Characterization of microbial communities of soils from gold mine tailings and identification of mercury-resistant strain

Molecular docking, molecular dynamics simulations and binding free energy studies of interactions between Mycobacterium tuberculosis Pks13, PknG and bioactive constituents of extremophilic bacteria

Mycobacterial pathogens present a significant challenge to disease control efforts globally due to their inherent resistance to multiple antibiotics. The rise of drug-resistant strains of Mycobacterium tuberculosis has prompted an urgent need for innovative therapeutic solutions. One promising way to discover new tuberculosis drugs is by utilizing natural products from the vast biochemical space. Multidisciplinary methods can used to harness the bioactivity of these natural products. This study aimed to evaluate the antimycobacterial efficacy of functional crude extracts from bacteria isolated from gold mine tailings in South Africa. Bacterial strains were identified using 16S rRNA sequencing. The crude extracts obtained from the bacteria were tested against Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. Untargeted HPLC-qTOF and molecular networking were used to identify the functional constituents present in extracts that exhibited inhibitory activity. A virtual screening workflow (VSW) was used to filter compounds that were strong binders to Mycobacterium tuberculosis Pks13 and PknG. The ligands returned from the VSW were subjected to optimization using density functional theory (DFT) at M06-2X/6-311++ (d,p) level of theory and basis set implemented in Gaussian16 Rev.C01. The optimized ligands were re-docked against Mycobacterium tuberculosis Pks13 and PknG. Molecular dynamics simulation and molecular mechanics generalized born surface area were used to evaluate the stability of the protein-ligand complexes formed by the identified hits. The hit that showed promising binding characteristics was virtually modified through multiple synthetic routes using reaction-driven enumeration. Three bacterial isolates showed significant activity against the two strains of Mycobacterium, while only two, Bacillus subtilis and Bacillus licheniformis, exhibited activity against both Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. The tentatively identified compounds from the bacterial crude extracts belonged to various classes of natural compounds associated with antimicrobial activity. Two compounds, cyclo-(L-Pro-4-OH-L-Leu) and vazabitide A, showed strong binding against PknG and Pks13, with pre-MD MM-GBSA values of - 42.8 kcal/mol and - 47.6 kcal/mol, respectively. The DFT-optimized compounds exhibited the same docking scores as the ligands optimized using the OPSL-4 force field. After modifying vazabitide A, its affinity to the Pks13 binding site increased to - 85.8 kcal/mol, as revealed by the post-MD MM-GBSA analysis. This study highlights the potential of bacteria isolates from gold mine tailings as a source of new scaffolds for designing and optimizing anti-Mycobacterium agents. These agents synthesized in-silico can be further tested in-vitro to evaluate their efficacy.

Microbial diversity and abundance of Hg related genes from water, sediment and soil the Colombian amazon ecosystems impacted by artisanal and small-scale gold mining

The Amazon region abounds in precious mineral resources including gold, copper, iron, and coltan. Artisanal and small-scale gold mining (ASGM) poses a severe risk in this area due to considerable mercury release into the surrounding ecosystems. Nonetheless, the impact of mercury on both the overall microbiota and the microbial populations involved in mercury transformation is not well understood. In this study we evaluated microbial diversity in samples of soil, sediment and water potentially associated with mercury contamination in two localities (Taraira and Tarapacá) in the Colombian Amazon Forest. To this end, we characterized the bacterial community structure and mercury-related functions in samples from sites with a chronic history of mercury contamination which today have different levels of total mercury content. We also determined mercury bioavailability and mobility in the samples with the highest THg and MeHg levels (up to 43.34 and 0.049 mg kg-1, respectively, in Taraira). Our analysis of mercury speciation showed that the immobile form of mercury predominated in soils and sediments, probably rendering it unavailable to microorganisms. Despite its long-term presence, mercury did not appear to alter the microbial community structure or composition, which was primarily shaped by environmental and physicochemical factors. However, an increase in the relative abundance of merA genes was detected in polluted sediments from Taraira. Several Hg-responsive taxa in soil and sediments were detected in sites with high levels of THg, including members of the Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes and Chloroflexi phyla. The results suggest that mercury contamination at the two locations sampled may select mercury-adapted bacteria carrying the merA gene that could be used in bioremediation processes for the region.

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

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.

