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Black shale is a type of sedimentary rocks that are enriched in rare earth elements (REEs). It is of both economic importance and environmental significance to understand REE mobility during black shale weathering. The present study approaches to this by analysing REEs in acid rock drainage (ARD) from black shale weathering system, fresh and weathered black shales, soils derived from black shales, and sequential extractants from black shales at Dongping town in Hunan province (China). Results showed that REEs had variable high concentrations in ARD as shown by total REE + Y (∑REY) concentrations from 162 to 4074 (µg/L). REEs in ARD displayed hat-shape NASC-normalized patterns with significant enrichments of middle REEs (MREE) relative to light REEs (LREE) and heavy REEs (HREE), and had significant negative Ce (Ce/Ce⁎ = 0.6) and positive Y (Y/Y⁎ = 1.5) anomalies. MREE enrichment in ARD could be evaluated using MREE/MREE⁎ values, which varied from 1.43 to 1.81 with a mean of 1.65, distinctly higher than those of whole rocks (around 1.0). 1 M HCl extraction results suggested that REEs were integratedly mobilized during shale weathering, while six-step extraction studies identified that REEs in ARD resulted from exchangeable and Fe-oxide fractions with MREE and HREE enrichment in shales respectively. MREE in exchangeable and HREE in Fe-oxide fractions were preferentially released during weathering, as illustrated by plots of MREE/MREE⁎ against HREE/LREE ratios of ARD and six-step extractants. Therefore, geochemical processes for REE mobility during black shale weathering included integrated mobilization and preferential release. Integrated REE mobilization resulted from the dissolution of REE-bearing minerals and oxidation of sulfides. Preferential REE release resulted from acid fluids produced by sulfide oxidation during weathering. Thus, a new model was proposed for interpreting geochemical processes of REE mobility during black shale weathering, and for understanding REE distribution in ARD from natural and anthropogenic systems.

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Green liquor dregs (GLD) is an alkaline by-product from the pulp and paper industry with a pH between 10 and 14. Today most of the produced GLD in Sweden is landfilled. As a fine-grained alkaline material, it might be possible to use it for acid-generating mining waste remediation. To increase the utilization, quality characteristics and environmental performance need to be determined. In this study samples were collected 5 times from 16 mills during a period of 2.5 years, and were characterized by analyzing dry matter content, loss on ignition (LOI) 550 °C and LOI 950 °C, elemental analysis, pH, electrical conductivity, and calorific value. The results were then evaluated using multivariate statistics (PCA) as well as being compared to other studies and Swedish till. The results show that even if GLD is heterogenous (both within a mill and between different mills) trends can be seen for samples from most mills. When samples do stand out, it is predominately related to the same four mills. Most of the studied parameters showed characteristics favorable for use as a remediant; however, TOC, sulfur, and some of the elements require further study. In general, this study concludes that GLD can be a viable option for the remediation of small orphaned sulfidic mining sites and thus worthy of further studies on the interaction between GLD and acidic mining waste.Overall, GLD can be a good alternative for cost-effective remediation of smaller orphaned mining sites. It is readily available in large quantities, has the qualities needed for remediation of many orphaned acidic mining sites, and can often be locally sourced near the mining site. The use of GLD for mining site remediation is likely also a more sustainable method compared to traditional remediation methods.

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The accelerated loss of glacial cover in the Cordillera Blanca in Áncash, Peru, exposes the underlying rocks with high concentrations of sulfides from the Chicama Formation to oxidation and leaching processes, generating acid rock drainage (ARD) in glacial and periglacial areas. These are transported by surface runoff, contaminating the surface water with high concentrations of metals and sulfates, as well as increasing the acidity, which poses a risk to human health and the ecosystem. Therefore, the risk indices for human health due to metal contamination were evaluated at 19 surface water sampling points distributed in the Río Negro sub-basin. Hydrochemical analyses revealed average metal concentrations in the following order: Fe (28.597 mg/L), Al (3.832 mg/L), Mn (1.085 mg/L), Zn (0.234 mg/L), Ni (0.085 mg/L), Co (0.053 mg/L), Li (0.036 mg/L), Cu (0.005 mg/L), and Pb (0.002 mg/L). The risk was determined by calculating the Heavy Metal Pollution Index (HPI) and the Hazard Index (HI). The average HPI value was 360.959, indicating a high level of contamination (HPI ≥ 150). The human health risk assessment indicated that adverse effects caused by iron, lithium, and cobalt in children and adults should be considered. Through the use of Pearson correlation analysis, principal component analysis, and cluster analysis, it was identified that SO42-, Fe, S, Al, Co, Mn, Ni, Zn, and Li originate from natural sources, associated with the generation of ARD in glacial and periglacial areas.

