmopolitan, and whether they are truly fire-adapted or simply opportunists adapted to rapidly occupy substrates and habitats made available by fires. We also discuss the possible inoculum sources of post-fire fungi and explore existing conceptual models and ecological frameworks that may be useful in generalizing fungal fire responses. We conclude with identifying research gaps and areas that may best transform the current knowledge and understanding of fungal responses to fire.

Biomineralization by Extremely Halophilic and Metal-Tolerant Community Members from a Sulfate-Dominated Metal-Rich Environment

The adaptation to adverse environmental conditions can lead to adapted microbial communities that may be screened for mechanisms involved in halophily and, in this case, metal tolerance. At a former uranium mining and milling site in Seelingstädt, Germany, microbial communities from surface waters and sediment soils were screened for isolates surviving high salt and metal concentrations. The high salt contents consisted mainly of chloride and sulfate, both in soil and riverbed sediment samples, accompanied by high metal loads with presence of cesium and strontium. The community structure was dominated by Chloroflexi, Proteobacteria and Acidobacteriota, while only at the highest contaminations did Firmicutes and Desulfobacterota reach appreciable percentages in the DNA-based community analysis. The extreme conditions providing high stress were mirrored by low numbers of cultivable strains. Thirty-four extremely halotolerant bacteria (23 Bacillus sp. and another 4 Bacillales, 5 Actinobacteria, and 1 Gamma-Proteobacterium) surviving 25 to 100 mM SrCl₂, CsCl, and Cs₂SO₄ were further analyzed. Mineral formation of strontium- or cesium-struvite could be observed, reducing bioavailability and thereby constituting the dominant metal and salt resistance strategy in this environment.

Ecological network analysis reveals distinctive microbial modules associated with heavy metal contamination of abandoned mine soils in Korea

Heavy metal pollution in soil around abandoned mine sites is one of the most critical environmental issues worldwide. Soil microbes form complex communities and perform ecological functions individually or in cooperation with other organisms to adapt to harsh environments. In this study, we investigated the distribution patterns of bacterial and fungal communities in non-contaminated and heavy metal-contaminated soil of the abandoned Samkwang mine in Korea to explore microbial interaction mechanisms and their modular structures. As expected, the bacterial and fungal community structures showed large differences depending on the degree of heavy metal contamination. The microbial network was divided into three modules based on the levels of heavy metal pollution: heavy metal-tolerant (HM-Tol), heavy metal-mid-tolerant (HM-mTol), and heavy metal-sensitive (HM-Sens) modules. Taxonomically, microbes assigned to Vicinamibacterales, Pedosphaeraceae, Nitrosomonadaceae, and Gemmatimonadales were the major groups constituting the HM-Tol module. Among the detected heavy metals (As, Pb, Cd, Cu, and Zn), copper concentrations played a key role in the formation of the HM-Tol module. In addition, filamentous fungi (Fusarium and Mortierella) showed potential interactions with bacteria (Nitrosomonadaceae) that could contribute to module stability in heavy metal-contaminated areas. Overall, heavy metal contamination was accompanied by distinct microbial communities, which could participate in the bioremediation of heavy metals. Analysis of the microbial interactions among bacteria and fungi in the presence of heavy metals could provide fundamental information for developing bioremediation mechanisms for the recovery of heavy metal-contaminated soil.

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.

Bacterial and fungal diversity in the lorandite (TlAsS2) mine 'Allchar' in the Republic of North Macedonia

The Allchar mineral mine is one of the oldest arsenic-antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.

Recent Advances in Biosorption of Copper and Cobalt by Filamentous Fungi

Copper (Cu) and Cobalt (Co) are among the most toxic heavy metals from mining and other industrial activities. Both are known to pose serious environmental concerns, particularly to water resources, if not properly treated. In recent years several filamentous fungal strains have been isolated, identified and assessed for their heavy metal biosorption capacity for potential application in bioremediation of Cu and Co wastes. Despite the growing interest in heavy metal removal by filamentous fungi, their exploitation faces numerous challenges such as finding suitable candidates for biosorption. Based on current findings, various strains of filamentous fungi have high metal uptake capacity, particularly for Cu and Co. Several works indicate that Trichoderma, Penicillium, and Aspergillus species have higher Cu and Co biosorption capacity compared to other fungal species such as Geotrichum, Monilia, and Fusarium. It is believed that far more fungal species with even higher biosorption capability are yet to be isolated. Furthermore, the application of filamentous fungi for bioremediation is considered environmentally friendly, highly effective, reliable, and affordable, due to their low technology pre-requisites. In this review, we highlight the capacity of various identified filamentous fungal isolates for biosorption of copper and cobalt from various environments, as well as their future prospects.