Fe/S Redox-Coupled Mercury Transformation Mediated by Acidithiobacillus ferrooxidans ATCC 23270 under Aerobic and/or Anaerobic Conditions

Bioleaching processes or microbially mediated iron/sulfur redox processes in acid mine drainage (AMD) result in mineral dissolution and transformation, the release of mercury and other heavy metal ions, and changes in the occurrence forms and concentration of mercury. However, pertinent studies on these processes are scarce. Therefore, in this work, the Fe/S redox-coupled mercury transformation mediated by Acidithiobacillus ferrooxidans ATCC 23270 under aerobic and/or anaerobic conditions was studied by combining analyses of solution behavior (pH, redox potential, and Fe/S/Hg ion concentrations), the surface morphology and elemental composition of the solid substrate residue, the Fe/S/Hg speciation transformation, and bacterial transcriptomics. It was found that: (1) the presence of Hg²⁺ significantly inhibited the apparent iron/sulfur redox process; (2) the addition of Hg²⁺ caused a significant change in the composition of bacterial surface compounds and elements such as C, N, S, and Fe; (3) Hg mainly occurred in the form of Hg⁰, HgS, and HgSO₄ in the solid substrate residues; and (4) the expression of mercury-resistant genes was higher in earlier stages of growth than in the later stages of growth. The results indicate that the addition of Hg²⁺ significantly affected the iron/sulfur redox process mediated by A. ferrooxidans ATCC 23270 under aerobic, anaerobic, and coupled aerobic-anaerobic conditions, which further promoted Hg transformation. This work is of great significance for the treatment and remediation of mercury pollution in heavy metal-polluted areas.

Physicochemical characteristics and microbial communities of rhizosphere in complex amendment-assisted soilless revegetation of gold mine tailings

Amendment-assisted soilless revegetation is a promissing ecological restoration method of mine tailings because of its eco-friendliness and low-cost. However, it is difficult to establish the plant community during ecological restoration because of its nutrient deficiency and heavy metal toxicity. In this study, the complex amendment, consisting of 1% peat, 1% sludge and 4% bentonite, was used to assist tall fescue to revegetate gold mine tailings. The variation in physicochemical characteristics and microbial community diversity and composition of rhizosphere tailings were investigated. The complex amendments significantly promoted tall fescue growth with an increase of 35.33% in shoot length and 27.19% in fresh weight. The improved plant growth was attributed to the reduction in heavy metal accumulation and the variation in the characteristics of rhizosphere tailing microecology. The heavy metal concentrations in plant tissues were decreased by 27.71-53.44% in the amended groups. Compared with the control, the available nitrogen (N), phosphorus (P) and potassium (K) levels in TA (without plant cultivation) and TPA (with plant cultivation) were also enhanced by 36.67-49.09% and 42.21-71.47%, respectively. Besides, the amendments introduced more exclusive operational taxonomic units (OTU) and increased the relative abundance of ecologically beneficial microbes in the rhizosphere. Overall, this study provides insight into amendment-assisted soilless revegetation and its effects on microecology to expand ecological restoration of gold mine tailings.

Isolation and Identification of Mercury-Tolerant Bacteria LBA119 from Molybdenum-Lead Mining Soils and Their Removal of Hg2

AIMS

To screen heavy metal-tolerant strains from heavy metal-contaminated soil in mining areas and determine the tolerance of the strains to different heavy metals and their removal rates through experiments.

METHODS

Mercury-resistant strain LBA119 was isolated from mercury-contaminated soil samples in Luanchuan County, Henan Province, China. The strain was identified by Gram staining, physiological and biochemical tests, and 16S rDNA sequences. The LBA119 strain showed good resistance and removal rates to heavy metals such as Pb²⁺, Hg²⁺, Mn²⁺, Zn²⁺, and Cd²⁺ using tolerance tests under optimal growth conditions. The mercury-resistant strain LBA119 was applied to mercury-contaminated soil to determine the ability of the strain to remove mercury from the soil compared to mercury-contaminated soil without bacterial biomass.

RESULTS

Mercury-resistant strain LBA119 is a Gram-positive bacterium that appears as a short rod under scanning electron microscopy, with a single bacterium measuring approximately 0.8 × 1.3 μm. The strain was identified as a Bacillus by Gram staining, physiological and biochemical tests, and 16S rDNA sequence analysis. The strain was highly resistant to mercury, with a minimum inhibitory concentration (MIC) of 32 mg/L for mercury. Under a 10 mg/L mercury environment, the optimal inoculation amount, pH, temperature, and salt concentration of the LBA119 strain were 2%, 7, 30 °C, and 20 g/L, respectively. In the 10 mg/L Hg²⁺ LB medium, the total removal rate, volatilization rate, and adsorption rate at 36 h were 97.32%, 89.08%, and 8.24%, respectively. According to tolerance tests, the strain showed good resistance to Pb²⁺, Mn²⁺, Zn²⁺, Cd²⁺, and other heavy metals. When the initial mercury concentration was 50 mg/L and 100 mg/L, compared with the mercury-contaminated soil that contained an LB medium without bacterial biomass, LBA119 inoculation increased 15.54-37.67% after 30 days of culture.

CONCLUSION

This strain shows high bioremediation potential for mercury-contaminated soil.

The Fashion Industry Needs Microbiology: Opportunities and Challenges

The fashion industry is the second most polluting industry in the world, representing a 2 trillion dollars and growing valuation. Fashion design practices have been perpetuating an industrial-focused approach, which relies mostly in the economic improvement through fast cycles of product development. Additionally, the fashion industry has also been closed to either multidisciplinary or transdisciplinary initiatives outside the scope of the artistic disciplines. Therefore, innovative approaches are needed to solve fashion industrial challenges. One of the most promising fields to tackle current environmental and technological problems in the fashion industry is microbiology. Through the emergent field of synthetic biology, the number of tools and approaches available is increasing and they can already be seen in niche applications. Despite the current advances and urgent need for change, there is still a long way until a more sustainable fashion industry is achieved.