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Streams impacted by historic mining activity are characterized by acidic pH, unique microbial communities, and abundant metal-oxide precipitation, all of which can influence groundwater-surface water exchange. We investigate how metal-oxide precipitates and hyporheic mixing mediate the composition of microbial communities in two streams receiving acid-rock and mine drainage near Silverton, Colorado, USA. A large, neutral pH hyporheic zone facilitated the precipitation of metal particles/colloids in hyporheic porewaters. A small, low pH hyporheic zone, limited by the presence of a low-permeability, iron-oxyhydroxide layer known as ferricrete, led to the formation of steep geochemical gradients and high dissolved-metal concentrations. To determine how these two hyporheic systems influence microbiome composition, we installed well clusters and deployed in situ microcosms in each stream to sample porewaters and sediments for 16S rRNA gene sequencing. Results indicated that distinct hydrogeochemical conditions were present above and below the ferricrete in the low pH system. A positive feedback loop may be present in the low pH stream where microbially mediated precipitation of iron-oxides contributes to additional clogging of hyporheic pore spaces, separating abundant, iron-oxidizing bacteria (Gallionella spp.) above the ferricrete from rare, low-abundance bacteria below the ferricrete. Metal precipitates and colloids that formed in the neutral pH hyporheic zone were associated with a more diverse phylogenetic community of nonmotile, nutrient-cycling bacteria that may be transported through hyporheic pore spaces. In summary, biogeochemical conditions influence, and are influenced by, hyporheic mixing, which mediates the distribution of micro-organisms and, thus, the cycling of metals in streams receiving acid-rock and mine drainage. IMPORTANCE: In streams receiving acid-rock and mine drainage, the abundant precipitation of iron minerals can alter how groundwater and surface water mix along streams (in what is known as the "hyporheic zone") and may shape the distribution of microbial communities. The findings presented here suggest that neutral pH streams with large, well-mixed hyporheic zones may harbor and transport diverse microorganisms attached to particles/colloids through hyporheic pore spaces. In acidic streams where metal oxides clog pore spaces and limit hyporheic exchange, iron-oxidizing bacteria may dominate and phylogenetic diversity becomes low. The abundance of iron-oxidizing bacteria in acid mine drainage streams has the potential to contribute to additional clogging of hyporheic pore spaces and the accumulation of toxic metals in the hyporheic zone. This research highlights the dynamic interplay between hydrology, geochemistry, and microbiology at the groundwater-surface water interface of acid mine drainage streams.

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There is a need to define mine tailings in a clear, precise, multidisciplinary, transdisciplinary, and holistic manner, considering not only geotechnical and hydraulic concepts but also integrating environmental and geochemical aspects with implications for the sustainability of mining. This article corresponds to an independent study that answers questions concerning the definition of mine tailings and the socio-environmental risks linked with mine tailings chemical composition by examining the practical experience of industrial-scale copper and gold mining projects in Chile and Peru. Definitions of concepts and analysis of key aspects in the responsible management of mine tailings, such as characterization of metallic-metalloid components, non-metallic components, metallurgical reagents, and risk identification, among others, are presented. Implications of potential environmental impacts from the generation of acid rock drainage (ARD) in mine tailings are discussed. Finally, the article concludes that mine tailings are potentially toxic to both communities and the environment, and cannot be considered as inert and innocuous materials; thus, mine tailings require safe, controlled, and responsible management with the application of the most high management standards, use of the best available technologies (BATs), use of best applicable practices (BAPs), and implementation of the best environmental practices (BEPs) to avoid risk and potential socio-environmental impact due to accidents or failure of tailings storage facilities (TSFs).

