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

Legacy copper/nickel mine tailings potentially harbor novel iron/sulfur cycling microorganisms within highly variable communities

The oxidation of sulfide-bearing mine tailings catalyzed by acidophilic iron and sulfur-oxidizing bacteria releases toxic metals and other contaminants into soil and groundwater as acid mine drainage. Understanding the environmental variables that control the community structure and metabolic activity of microbes indigenous to tailings (especially the abiotic stressors of low pH and high dissolved metal content) is crucial to developing sustainable bioremediation strategies. We determined the microbial community composition along two continuous vertical gradients of Cu/Ni mine tailings at each of two tailings impoundments near Sudbury, Ontario. 16S rRNA amplicon data showed high variability in community diversity and composition between locations, as well as at different depths within each location. A temporal comparison for one tailings location showed low fluctuation in microbial communities across 2 years. Differences in community composition correlated most strongly with pore-water pH, Eh, alkalinity, salinity, and the concentration of several dissolved metals (including iron, but not copper or nickel). The relative abundances of individual genera differed in their degrees of correlation with geochemical factors. Several abundant lineages present at these locations have not previously been associated with mine tailings environments, including novel species predicted to be involved in iron and sulfur cycling.IMPORTANCEMine tailings represent a significant threat to North American freshwater, with legacy tailings areas generating acid mine drainage (AMD) that contaminates rivers, lakes, and aquifers. Microbial activity accelerates AMD formation through oxidative metabolic processes but may also ameliorate acidic tailings by promoting secondary mineral precipitation and immobilizing dissolved metals. Tailings exhibit high geochemical variation within and between mine sites and may harbor many novel extremophiles adapted to high concentrations of toxic metals. Characterizing the unique microbiomes associated with tailing environments is key to identifying consortia that may be used as the foundation for innovative mine-waste bioremediation strategies. We provide an in-depth analysis of microbial diversity at four copper/nickel mine tailings impoundments, describe how communities (and individual lineages) differ based on geochemical gradients, predict organisms involved in AMD transformations, and identify taxonomically novel groups present that have not previously been observed in mine tailings.

Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches

The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.

The efficient applications of native flora for phytorestoration of mine tailings: a pan-global survey

Mine tailings are the discarded materials resulting from mining processes after minerals have been extracted. They consist of leftover mineral fragments, excavated land masses, and disrupted ecosystems. The uncontrolled handling or discharge of tailings from abandoned mine lands (AMLs) poses a threat to the surrounding environment. Numerous untreated mine tailings have been abandoned globally, necessitating immediate reclamation and restoration efforts. The limited feasibility of conventional reclamation methods, such as cost and acceptability, presents challenges in reclaiming tailings around AMLs. This study focuses on phytorestoration as a sustainable method for treating mine tailings. Phytorestoration utilizes existing native plants on the mine sites while applying advanced principles of environmental biotechnology. These approaches can remediate toxic elements and simultaneously improve soil quality. The current study provides a global overview of phytorestoration methods, emphasizing the specifics of mine tailings and the research on native plant species to enhance restoration ecosystem services.

Role of indigenous microbial communities in the mobilization of potentially toxic elements and rare-earth elements from alkaline mine waste

This study aims to evaluate the role of indigenous microorganisms in the mobilization of potentially toxic elements (PTE) and rare-earth elements (REE), the influence of the bioavailability of carbon sources that might boost microbial leaching, and the generation of neutral/alkaline mine drainage from alkaline tailings. These tailings, with significant concentrations of total organic carbon (TOC), were mainly colonized by bacteria belonging to the genera Sphingomonas, Novosphingobium and Solirubrobacter, and fungi of the genera Alternaria, Sarocladium and Aspergillus. Functionality analysis suggests the capability of these microorganisms to leach PTE and REE. Bio-/leaching tests confirmed the generation of neutral mine drainage, the influence of organic substrate, and the leaching of higher concentrations of PTE and REE due to the production of organic acids and siderophores by indigenous microorganisms. In addition, this study offers some insights into a sustainable alternative for reprocessing PMC alkaline tailings to recover REE.