Study on potential microbial community to the waste water treatment from bauxite desilication process

Discharging waste water from the bauxite desilication process will bring potential environmental risk from the residual ions and organic compounds, especially hydrolyzed polyacrylamide. Characterization of the microbial community diversity in waste water plays an important role in the biological treatment of waste water. In this study, eight waste water samples from five flotation plants in China were investigated. The microbial community and functional profiles within the waste water were analyzed by a metagenomic sequencing method and associated with geochemical properties. The results revealed that Proteobacteria and Firmicutes were the dominant bacterial phyla. Both phylogenetical and clusters of orthologous groups' analyses indicated that Tepidicella, Paracoccus, Pseudomonas, and Exiguobacterium could be the dominant bacterial genera in the waste water from bauxite desilication process for their abilities to biodegrade complex organic compounds. The results of the microbial community diversity and functional gene compositions analyses provided a beneficial orientation for the biotreatment of waste water, as well as regenerative using of water resources. Besides, this study revealed that waste water from bauxite desilication process was an ideal ecosystem to find novel microorganisms, such as efficient strains for bio-desilication and bio-desulfurization of bauxite.

Impact of environmental factors on the ammonia-oxidizing and denitrifying microbial community and functional genes along soil profiles from different ecologically degraded areas in the Siding mine

Ammonia oxidizers (ammonia-oxidizing bacteria (AOB amoA) and ammonia-oxidizing archaea (AOA amoA)) and denitrifiers (encoded by nirS, nirK and nosZ) in the soil nitrogen cycle exist in a variety of natural ecosystems. However, little is known about the contribution of these five N-related functional genes to nitrification and denitrification in the soil profile in severely ecologically degraded areas. Therefore, in the present study, the abundance, diversity and community composition of AOA, AOB, nirS, nirK and nosZ were investigated in the soil profiles of different ecologically degraded areas in the Siding mine. The results indicated that, at the phylum level, the dominant archaea were Crenarchaeota and Thaumarchaeota and the dominant bacteria were Proteobacteria. Heavy metal contents had a great impact on AOA amoA, nirS and nirK gene abundances. AOA amoA contributed more during the ammonia oxidation process and was better adapted for survival in heavy metal-contaminated environments. In addition to heavy metals, the soil organic matter (SOM) content and C/N ratio had strong effects on the AOA and AOB community diversity and structure. In addition, variations in the net ammonification and nitrification rates were proportional to AOA amoA abundance along the soil profile. The soil C/N ratio, soil available phosphorus content and soil moisture influenced the denitrification process. Both soil available phosphorus and moisture were more strongly related to nosZ than to nirS and nirK. In addition, nosZ presented a higher correlation with the nosZ/(nirS + nirK) ratio. Moreover, nosZ/(nirS + nirK) was the key functional gene group that drove the major processes for NH₄⁺-N and NO₃^--N transformation. This study demonstrated the role and importance of soil property impacts on N-related microbes in the soil profile and provided a better understanding of the role and importance of N-related functional genes and their contribution to soil nitrification and denitrification processes in highly degraded areas in the Siding mine.

Heavy metal(loid)s shape the soil bacterial community and functional genes of desert grassland in a gold mining area in the semi-arid region

Gold mining can create serious environmental problems, such as soil pollution by heavy metal (loid)s. In this study, we assessed the ecological risk of Hatu gold mining activities and synchronously investigated the bacterial community structure, distribution of soil nutrient-element cycling genes (CNPS) and heavy metal resistance genes (MRG) in adjacent desert grassland soil. The study area was above the moderate risk level, with the ecological risk index (RI) of each sampling site greater than 150. Arsenic, mercury and copper were the main pollutants. Proteobacteria, Actinobacteria and Firmicutes dominated the phyla of the bacterial communities. Species turnover rather than nestedness accounted for the significant differences in community structure among various regions in the mining area. In addition, the bioavailable heavy metal (loid)s (AHM) content had a strong correlation with beta diversity and species turnover of the bacterial community (p < 0.05). No clear difference was found in the total abundance of CNPS genes among various functional regions, but eight specific functional genes were identified from downwind grasslands with lower pollution levels. Among the MRGs, Hg MRG had the highest average total relative abundance, followed by Cu, Co/Zn/Cd and As. The mercury resistance gene subtype hgcAB was positively related to the diversity of the bacterial community, and the bacterial community of grassland soil showed congruency with the MRGs in the Hatu mining area. Total Hg (THg) showed the highest influence affecting the bacterial community, while NH₄⁺-N had the greatest effect on CNPS genes and MRGs. These results highlighted the role of heavy metal (loid)s in shaping the bacterial community and functional genes in arid and semiarid desert grassland soil in gold mining regions.