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Sulphate reducing bacteria (SRB) offer promise for the treatment of mine waste due to their effectiveness removing toxic heavy metals as highly insoluble metal sulphides and their ability to generate alkalinity. The main objective of this study was to develop a treatment composed of a sulphate-reducing bioreactor with a limestone precolumn for the removal of Cu(II) from a synthetic ARD. The purpose of the limestone column was to increase the pH values and decrease the level of Cu in the effluent to prevent SRB inhibition. The system was fed with a pH-2.7 synthetic ARD containing Cu(II) (10-40 mg/L), sulphate (2000 mg/L) and acetate (2.5 g COD/L) for 150 days. Copper removal efficiencies in the two-stage system were very high (95-99%), with a final concentration of 0.53 mg/L Cu, and almost complete removal occurred in the limestone precolumn. In the same manner, the acidity of the synthetic ARD was effectively reduced in the limestone precolumn to 7.3 and the pH was raised in the bioreactor (7.3-8.0). COD consumption by methanogens was predominant from day 0-118, but SRB dominated at the end of the experiment (day 150) when the average COD removal and sulphide production were 74.8% and 61.7%, respectively. Study of the microbial taxonomic composition in the bioreactor revealed that Methanosarcina and Methanosaeta were the most prevalent methanogens while the genera Desulfotomaculum and Syntrophobacter were the dominant SRB. Among the SRB identified Desulfotomaculum intricatum (99% identity) and Desulfotomaculum acetoxidans (96%) were the most abundant sequences of bacteria capable of using acetate.

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Industrial processes typically produce large wastewater volumes, which, if left untreated, greatly affect receiving ecosystems. However, wastewater treatment can be costly and energy-intensive, with the developing world particularly struggling with wastewater management. As such, simple and cost-effective solutions are urgently required with the passive (no energy or reagents) co-treatment of different wastewater matrices holding great promise. Here, wastewater from a phosphorus recovery system (chemical precipitation) was co-treated with acid mine drainage (AMD). Specifically, phosphorus-rich municipal wastewater was treated with hydrated lime, as to synthesize a wastewater-derived phosphorus product, i.e., calcium phosphate (Ca3(PO4)2), also producing a phosphorous-depleted alkaline effluent. The feasibility of valorising this effluent is examined here by using it for the passive co-treatment of real AMD. Different liquid-to-liquid (v/v) ratios were considered, with the optimum ratio (AMD to phosphate-depleted wastewater) being 1:9. The pH of the co-treated effluent was adjusted to 8.4 (from an initial value of 11.5 in the phosphorus-depleted wastewater and 2.2 in AMD), while metals (∼100% reduction of Fe, Mn, Ni, Cu, Pb, ≥99.5 for Al, Zn, and Mg, 80% for Cr, and 75% for As) and sulphate (89.26% reduction) contained in AMD were greatly removed. This was also the case for the remaining orthophosphate that was contained in the phosphorus-depleted wastewater (93.75% reduction). The electrical conductivity was also reduced in both the AMD (88.75%) and the phosphorus-depleted wastewater (69.21%), suggesting the removal of contaminants from both matrices. Results were underpinned by state-of-the-art analytical techniques, including FE-SEM/FIB/EDX, FTIR, and XRD, along with geochemical modelling (PHREEQC). Contaminants were removed through complexation, (co)adsorption, crystallization, and (co)precipitation. Overall, results suggest that the co-treatment of these wastewater matrices is feasible and could be directly scaled up (e.g., using waste stabilization ponds), while opportunities for the beneficiation of the produced sludge and for water reclamation (e.g., through membrane filtration) could also arise, further promoting the sustainably of this passive co-treatment method.