Mechanisms of arsenic assimilation by plants and countermeasures to attenuate its accumulation in crops other than rice

Arsenic is a ubiquitous metalloid in the biosphere, and its origin can be either geogenic or anthropic. Four oxidation states (-3, 0, +3 and + 5) characterize organic and inorganic As- compounds. Although arsenic is reportedly a toxicant, its harmful effects are closely related to its chemical form: inorganic compounds are most toxic, followed by organic ones and finally by arsine gas. Although drinking water is the primary source of arsenic exposure to humans, the metalloid enters the food chain through its uptake by crops, the extent of which is tightly dependent on its phytoavailability. Arsenate is taken up by roots via phosphate carriers, while arsenite is taken up by a subclass of aquaporins (NIP), some of which involved in silicon (Si) transport. NIP and Si transporters are also involved in the uptake of methylated forms of As. Once taken up, its distribution is regulated by the same type of transporters albeit with mobility efficiencies depending on As forms and its accumulation generally occurs in the following decreasing order: roots > stems > leaves > fruits (seeds). Besides providing a survey on the uptake and transport mechanisms in higher plants, this review reports on measures able to reducing plant uptake and the ensuing transfer into edible parts. On the one hand, these measures include a variety of plant-based approaches including breeding, genetic engineering of transport systems, graft/rootstock combinations, and mycorrhization. On the other hand, they include agronomic practices with a particular focus on the use of inorganic and organic amendments, treatment of irrigation water, and fertilization.

Effect of depleted uranium on a soil microcosm fungal community and influence of a plant-ectomycorrhizal association

Fungi are one of the most biogeochemically active components of the soil microbiome, becoming particularly important in metal polluted terrestrial environments. There is scant information on the mycobiota of uranium (U) polluted sites and the effect of metallic depleted uranium (DU) stress on fungal communities in soil has not been reported. The present study aimed to establish the effect of DU contamination on a fungal community in soil using a culture-independent approach, fungal ribosomal intergenic spacer analysis (F-RISA). Experimental soil microcosms also included variants with plants (Pinus silvestris) and P. silvestris/Rhizopogon rubescens ectomycorrhizal associations. Soil contamination with DU resulted in the appearance of RISA bands of the ITS fragments of fungal metagenomic DNA that were characteristic of the genus Mortierella (Mortierellomycotina: Mucoromycota) in pine-free microcosms and for ectomycorrhizal fungi of the genus Scleroderma (Basidiomycota) in microcosms with mycorrhizal pines. The precise taxonomic affinity of the ITS fragments from the band appearing for non-mycorrhizal pines combined with DU remained uncertain, the most likely being related to the subphylum Zoopagomycotina. Thus, soil contamination by thermodynamically unstable metallic depleted uranium can cause a significant change in a soil fungal community under experimental conditions. These changes were also strongly affected by the presence of pine seedlings and their mycorrhizal status which impacted on DU biocorrosion and the release of bioavailable uranium species.

Microbial diversity along a gradient in peatlands treating mining-affected waters

Peatlands are used for the purification of mining-affected waters in Northern Finland. In Northern climate, microorganisms in treatment peatlands (TPs) are affected by long and cold winters, but studies about those microorganisms are scarce. Thus, the bacterial, archaeal and fungal communities along gradients of mine water influence in two TPs were investigated. The TPs receive waters rich in contaminants, including arsenic (As), sulfate (SO42-) and nitrate (NO3-). Microbial diversity was high in both TPs, and microbial community composition differed between the studied TPs. Bacterial communities were dominated by Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria, archaeal communities were dominated by Methanomicrobia and the Candidate phylum Bathyarchaeota, and fungal communities were dominated by Ascomycota (Leotiomycetes, Dothideomycetes, Sordariomycetes). The functional potential of the bacterial and archaeal communities in TPs was predicted using PICRUSt. Sampling points affected by high concentrations of As showed higher relative abundance of predicted functions related to As resistance. Functions potentially involved in nitrogen and SO42- turnover in TPs were predicted for both TPs. The results obtained in this study indicate that (i) diverse microbial communities exist in Northern TPs, (ii) the functional potential of the peatland microorganisms is beneficial for contaminant removal in TPs and (iii) microorganisms in TPs are likely well-adapted to high contaminant concentrations as well as to the Northern climate.

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

Distribution and biodiversity of soil microscopic fungi in 5 areas of old environmental loads in Slovakia were studied in relation to very low amount of organic matter (%TOC from 0.2 to 3.54) and to the pH gradient from ultra-acidic (< 3.5) to very strongly alkaline (> 9.0). All soil samples were affected by several hundred years of mining activities and contained heavy metals and other toxic elements: arsenic, cadmium, copper, zinc, antimony, lead. Concentrations of toxicants highly exceeded their limited values. Fifty-three genera and 112 species of microscopic fungi were identified. Among them, Zygomycota occurred very rarely (8 genera and 12 species), except of samples with the highest content of TOC (2.01-3.54% - samples 2 and 6), regardless their pH. Though, on the other hand, from some similar samples (3, 5 and 9), incl. those with relatively high TOC (0.14-2.62%), the lower fungi were not recovered. Forty one genera and 95 species of Ascomycota represented the most abundant fungal phylum in all investigated samples. Among them, Penicillium chrysogenum var. chrysogenum, Aspergillus niger and Neosartorya fischeri were isolated the most often. Phytopathogenic moulds of Bionectria ochroleuca, Lewia infectoria, Phoma macrostoma and Phlebia acerina were also occurred frequently. The highest biodiversity of microfungal community was recorded in the extreme acidic environment, followed by the neutral, ultra-acidic and the very strong acidic ones. There was no similarity in microfungal spectrum found in the samples studied. Except of the ultra acidic and extreme acidic samples (1-2) as well as the ultra acidic and strong acidic ones (1-4) with the most rich mycobiota, that may indicate a certain similarity degree.