Current advances and research prospects for agricultural and industrial uses of microbial strains available in world collections

Microorganisms are an important component of the ecosystem and have an enormous impact on human lives. Moreover, microorganisms are considered to have desirable effects on other co-existing species in a variety of habitats, such as agriculture and industries. In this way, they also have enormous environmental applications. Hence, collections of microorganisms with specific traits are a crucial step in developing new technologies to harness the microbial potential. Microbial culture collections (MCCs) are a repository for the preservation of a large variety of microbial species distributed throughout the world. In this context, culture collections (CCs) and microbial biological resource centres (mBRCs) are vital for the safeguarding and circulation of biological resources, as well as for the progress of the life sciences. Ex situ conservation of microorganisms tagged with specific traits in the collections is the crucial step in developing new technologies to harness their potential. Type strains are mainly used in taxonomic study, whereas reference strains are used for agricultural, biotechnological, pharmaceutical research and commercial work. Despite the tremendous potential in microbiological research, little effort has been made in the true sense to harness the potential of conserved microorganisms. This review highlights (1) the importance of available global microbial collections for man and (2) the use of these resources in different research and applications in agriculture, biotechnology, and industry. In addition, an extensive literature survey was carried out on preserved microorganisms from different collection centres using the Web of Science (WoS) and SCOPUS. This review also emphasizes knowledge gaps and future perspectives. Finally, this study provides a critical analysis of the current and future roles of microorganisms available in culture collections for different sustainable agricultural and industrial applications. This work highlights target-specific potential microbial strains that have multiple important metabolic and genetic traits for future research and use.

Effects of Mercury Contamination on Microbial Diversity of Different Kinds of Soil

Soil microorganisms promote the recovery of contaminated soil by influencing the cyclic transformation of various substances. In this study, we investigated the impact of mercury pollution on the structure, composition, and main populations of soil microbial communities using a high-throughput sequencing method and observed that mercury pollution significantly influenced the diversity, structure, and distribution pattern of microbial communities. Furthermore, during mercury pollution, the Shannon and Chao indices decreased for the bacterial communities and increased for the fungal communities. Mercury pollution mainly reduced the relative abundances of Proteobacteria (16.2−30.6%), Actinomycetes (24.7−40.8%), and other dominant bacterial phyla. The relative abundance of Ascomycota decreased by 17.4% and 16.7% in alkaline and neutral soils, respectively, whereas the relative abundance of unclassified_k_Fungi increased by 26.1% and 28.6%, respectively. In acidic soil, Ascomycota increased by 106.3% and unclassified_k_Fungi decreased by 71.2%. The results of redundancy and correlation analyses suggested that soil microbial diversity was significantly correlated with soil properties such as pH, cation exchange capacity, soil organic carbon, and total nitrogen (p < 0.05) under different treatments. Our findings highlight the impact of Hg pollution on soil microbial communities, thereby providing a theoretical foundation for the bioremediation of soil Hg pollution.

Indigenous microbial populations of abandoned mining sites and their role in natural attenuation

Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.

Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics

Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo [ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petrochemical wastes in the landfill. The levels of the total toxic benzo [a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.

Distribution characteristics and risk of heavy metals and microbial community composition around the Wanshan mercury mine in Southwest China

The Wanshan mercury (Hg) mine in Guizhou Province is one of the main Hg-producing mines in China, resulting in serious Hg pollution in soil and wastewater. Therefore, the present study is mainly aimed to investigate the current degree of heavy metal pollution and compared the microbial diversity in the Wanshan Hg mine and its surrounding environment. The results showed the distribution of the pollution load index values was low in the west and high in the east. The northwestern (Aozhai River), northern (Meizi Stream), and southwestern parts of the study area and the area surrounding Erkeng did not reach moderate pollution. Mercury accounted for the majority of the potential ecological risk index values, reaching 67.62%, while the proportions of Cd and As were 15.75% and 10.75%, respectively. Mercury was found mainly in a residual state, which had an average proportion of 71.09%. In the three regions, Proteobacteria and Actinobacteria had the highest relative abundances. According to linear discriminant analysis effect size, the indicator species in the Hg mining area, woodland and cultivated land was f__67-14 (belonging to a family of Solirubrobacterales), Reyranellales and Reyranellaceae, Intrasporangiaceae, respectively. In summary, this study for the very first time estimated that the higher Hg, Cd and As pollution existed in Wanshan Hg mine since their concentration in the all soil samples totally exceeded the standard value (GB15618-2018), while Cd and As pollution in soil was commonly ignored by the previous study. The cultivated land had higher community richness than the mercury mining district and woodland. Our results suggested that the relevant local departments need to take more active measures to solve the problem of high levels of Hg, Cd, and As in the local soil, and prevent their adverse effects on humans.