Bacterial tolerance and detoxification of cyanide, arsenic and heavy metals: Holistic approaches applied to bioremediation of industrial complex wastes

Cyanide is a highly toxic compound that is found in wastewaters generated from different industrial activities, such as mining or jewellery. These residues usually contain high concentrations of other toxic pollutants like arsenic and heavy metals that may form different complexes with cyanide. To develop bioremediation strategies, it is necessary to know the metabolic processes involved in the tolerance and detoxification of these pollutants, but most of the current studies are focused on the characterization of the microbial responses to each one of these environmental hazards individually, and the effect of co-contaminated wastes on microbial metabolism has been hardly addressed. This work summarizes the main strategies developed by bacteria to alleviate the effects of cyanide, arsenic and heavy metals, analysing interactions among these toxic chemicals. Additionally, it is discussed the role of systems biology and synthetic biology as tools for the development of bioremediation strategies of complex industrial wastes and co-contaminated sites, emphasizing the importance and progress derived from meta-omic studies.

Extremophiles: the species that evolve and survive under hostile conditions

Extremophiles possess unique cellular and molecular mechanisms to assist, tolerate, and sustain their lives in extreme habitats. These habitats are dominated by one or more extreme physical or chemical parameters that shape existing microbial communities and their cellular and genomic features. The diversity of extremophiles reflects a long list of adaptations over millions of years. Growing research on extremophiles has considerably uncovered and increased our understanding of life and its limits on our planet. Many extremophiles have been greatly explored for their application in various industrial processes. In this review, we focused on the characteristics that microorganisms have acquired to optimally thrive in extreme environments. We have discussed cellular and molecular mechanisms involved in stability at respective extreme conditions like thermophiles, psychrophiles, acidophiles, barophiles, etc., which highlight evolutionary aspects and the significance of extremophiles for the benefit of mankind.

Long-term comparison of the performance of biostimulation and phytoextraction in soil contaminated with diesel and heavy metals

The long-term remediation performance under the natural conditions is required to establish the appropriate remediation strategy for contaminated soil. The objective of this study was to compare the long-term remediation efficiency of biostimulation and phytoextraction in contaminated soil containing petroleum hydrocarbons (PHs) and heavy metals. Two types of contaminated soil (soil contaminated with diesel only and co-contaminated with diesel and heavy metals) were prepared. For the biostimulation treatments, the soil was amended with compost, whereas maize, a representative phytoremediation plant, was cultivated for the phytoextraction treatments. There was no significant difference in remediation performance of biostimulation and phytoextraction in the diesel-contaminated soil, in which the maximum total petroleum hydrocarbon (TPH) removability was 94-96% (p < 0.05). However, phytoextraction exhibited the higher removability for TPH and heavy metals than biostimulation in the co-contaminated soil. There was no considerable change in the TPH removal in biostimulation (16-25%), while phytoextraction showed a 75% of TPH removal rate in the co-contaminated soil. Additionally, no significant changes were observed in heavy metals concentration of biostimulation, whereas the removability of heavy metals was 33-63% in phytoextraction. Meanwhile, maize, which is a suitable plant for phytoextraction, showed a translocation factor (translocating efficiency from roots to shoots) value of >1. Correlation analysis revealed that soil properties (pH, water content, and organic content) negatively correlated with pollutants removal. Additionally, the soil bacterial communities were changed over the investigated period, and the types of pollutants exerted a significant influence on the bacterial community dynamics. This study performed a pilot-scale comparison of two types of biological remediation technologies under natural environmental conditions and provided information on changes in the bacterial community structures. This study can be useful for establishing appropriate biological remediation methods to restore soil contaminated with PHs and heavy metals.

Dynamics of vanadium and response of inherent bacterial communities in vanadium-titanium magnetite tailings to beneficiation agents, temperature, and illumination