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Previous studies have addressed the occurrence of Acid Rock Drainage (ARD) affecting La Silva stream due to the generation of large dumps of Middle Ordovician black shales during the construction of a highway close to El Bierzo (León, Spain). This ARD was characterized by sulphated acid waters with high concentration of heavy metals and anomalies in dissolved thorium (Th) and uranium (U). In the present study, we analyse in depth black shales and water, streambed sediments and precipitates of La Silva stream and its tributaries using different petrographic, mineralogical and geochemical approaches. Black shales, with average Th and U contents of 20 and 3 µg/g respectively contain disseminated detritic micro-grains of high weathering-resistant minerals, such as monazite and xenotime, that present smaller amounts of yttrium and rare earth elements (REY) and other elements as Ca, U, Th, Si and F. Results of the affected waters by ARD show an enrichment in dissolved Th, U and REY of several orders of magnitude with respect to natural waters. Sampled precipitates were mainly schwertmannite (Fe8O8(OH)8-2x (SO4)xO16•nH2O) and goethite (α-Fe3+O(OH)) that showed an enrichment of Th (up to 798 µg/g) and REY, due to the presence of dissolved anionic species (e.g. [Formula: see text] , [Formula: see text] ) that enables their adsorption. Furthermore, these black shales show a clear enrichment in REE (Rare Earth Elements) with respect to NASC (North American Shales Composite) normalized REE patterns. Likewise, normalized REE patterns of stream waters and precipitates clearly show convex curvatures in middle-REE (MREE) with respect to light- and something less than heavy-REE, indicating the trend towards MREE enrichment. These findings are essential to evaluate the impact of ARD of Mid Ordovician shales in the surrounding environment, and to start considering these site as potential source of REE and critical raw materials, activating a Circular Economy.

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Biological sulfate reduction (BSR) is an attractive approach for the bioremediation of sulfate-rich wastewater streams. Many sulfate-reducing microorganisms (SRM), which facilitate this process, have been well-studied in pure culture. However, the role of individual members of microbial communities within BSR bioreactors remains understudied. In this study we investigated the performance of two up-flow anaerobic packed bed reactors (UAPBRs) supplemented primarily with acetate and with lactate, respectively, during a hydraulic retention time (HRT) study set up to remediate sulfate-rich synthetic wastewater over the course of 1,000 + days. Plug-flow hydrodynamics led to a continuum of changing volumetric sulfate reduction rates (VSRRs), available electron donors, degrees of biomass retention and compositions of microbial communities throughout these reactors. Microbial communities throughout the successive zones of the reactors were resolved using 16S rRNA gene amplicon sequencing which allowed the association of features of performance with discrete microorganisms. The acetate UAPBR achieved a maximum VSRR of 23.2 mg.L-1. h-1 at a one-day HRT and a maximum sulfate conversion of the 1 g/L sulfate of 96% at a four-day HRT. The sulfate reduction reactions in this reactor could be described with a reaction order of 2.9, an important observation for optimisation and future scale-up. The lactate UAPBR achieved a 96% sulfate conversion at one-day HRT, corresponding with a VSRR of 40.1 mg.L-1. h-1. Lactate was supplied in this reactor at relatively low concentrations necessitating the subsequent use of propionate and acetate, by-products of lactate fermentation with acetate also a by-product of incomplete lactate oxidation, to achieve competitive performance. The consumption of these electron donors could be associated with specific SRM localised within biofilms of discrete zones. The sulfate reduction rates in the lactate UAPBR could be modelled as first-order reactions, indicating effective rates were conferred by these propionate- and acetate-oxidising SRM. Our results demonstrate how acetate, a low-cost substrate, can be used effectively despite low associated SRM growth rates, and that lactate, a more expensive substrate, can be used sparingly to achieve high VSRR and sulfate conversions. We further identified the preferred environment of additional microorganisms to inform how these microorganisms could be enriched or diminished in BSR reactors.