Microbial community profiles in soils adjacent to mining and smelting areas: Contrasting potentially toxic metals and co-occurrence patterns

Mining and smelting activities have introduced severe potentially toxic metals (PTMs) contamination into surrounding soil settings. Influences of PTMs on microbial diversity have been widely studied. However, variations of microbial communities, network structures and community functions in different levels of PTMs contaminated soils adjacent to mining and smelting aera are still poorly investigated. In this study, microbial communities of soils around different levels of PTMs contamination were comprehensively studied by 16S rRNA gene amplicons high-throughput sequencing. Microbial interactions and module functions were also exploited to ascertain the discrepancies of PTMs concentration levels on microbial ecological functions. Results indicated that the microbial community composition was significantly distinct attributed to the phylum Protebacteria (p = 0.002) dominating in soil with high level PTMs contents but Actinobacteria (p = 0.002) in low level of PTMs-contaminated soil. Microbial α diversity was not significantly influenced by different levels of PTMs contaminations. Microorganisms proactively responded to PTMs content levels by means of strengthening network complexities and modularities among microbe-microbe interactions. The functions of main network modules were predicted associating membrane transport, amino acid metabolism, energy metabolism and carbohydrate metabolism. The PTMs detoxification and anti-oxidation were significantly strengthened at the high level of PTMs contamination. The present study demonstrated that modification of microbial community by the adaptive adjustment of microbial compositions and strengthening their network complexity and modularity.

The Microbiology of Metal Mine Waste: Bioremediation Applications and Implications for Planetary Health

Mine wastes pollute the environment with metals and metalloids in toxic concentrations, causing problems for humans and wildlife. Microorganisms colonize and inhabit mine wastes, and can influence the environmental mobility of metals through metabolic activity, biogeochemical cycling and detoxification mechanisms. In this article we review the microbiology of the metals and metalloids most commonly associated with mine wastes: arsenic, cadmium, chromium, copper, lead, mercury, nickel and zinc. We discuss the molecular mechanisms by which bacteria, archaea, and fungi interact with contaminant metals and the consequences for metal fate in the environment, focusing on long-term field studies of metal-impacted mine wastes where possible. Metal contamination can decrease the efficiency of soil functioning and essential element cycling due to the need for microbes to expend energy to maintain and repair cells. However, microbial communities are able to tolerate and adapt to metal contamination, particularly when the contaminant metals are essential elements that are subject to homeostasis or have a close biochemical analog. Stimulating the development of microbially reducing conditions, for example in constructed wetlands, is beneficial for remediating many metals associated with mine wastes. It has been shown to be effective at low pH, circumneutral and high pH conditions in the laboratory and at pilot field-scale. Further demonstration of this technology at full field-scale is required, as is more research to optimize bioremediation and to investigate combined remediation strategies. Microbial activity has the potential to mitigate the impacts of metal mine wastes, and therefore lessen the impact of this pollution on planetary health.

Co-remediation of PTEs contaminated soil in mining area by heat modified sawdust and herb

Exploring efficient remediation technologies to remediate potentially toxic element (PTE) in soil around the mining area has become a trendy research topic. This study conducted material composed of sawdust ash (SA) and sawdust biochar (SB) with mass ratio of SA:SB = 1:2 in combination with Medicago sativa L. and Festuca arundinacea to remediate soil contaminated by zinc (Zn), cadmium (Cd), and arsenic (As) in a mining area. The result showed that the removal rates of Zn, Cd, and As were the highest under the treatment of Festuca arundinacea combined with 5% material with values of 22.15%, 22.05%, and 12.47%, respectively. Festuca arundinacea had the most potent ability to absorb and tolerate composite PTEs, and the co-remediation process could remarkably improve soil enzyme environment and microbial community diversity. The distribution of PTEs in plant subcellular showed that the accumulation of Zn, Cd, and As in the cell wall of Festuca arundinacea root was significantly increased by adding 2% materials. The concentrations of Zn, Cd, and As in the cell wall were 4486.25, 33.59, and 124.15 mg/kg, respectively. The combination of 2% material and Festuca arundinacea could effectively remove PTEs in soil and enhance the detoxification ability of the plant, thus effectively improving the soil environment and remediating PTEs pollution. This study provided insights into the remediation of PTE-contaminated soil in mining area by combining materials and plants.

Relationships Between the Microbial Composition and the Geochemistry and Mineralogy of the Cobalt-Bearing Legacy Mine Tailings in Northeastern Ontario