Vanadium-titanium (V-Ti) magnetite tailings contain toxic metals that could potentially pollute the surrounding environment. However, the impact of beneficiation agents, an integral part of mining activities, on the dynamics of V and the microbial community composition in tailings remains unclear. To fill this knowledge gap, we compared the physicochemical properties and microbial community structure of V-Ti magnetite tailings under different environmental conditions, including illumination, temperature, and residual beneficiation agents (salicylhydroxamic acid, sodium isobutyl xanthate, and benzyl arsonic acid) during a 28-day reaction. The results revealed that beneficiation agents exacerbated the acidification of the tailings and the release of V, among which benzyl arsonic acid had the greatest impact. The concentration of soluble V in the leachate of tailings with benzyl arsonic acid was 6.4 times higher than that with deionized water. Moreover, illumination, high temperatures, and beneficiation agents contributed to the reduction of V in V-containing tailings. High-throughput sequencing revealed that Thiobacillus and Limnohabitans adapted to the tailings environment. Proteobacteria was the most diverse phylum, and the relative abundance was 85.0%-99.1%. Desulfovibrio, Thiobacillus, and Limnohabitans survived in the V-Ti magnetite tailings with residual beneficiation agents. These microorganisms could contribute to the development of bioremediation technologies. The main factors affecting the diversity and composition of bacteria in the tailings were Fe, Mn, V, SO₄^2-, total nitrogen, and pH of the tailings. Illumination inhibited microbial community abundance, while the high temperature (39.5 °C) stimulated microbial community abundance. Overall, this study strengthens the understanding of the geochemical cycling of V in tailings influenced by residual beneficiation agents and the application of inherent microbial techniques in the remediation of tailing-affected environments.

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.

Proteomic Analysis of Arsenic Resistance during Cyanide Assimilation by Pseudomonas pseudoalcaligenes CECT 5344

Wastewater from mining and other industries usually contains arsenic and cyanide, two highly toxic pollutants, thereby creating the need to develop bioremediation strategies. Here, molecular mechanisms triggered by the simultaneous presence of cyanide and arsenite were analyzed by quantitative proteomics, complemented with qRT-PCR analysis and determination of analytes in the cyanide-assimilating bacterium Pseudomonas pseudoalcaligenes CECT 5344. Several proteins encoded by two ars gene clusters and other Ars-related proteins were up-regulated by arsenite, even during cyanide assimilation. Although some proteins encoded by the cio gene cluster responsible for cyanide-insensitive respiration decreased in the presence of arsenite, the nitrilase NitC required for cyanide assimilation was unaffected, thus allowing bacterial growth with cyanide and arsenic. Two complementary As-resistance mechanisms were developed in this bacterium, the extrusion of As(III) and its extracellular sequestration in biofilm, whose synthesis increased in the presence of arsenite, and the formation of organoarsenicals such as arseno-phosphoglycerate and methyl-As. Tetrahydrofolate metabolism was also stimulated by arsenite. In addition, the ArsH2 protein increased in the presence of arsenite or cyanide, suggesting its role in the protection from oxidative stress caused by both toxics. These results could be useful for the development of bioremediation strategies for industrial wastes co-contaminated with cyanide and arsenic.

Stability of Aquatic Nitrogen Cycle Under Dramatic Changes of Water and Sediment Inflows to the Three Gorges Reservoir

Stability of nitrogen cycle is a key indicator to aquatic health. In recent years, water and sediment inflows to the Three Gorges Reservoir (TGR) have changed significantly. To reveal the effects of such dramatic hydrological changes on aquatic nitrogen cycle, this paper at first analyzed the changing trends of water and suspended sediment discharges of TGR based on dynamic harmonic regression, and found that the intra-year distribution of water flow was significantly homogenized between flood and dry seasons, with the seasonal variations narrowed by 43.5%-69.9% during 2007-2016, while sediment concentration sharply dropped (the non-periodic term decreased by 1.48%-2.07%/month). Modified with the effects of sediment concentration variations on nitrification/denitrification rates, the proposed numerical model surprisingly showed that ammonia nitrogen and total nitrogen concentrations in TGR were insensitive to either water flow homogenization or sediment reduction, implying relative stability of microbial community related to nitrogen cycle, which is a positive sign for aquatic health. However, N₂ emission varied more violently. The variation range of nitrogen gas (N₂) emitted from TGR enlarged by 30% with the homogenization of water inflow from 2010 to 2016, while the annual total N₂ emission decreased by 7% due to the reduction of sediment concentration, indicating quick response and strong adaption of the microbial N₂ producing process to the environmental changes of TGR, which is beneficial for maintaining ecological functions related to nitrogen cycling. This work helps understanding nitrogen cycle of reservoirs experiencing dramatic changes in water and sediment inflows.

