Bioremediation of copper using indigenous fungi Aspergillus species isolated from an abandoned copper mine soil

The expansion of fungal organisms in environmental biotechnology

Fungal organisms hold vital roles in ecosystem processes. Despite their intricate entanglement with most life on earth and their powerful metabolic capacities, they remain under-represented in environmental biotechnology. The interest in applying fungal biotechnologies to different environments is growing, as light is shed on their versatile potential. A diversity of fungi can be harnessed to promote crop yield, remediate pollutants from terrestrial and aquatic environments, and mitigate climate change impacts. Current technological advancements, such as the increase in high-accuracy 'omics pipelines, provide improvement. However, it is emphasized that there are many knowledge gaps regarding applying fungal biotechnology at scale where other organisms are inherently present. Hence, there is a dire need to increase funding that enables in-depth studies on fungal processes, such as degradation capacities, metabolite production, and cross-kingdom interactions, that promote climate-smart biotechnologies.

Mechanisms of microbial diversity modulation of mineral black clay to achieve ecological restoration of open-pit mine dump

The harsh climatic conditions and severe scarcity of surface soil present significant challenges to ecological restoration in open-pit mine dumps within China's type II plant cold resistance zone. To address the topsoil shortage, mineral black clay was used to create synthetic soil. This study explored the application of an ecological restoration bacteria (ERB) consortium to accelerate the ecological restoration of synthetic soil-covered areas by enhancing soil ecosystem construction. The results demonstrated that ERB significantly influenced the native bacterial community structure in mixed black clay. Specifically, ERB disrupted the inhibitory effects of the Actinobacterota phylum on the development of native bacterial diversity, leading to an increase in unclassified_o_Solirubrobacterales sp., norank_f_norank_o_norank_c_KD4-96 sp., Sphingomonas sp., Luteitalea sp., norank_f_Vicinamibacteraceae sp., and other aerobic and anaerobic bacteria. These alterations in soil microbial structure directly impacted soil composition and vegetation diversity. The plant diversity survey and metabolomics analysis revealed that the reduction of harmful substances, such as HPED, HODE, and HOME, in black clay soil improved the growth and distribution of Salsola collina Pall. and Medicago sativa L. This increase facilitated the cycling of key nutrients, such as nitrogen (N) and phosphorus (P), and promoted the establishment of symbiotic relationships between plants, microorganisms, and soil. Ultimately, the ecological remediation of the synthetic soil was achieved through the synergistic effects of ERB, which included the degradation of inhibitory soil components, enhanced nutrient consumption by microbiota and plants, and the overall promotion of ecosystem stability in the reclamation area.

Microbial Removal of Heavy Metals from Contaminated Environments Using Metal-Resistant Indigenous Strains

Contamination of soil with heavy metals has become a matter of global importance due to its impact on agriculture, environmental integrity, and therefore human health and safety. Several microbial strains isolated from soil contaminated by long-term chemical and petrochemical activities were found to manifest various levels of tolerance to Cr, Pb, and Zn, out of which Bacillus marisflavi and Trichoderma longibrachiatum exhibited above-moderate tolerance. The concentrations of target heavy metals before and after bioremediation were determined using electrochemical screen-printed electrodes (SPE) modified with different nanomaterials. The morpho-structural SEM/EDX analyses confirmed the presence of metal ions on the surface of the cell, with metal uptake being mediated by biosorption with hydroxyl, carboxyl, and amino groups as per FTIR observations. T. longibrachiatum was observed to pose a higher bioremediation potential compared to B. marisflavi, removing 87% of Cr and 67% of Zn, respectively. Conversely, B. marisflavi removed 86% of Pb from the solution, compared to 48% by T. longibrachiatum. Therefore, the fungal strain T. longibrachiatum could represent a viable option for Cr and Zn bioremediation strategies, whereas the bacterial strain B. marisflavi may be used in Pb bioremediation applications.