Mine tailings host dynamic biogeochemical processes that can mobilize a range of elements from the host material and release them into the environment through acidic, neutral, or alkaline mine drainage. Here we use a combination of mineralogical, geochemical, and microbiological techniques that provide a better understanding of biogeochemical processes within the surficial layers of neutral cobalt and arsenic-rich tailings material at Cobalt, ON, Canada. Tailings material within 30-cm depth profiles from three tailings sites (sites A, B, and C) were characterized for their mineralogical, chemical and microbial community compositions. The tailings material at all sites contains (sulf)arsenides (safflorite, arsenopyrite), and arsenates (erythrite and annabergite). Site A contained a higher and lower amount of (sulf)arsenides and arsenates than site B, respectively. Contrary to site A and B, site C depicted a distinct zoning with (sulf)arsenides found in the deeper reduced zone, and arsenates occurring in the shallow oxidized zone. Variations in the abundance of Co+As+Sb+Zn (Co#), Fe (Fe#), total S (S#), and average valence of As indicated differences in the mineralogical composition of the tailings material. For example, material with a high Co#, lo Fe# and high average valence of As commonly have a higher proportion of secondary arsenate to primary (sulf)arsenide minerals. Microbial community profiling indicated that the Cobalt tailings are primarily composed of Actinobacteria and Proteobacteria, and known N, S, Fe, methane, and possible As-cycling bacteria. The tailings from sites B and C had a larger abundance of Fe and S-cycling bacteria (e.g., Sulfurifustis and Thiobacillus), which are more abundant at greater depths, whereas the tailings of site A had a higher proportion of potential As-cycling and -resistant genera (e.g., Methylocystis and Sphingomonas). A multi-variate statistical analysis showed that (1) distinct site-specific groupings occur for the Co # vs. Fe #, Co# vs. S#'s and for the microbial community structure and (2) microbial communities are statistically highly correlated to depth, S#, Fe#, pH and the average valence of As. The variation in As valence correlated well with the abundance of N, S, Fe, and methane-cycling bacteria. The results of this study provide insights into the complex interplay between minerals containing the critical element cobalt, arsenic, and microbial community structure in the Cobalt Mining Camp tailings.

Soil aggregate-associated mercury (Hg) and organic carbon distribution and microbial community characteristics under typical farmland-use types

In order to get insight into the distribution characteristics of mercury (Hg) and organic carbon in soil aggregates, and the diversity and composition of soil microbial community under different farmland-use types (soil form three adjacent cultivation systems, i.e., corn, vegetable, and rice fields, named as CFS, VFS, and RFS), a field investigation close to Wanshan Hg mining area was conducted. Results indicated that soil total Hg (0-20 cm) presented in decreasing order of RFS (5.27 mg kg^-1) > VFS (4.32 mg kg^-1) > CFS (2.21 mg kg^-1), implying soils from rice field with higher ability of Hg accumulation. Soil aggregate-associated Hg and organic carbon enriched with the decrease of particle size under all farmland-use types, with the maximum at microaggregates (<0.053 mm). Due to the mass ratio of soil aggregates fraction, soil aggregate-associated Hg and organic carbon mainly distributed in >2 mm particles for RFS, whereas 0.25-2 mm particles for CFS and VFS. Furthermore, 16S rRNA results revealed the obvious differences in RFS and dry land soils (CFS and VFS), such as the observed species and unique OUTs, Shannon index, relative abundance at phylum and genus, which implied the diversity and composition of soil microbial community were greatly affected by farmland-use types. Spearman correlation and RDA results suggested farmland-use types, pH and total Hg were main drives for differences in soil microbial community. These findings provide evidence that farmland-use type is an important factor that affects soil total Hg accumulation, soil aggregate-associated Hg and organic carbon distribution, as well as the indigenous microbial community profiles.

The evaluation of long term performance of microbial fuel cell based Pb toxicity shock sensor

Microbial fuel cell (MFC) sensor exhibits attractive prospects for online monitoring of water toxicity as an early warning device. However, the accumulation of dead cells in anode biofilm might decrease the sensing sensitivity of MFC during long term operation. In addition, with repeated exposure to toxins, the microbial community of anode biofilm would also adjust to build up higher endurance to environmental toxicity. In this study, the long term sensing sensitivity of MFC sensor and the microbial community changes were characterized with Pb²⁺ as the target toxin. The results show that newly formed biofilm with higher live/dead cell ratio exhibited higher sensitivity than mature biofilm. Modification of anodic biofilm via high current stimulation was applied to increase the ratio of live cells, which led to enhanced sensing sensitivity of MFC with mature anode biofilm. However, the enhancement was relatively limited for biofilm that was previously exposed to repeated Pb²⁺ shocks. Microbial community analysis revealed that the proportions of microbial species possessing higher environmental robustness, such as Hyphomicrobiaceae and Cloacibacillus, significantly increased in the anode biofilm after long term repeated Pb²⁺ shocks.

Soilless revegetation: An efficient means of improving physicochemical properties and reshaping microbial communities of high-salty gold mine tailings