Evolution of Sulfidic Legacy Mine Tailings: A Review of the Wheal Maid Site, UK

Historic tailings dams and their associated mine waste can pose a significant risk to human and environmental health. The Wheal Maid mine site, Cornwall, UK, serves as an example of the temporal evolution of a tailings storage facility after mining has ceased and the acid-generating waste subjected to surficial processes. This paper discusses its designation as a contaminated land site and reviews our current understanding of the geochemistry, mineralogy, and microbiology of the Wheal Maid tailings, from both peer-reviewed journal articles and unpublished literature. We also present new data on waste characterisation and detailed mineral chemistry and data from laboratory oxidation experiments. Particularly of interest at Wheal Maid is the presence of pyrite-bearing “Grey Tailings”, which, under typical environmental conditions at the Earth’s surface, would be expected to have undergone oxidation and subsequently formed acidic and metalliferous mine drainage (AMD). The results identified a number of mechanisms that could explain the lack of pyrite oxidation in the Grey Tailings, including a lack of nutrients inhibiting microbial Fe(II) oxidation, passivation of pyrite mineral surfaces with tailings processing chemicals, and an abundance of euhedral pyrite grains. Such research areas need further scrutiny in order to inform the design of future tailings facilities and associated AMD management protocols.

Multiple heavy metal distribution and microbial community characteristics of vanadium-titanium magnetite tailing profiles under different management modes

Vanadium-titanium (V-Ti) magnetite tailings have caused great concern due to their safety hazards and environmental risks. However, the microbial community structure and the key geochemical factors of V-Ti magnetite tailing profiles under different management modes remain unclear. Therefore, we investigated the heavy metal distribution and the microbial community structure of the soils and tailings at varied depths of V-Ti magnetite tailing profiles with and without soil coverage. The results indicated that the topsoil covering measures retarded the acidification of tailings during stockpiling. However, As, Mn, and V in tailings have the ability to migrate to the overlying soil. Based on 16S rRNA gene amplicon sequencing, Proteobacteria was the dominant genus in the topsoil-covered tailings, whereas the most abundant genus in the exposed tailings was Betaproteobacteria. Furthermore, Rhodobacter, Hydrogenophaga, Novosphingobium, and Geobacter enriched in tailings may potentially contribute to V(V) biotransformation and the development of mine bioreremediation technologies. RDA and Spearman correlation analysis showed that pH, EC, Cd, Mn, Pb, and V were the main influencing factors regulating microbial community composition. Overall, this study provides insights for evaluating the soil covering management mode and the engineering applications of microbial technologies to manage V-Ti magnetite tailings.

Thermoacidophilic Bioleaching of Industrial Metallic Steel Waste Product

The continuous deposition of hazardous metalliferous wastes derived from industrial steelmaking processes will lead to space shortages while valuable raw metals are being depleted. Currently, these landfilled waste products pose a rich resource for microbial thermoacidophilic bioleaching processes. Six thermoacidophilic archaea (Sulfolobus metallicus, Sulfolobus acidocaldarius, Metallosphaera hakonensis, Metallosphaera sedula, Acidianus brierleyi, and Acidianus manzaensis) were cultivated on metal waste product derived from a steelmaking process to assess microbial proliferation and bioleaching potential. While all six strains were capable of growth and bioleaching of different elements, A. manzaensis outperformed other strains and its bioleaching potential was further studied in detail. The ability of A. manzaensis cells to break down and solubilize the mineral matrix of the metal waste product was observed via scanning and transmission electron microscopy. Refinement of bioleaching operation parameters shows that changes in pH influence the solubilization of certain elements, which might be considered for element-specific solubilization processes. Slight temperature shifts did not influence the release of metals from the metal waste product, but an increase in dust load in the bioreactors leads to increased element solubilization. The formation of gypsum crystals in course of A. manzaensis cultivation on dust was observed and clarified using single-crystal X-ray diffraction analysis. The results obtained from this study highlight the importance of thermoacidophilic archaea for future small-scale as well as large-scale bioleaching operations and metal recycling processes in regard to circular economies and waste management. A thorough understanding of the bioleaching performance of thermoacidophilic archaea facilitates further environmental biotechnological advancements.