Evaluation of copper-tolerant fungi isolated from Sarcheshmeh copper mine of Iran

Mycoremediation, a subset of bioremediation, is considered an advanced method to eliminate environmental contaminations. To identify tolerant fungi to copper contamination and study the related gene expression, sampling was carried out from the soil of "Sarcheshmeh Copper Mine," which is one of the biggest open-cast copper mines in the world. A total of 71 fungal isolates were obtained and purified. Afterward, the inhibitory effect of different concentrations (1000, 1500, 3500, 4000, and 5500 ppm) of copper sulfate on mycelial growth was evaluated. Results indicated that only 5500 ppm of copper sulfate inhibited fungal growth compared to the control. Based on the bioassay experiments, three isolates including S3-1, S3-21, and S1-7, which were able to grow on solid and broth medium containing 5500 ppm of copper sulfate at different pH conditions, were selected and identified using molecular approaches. Also, laccase and metallothionein gene expression has been assessed in these isolates. According to the molecular identification using ITS1-5.8S- ITS2 region, isolates S3-1 and S1-7 were identified as Pleurotus eryngii, and isolate S3-21 belonged to the genus Sarocladium. In addition, P. eryngii showed laccase gene expression reduction after 8 days of exposure to copper sulfate. While in the genus Sarocladium, it increased (almost 2 times) from 6 to 8 days. Besides, metallothionein gene expression has increased from 6 to 8 days of copper sulfate treatment compared to the control which reveals its role in copper tolerance of all studied isolates. In this study, Pleurotus eryngii and Sarocladium sp. are introduced as heavy metal tolerant fungi and the related gene expression to copper tolerance was studied for the first time in Iran.

Copper-Contaminated Substrate Biosorption by Penicillium sp. Isolated from Kefir Grains

In this bioremediation study, the fungus Penicillium sp. isolated from kefir grains was evaluated for its resistance to copper in the culture medium. Penicillium sp. was cultivated in liquid medium prepared using 2% malt-agar at pH 7.0. Biomass of the fungus was significantly reduced, but only when 800 mg·L^-1 of Cu(NO₃)₂ copper nitrate was used. The effect on radial growth of the fungus in experiments combining different pH values and the inorganic contaminant showed an inhibition of 73% at pH 4.0, 75% at pH 7.0 and 77% at pH 9.0 in liquid medium. Thus, even though the growth of Penicillium sp. could be inhibited with relatively high doses of copper nitrate, images obtained with scanning electron microscopy showed the preservation of fungal cell integrity. Therefore, it can be concluded that Penicillium sp. isolated from kefir grains can survive while performing bioremediation to minimize the negative effects of copper on the environment through biosorption.

Genome sequencing of Cladophialophora exuberans, a novel candidate for bioremediation of hydrocarbon and heavy metal polluted habitats

Cladophialophora exuberans is a filamentous fungus related to black yeasts in the order Chaetothyriales. These melanized fungi are known for their 'dual ecology', often occurring in toxic environments and also being frequently involved in human infection. Particularly Cladophialophora exuberans, C. immunda, C. psammophila, and Exophiala mesophila have been described with a pronounced ability to degrade aromatic compounds and xenobiotic volatiles, such as benzene, toluene, ethyl-benzene, and xylene, and are candidates for bioremediation applications. The objective of the present study is the sequencing, assembly, and description of the whole genome of C. exuberans focusing on genes and pathways related to carbon and toxin management, assessing the tolerance and bioremediation of lead and copper, and verifying the presence of genes for metal homeostasis. Genomic evaluations were carried out through a comparison with sibling species including clinical and environmental strains. Tolerance of metals was evaluated via a microdilution method establishing minimum inhibitory (MIC) and fungicidal concentrations (MFC), and agar diffusion assays. Heavy metal bioremediation was evaluated via graphite furnace atomic absorption spectroscopy (GFAAS). The final assembly of C. exuberans comprised 661 contigs, with genome size of 38.10 Mb, coverage of 89.9X and a GC content of 50.8%. In addition, inhibition of growth was shown at concentrations of 1250 ppm for copper and at 625 ppm for lead, using the MIC method. In the agar tests, the strain grew at 2500 ppm of copper and lead. In GFAAS tests, uptake capacities were observed of 89.2% and 95.7% for copper and lead, respectively, after 21 experimental days. This study enabled the annotation of genes involved in heavy metal homeostasis and also contributed to a better understanding of the mechanisms used in tolerance of and adaptation to extreme conditions.