Soilless revegetation is a cost-effective and eco-friendly method for the ecological restoration of gold mine tailings. However, due to gold mine tailings are high-salty, alkaline and low-nutrient, little research has been done on soilless revegetation of gold mine tailings. The aim of study was to apply soilless revegetation to gold mine tailings, and investigate the changes of physicochemical properties and microbial communities of tailings after soilless revegetation. Six selected herbaceous plants (Melilotus officinalis, Xanthium sibiricum, Festuca elata, Zoysia japonica, Amaranthus tricolor L., Artemisia desertorum) grew well on the bare tailings, and their heights reached as high as 16.28 cm after 90 days. After soilless revegetation, tailings salinity dramatically dropped from 547.15 to 129.24 μS cm^-1, and pH went down from 8.68 to 7.59 at most. The content of available phosphorus (AP), available nitrogen (AN) and organic matter (OM) in tailings gradually improved, especially the content of AP and OM increased 53.36% and 52.58%, respectively. Furthermore, microbial metabolic activity and diversity in tailings obviously increased 70.33-264.70% and 1.64-13.97% respectively. The relative abundance of potential plant growth-promoting bacteria increased 1.40-3.05%, while the relative abundance of opportunistic pathogens and halophilic bacteria decreased 10.58-17.03% and 2.98-6.52% respectively. Such variations of microbial communities were beneficial for tailings restoration. This study provided insight into soilless revegetation and its impact on tailings microorganisms, which could be a new strategy for ecological restoration of gold mine tailings.

Deciphering the toxic effects of metals in gold mining area: Microbial community tolerance mechanism and change of antibiotic resistance genes

Mine tailing dumps represent significant threats to ecological environments due to the presence of toxic substances. The present work investigated the relationship among microbial activity, the community, antibiotic resistance genes (ARGs) and trace metals in soil surrounding gold mine tailings. Using microbial metabolic activity and high-throughput sequencing analysis, we found the trace metals Cd and Hg could be main factors influencing the microbial community. According to bacterial co-occurrence pattern analysis, the effects of total cadmium and total mercury on bacterial diversity are potentially mediated by influencing bacteria community in the keystone module II. Additionally, most of metal-resistant bacteria belong to Actinobacteria and Proteobacteria, and the metal tolerance suggested to be linked with various functions including replication, recombination and repair, as well as inorganic ion transport and metabolism based on PICRUSt2 analysis. We also found that metals generated by mining activity may trigger the co-selection of antibiotic resistance in the phyla Actinobacteria and Proteobacteria due to co-resistance or cross resistance. Additionally, PLS-PM analysis revealed that metals could indirectly affect ARGs by influencing bacterial diversity in gold mining areas.

Mercury detoxification by absorption, mercuric ion reductase, and exopolysaccharides: a comprehensive study

Mercury (Hg), the environmental toxicant, is present in the soil, water, and air as it is substantially distributed throughout the environment. Being extremely toxic even at low concentration, its remediation is utterly important. Therefore, it is necessary to detoxify the contaminant within the acceptable limits before threatening the environment. Although various conventional methods are being used, irrespective of high cost, it produces intermediate toxic by-product too. Biological methods are eco-friendly, clean, greener, and safer for the remediation of heavy metals corresponding to the conventional remediation due to their economic and high-tech constraints. Bioremediation is now being used for Hg (II) removal, which involves biosorption and bioaccumulation mechanisms or both, also mercuric ion reductase, exopolysaccharide play significant role in detoxification of mercury by acting a potential instrument for the remediation of heavy metals. In this review paper, we shed light on problems caused by mercury pollution, mercury cycle, and its global scenario and detoxification approaches by biological methods and result found in the literature.

Stabilization process and potential of agro-industrial waste on Pb-Contaminated soil around Pb-Zn mining

Sawdust wastes were used as precursors to prepare adsorbents by combustion and pyrolysis for experimental and mechanism studies and determine the potential of biomass extracted from agro-industrial residues for Pb-polluted soil remediation. Pot experiments were conducted on contaminated soils near Pb-Zn mining with sawdust ash (SA) and sawdust biochar (SB) in different proportions and dosage ratios. Studies have indicated that the application of biomass materials can enhance the adsorption, complexation and precipitation of Pb cations in soil and reduce the mobility of Pb. The concentrations of SPLP-Pb and DTPA-extractable Pb in amended soils were the lowest under 1% 1:2 and 5% 1:1 treatment, respectively. Results of fraction extraction and XANES analysis showed that the materials change the main forms of Pb in soil. Moreover, the binding behavior of Pb with organic matter increases the proportion of Pb (Ac)₂, leading to the transformation of high toxicity Pb-compounds into precipitates and complexes. The remediation methods of 2% 1:2 and 5% 1:2 were better than those of other methods in stabilizing Pb in soil. This study indicated that heat-treated sawdust can be used for Pb-polluted soil remediation, which is a type of environmental remediation measure with considerable ecological potential.

Co-remediation of Pb Contaminated Soils by Heat Modified Sawdust and Festuca arundinacea

This research aimed to explore the potential and mechanism of heat modified sawdust combined with Festuca arundinacea for the remediation of Pb-contaminated soil. We determined Pb concentration and biochemical indices in plants and soils, analyzed microbial communities in soil, and studied Pb distribution in subcellular and tissues. Under co-remediation of 5% material addition and Festuca arundinacea, the concentration of Pb in soil decreased. Pb toxicity of Festuca arundinacea was alleviated by 2% material addition through the promotion of plant growth and reduction of oxidative stress. In addition, soil enzyme activities and microbial community in contaminated soil were promoted by the application of co-remediation. Festuca arundinacea cell wall accumulated a large amount of Pb, and the addition of material promoted the accumulation of Pb in Festuca arundinacea root. The concentration of Pb in the shoot of the plant treated with 2% material was higher than that of the plant treated with 5% material, and the damage of Festuca arundinacea leaves was lower under 2% treatment. The combination of heat modified sawdust and Festuca arundinacea promoted the adsorption of Pb by plants, and protected the growth of plants.