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Protozoa play important roles in microbial communities, regulating populations via predation and contributing to nutrient cycling. While amoebae have been identified in acid rock drainage (ARD) systems, our understanding of their symbioses in these extreme environments is limited. Here, we report the first isolation of the amoeba Stemonitis from an ARD environment as well as the genome sequence and annotation of an associated bacterium, Dyella terrae strain Ely Copper Mine, from Ely Brook at the Ely Copper Mine Superfund site in Vershire, Vermont, United States. Fluorescent in situ hybridization analysis showed this bacterium colonizing cells of Stemonitis sp. in addition to being outside of amoebal cells. This amoeba-resistant bacterium is Gram-negative with a genome size of 5.36 Mbp and GC content of 62.5%. The genome of the D. terrae strain Ely Copper Mine encodes de novo biosynthetic pathways for amino acids, carbohydrates, nucleic acids, and lipids. Genes involved in nitrate (1) and sulfate (7) reduction, metal (229) and antibiotic resistance (37), and secondary metabolite production (6) were identified. Notably, 26 hydrolases were identified by RAST as well as other biomass degradation genes, suggesting roles in carbon and energy cycling within the microbial community. The genome also contains type IV secretion system genes involved in amoebae resistance, revealing how this bacterium likely survives predation from Stemonitis sp. This genome analysis and the association of D. terrae strain Ely Copper Mine with Stemonitis sp. provide insight into the functional roles of amoebae and bacteria within ARD environments.

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Biological treatment using sulfate-reducing bacteria (SRB) is a promising approach to remediate acid rock drainage (ARD). Our purpose was to assess the performance of a sequential system consisting of a limestone bed filter followed by a sulfate-reducing bioreactor treating synthetic ARD for 375 days and to evaluate changes in microbial composition. The treatment system was effective in increasing the pH of the ARD from 2.7 to 7.5 and removed total Cu(II) and Zn(II) concentrations by up to 99.8% and 99.9%, respectively. The presence of sulfate in ARD promoted sulfidogenesis and changed the diversity and structure of the microbial communities. Methansarcina spp. was the most abundant amplicon sequence variant (ASV); however, methane production was not detected. Biodiversity indexes decreased over time with the bioreactor operation, whereas SRB abundance remained stable. Desulfobacteraceae, Desulfocurvus, Desulfobulbaceae and Desulfovibrio became more abundant, while Desulfuromonadales, Desulfotomaculum and Desulfobacca decreased. Geobacter and Syntrophobacter were enriched with bioreactor operation time. At the beginning, ASVs with relative abundance <2% represented 65% of the microbial community and 21% at the end of the study period. Thus, the results show that the microbial community gradually lost diversity while the treatment system was highly efficient in remediating ARD.

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Although the environmental significance of acid rock drainage (ARD) generated from mining wastes is well known, selecting the appropriate ARD management strategy can prove a complicated task. Chemical methods are favored for initial mine waste characterization but using these exclusively can overlook key factors, e.g., mineralogy, which controls the formation and elution of ARD. This paper first presents an ARD waste rock classification developed on Triple Characterization Criteria (TCC) which considers three input parameters: neutralizing potential ratio (NPR), net acid generation (NAG pH), and modal mineralogy weathering index (MMWI) values. Second, a new mixed-integer programming (MIP) model to guide waste dump construction with the dual aim of preventing ARD across the life-of-mine (LOM) and reducing waste rock re-handling, is introduced. Last, the spatial distribution of TCC in a planned waste dump is simulated via geo-statistical techniques to evaluate the MIP model. The proposed waste rock classification and dump planning model has been tested at an iron mine. The results of the MIP modeling and simulation of TCC showed the successful prevention of ARD by achieving large values of TCC (NPR ≥2, NAG pH ≥ 4.5, and MMWI ≥4.7) for dump cells, with the planned mine production maintained. The integrated TCC approach introduced in this study is intended to enable mine operators, at the start of the LOM, to effectively forecast ARD from future waste rock. Further, the MIP model will facilitate development of a mine schedule that optimizes the use of the waste materials based on TCC values. If used correctly, the TCC and MIP model have the potential to enable mine operators to reduce their environmental footprint across the entire LOM.