Comparison of Bacterial Community Structure and Diversity in Traditional Gold Mining Waste Disposal Site and Rice Field by Using a Metabarcoding Approach

Traditional small-scale gold mining mostly use mercury to extract the gold from ores. However, mercury contamination in the environment can affect the composition and structure of the bacterial community. The purpose of this study was to determine the effect of mercury contamination on the bacterial community in the traditional gold mining waste disposal site and in the rice field. Mercury analysis was carried out using the CVAFS method. Analysis of bacterial communities and structure was carried out based on the results of metabarcoding of the V3-V4 16S rRNA regions obtained from paired-end Illumina MiSeq reads. The results showed that the sample from the mining waste disposal site had a mercury level of 230 mg/kg, while the sample from the rice field had 3.98 mg/kg. The results showed that there were differences in microbial composition and community structure in both locations. With the total reads of 57,031, the most dominant phylum was Firmicutes in the mining disposal site sample. Meanwhile, with the total reads of 33,080, the sample from rice field was dominated by Planctomycetes. The abundant classes of bacteria in the mining waste disposal site, from the highest were Bacilli, Gammaproteobacteria and Planctomycetia, while the sample from the rice field was dominated by the Planctomycetia and Acidobacteria subdivision 6. The families that dominated the sample in disposal site were Bacillaceae and Aeromonadaceae, while the sample from the rice field was dominated by Gemmataceae. The abundant genera in both locations were Bacillus and Gemmata. This study concluded that the high level of mercury in the soil reduced the richness and diversity of bacterial phyla and lower taxa. There was also a shift in the dominance of phyla and lower taxa in both locations. This study provides an understanding of the microbial community structure in the area that is highly contaminated with mercury to open insight into the potential of these bacteria for mercury bioremediation.

Physiological responses and accumulation characteristics of turfgrasses exposed to potentially toxic elements

The tolerance and enrichment of potentially toxic elements (PTEs) in plants are the most important basis of phytoremediation technology for mining area soils. The aim of this research was to study PTEs tolerance, translocation and accumulation differences in three turfgrass species and the biochemical changes of plants and soils. Three turfgrass species were cultured on soils contaminated by single and compound PTEs. Pb, Zn, Cd and As concentrations and biochemical indicators in plant (root and shoot) and soil were determined. Moreover, the microbial communities in rhizosphere soil were analyzed. The studied plants showed strong tolerance and high enrichment ability to Pb, Zn, Cd and As in soil under different PTE concentration gradient stress. Festuca arundinacea had the strongest tolerance to PTEs, whereas Medicago sativa L. had the best tolerance to PTEs. Among all the measured growth or biochemical indicators, the relative growth rate and enzymatic activity of Orychophragmus violaceus were most sensitive to stress. The bioconcentration and translocation factors of Medicago sativa L. for Cd were 1.60 and 1.17, respectively, indicating that it was the most suitable plant for extracting Cd. Compared with other plants, Festuca arundinacea had the most significant effect on soil environment improvement, increasing the soil enzyme activities and microbial community after phytoremediation. This study indicates that Medicago sativa L. can be a potential phytoextraction plant to remove Cd, whereas Festuca arundinacea is more suitable as a cover plant to prevent the dispersion of contaminants in polluted soil.

Nonferrous metal (loid) s mediate bacterial diversity in an abandoned mine tailing impoundment

Migration and transformation of toxic metal (loid) s in tailing sites inevitably lead to ecological disturbances and serious threats to the surroundings. However, the horizontal and vertical distribution of bacterial diversity has not been determined in nonferrous metal (loid) tailing ponds, especially in Guangxi China, where the world's largest and potentially most toxic sources of metal (loid) s are located. Distribution of bacterial communities was stable at horizontal levels. At the surface (0-10 cm), the stability was most attributed to Bacillus and Enterococcus, while bacterial communities at the subsurface (50 cm) were mainly contributed by Nitrospira and Sulfuricella. Variable vertical distribution of bacterial communities has led to the occurrence of specific genera and specific predicted functions (such as transcription regulation factors). Sulfurifustis (a S-oxidizing and inorganic carbon fixing bacteria) genera were specific at the surface, whereas Streptococcus-related genera were found at the surface and subsurface, but were more abundant in the latter depth. Physical-chemical parameters, such as pH, TN, and metal (loid) (As, Cd, Pb, Cu, and Zn) concentrations were the main drivers of bacterial community abundance, diversity, composition, and metabolic functions. These results increase our understanding of the physical-chemical effects on the spatial distribution of bacterial communities and provide useful insight for the bioremediation and site management of nonferrous metal (loid) tailings.