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Acid mine drainage (AMD), a waste product of mining activities containing sulfates, iron and heavy metals, causes severe environmental degradation and pose risks to human health and sustainable development. Areas impacted by AMD are lacking remediation techniques that holistically address the ecologic, social, and economic needs of affected communities, for which phytoremediation is a promising solution. This review article introduces AMD and AMD-impacted environments and critically discusses phytomanagement, phytoprotection, and phytorestoration approaches towards AMD-impacted environments. Continued research and application of such approaches will help optimize resource and revenue-generating potentials, address biodiversity loss and carbon storage concerns of climate change, and promote sustainable agricultural management. With a focus on energy crops, phytomining critical elements, carbon storage, co-cropping, allelopathy, and ecosystem restoration, this review examines phytoremediation research that addresses positive economic and environmental opportunities for AMD-impacted environments.

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The co-management of different wastewater matrices can lead to synergistic effects in terms of pollutants removal. Here, the co-treatment of real municipal wastewater (MWW) and acid mine drainage (AMD) is comprehensively examined. Under the identified optimum co-treatment condition, i.e., 15 min contact time, 1:7 AMD to MWW liquid-to-liquid ratio, and ambient temperature and pH, the metal content of AMD (e.g., Al, Fe, Mn, Zn) was grossly (~95%) reduced along with sulphate (~92%), while MWW's phosphate content was practically removed (≥99%). The PHREEQC geochemical model predicted the formation of (oxy)-hydroxides, (oxy)-hydro-sulphates, metals hydroxides, and other mineral phases in the produced sludge, which were confirmed using state-of-the-art analytical techniques such as FE-SEM-EDS and XRD. The key mechanisms governing pollutants removal include dilution, precipitation, co-precipitation, adsorption, and crystallization. Beneficiation and valorisation of the produced sludge and co-treated effluent could promote resource recovery paradigms in wastewater management. Overall, the co-treatment of AMD and MWW appear to be feasible, yet not practical due to the excessive volume of MWW that is required to attain the desired treatment quality. Future research could focus on chemical addition for the control of the pH and the use of (photo)-Fenton for enhancing treatment efficiency.

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Reactive transport models have proven abilities to simulate the quantity and quality of drainage from mine waste rock. Tracer experiments indicate the presence of fast and slow flow regimes in many heterogeneous waste-rock piles. Although multidomain models have been developed specifically for systems with such distinctive hydrodynamics, there have been limited applications of multidomain reactive transport models to simulate composite drainage chemistries from waste-rock piles to date. This work evaluated the ability of dual-domain multicomponent reactive transport models (DDMRTMs) to reproduce breakthrough curves of conservative (chloride) and reactive (molybdenum) solutes observed at a well-characterized experimental waste-rock pile at the Antamina Mine, Peru. We found that the DDMRTM simulations quantitatively matched eight-year-long records of conservative transport through the waste-rock pile when parameterized mainly with field-measured properties obtained from the site and limited calibration. The DDMRTM model also provided a reasonable match to field observations of the reactive solute. The limited calibrated parameters are physically realistic, corroborating the ability of these multidomain models to reproduce the complex reactive-transport processes governing polluted rock drainage from large-scale waste-rock piles.

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In waste rock piles, the leaching process involved in acid rock drainage is mainly controlled by water flow. This paper (Part 2) investigates the effects of heterogeneities on the water flow patterns by applying probability density functions to hydrogeological properties. In this study, a piecewise constant distribution is proposed to describe the permeability inside waste rock piles, which reflects the effect of both finer and coarser pores. Compared with uniform water flow obtained from traditional homogeneous modeling, various water flow patterns and their pathways inside waste rock piles can be simulated by the proposed model. In addition, the leaching process is also investigated by coupling the calculated water flow with the geochemical reaction based on the water film model proposed in part 1. For demonstration, these models are integrated and applied to the full-scale waste rock pile at Equity Silver mine in British Columbia, Canada. Because the iron loading is highly correlated to the acidity at this site, it is found that the fluctuation of annual lime consumption for neutralization at this site can be well predicted by the integrated model. In addition, the results indicate that waste rock piles with different spatial patterns of permeability distribution, but with the same probability density function, may have different water flow patterns and spatial distributions of iron concentrations inside the pile. However, the total water flow discharge rate and iron loading profiles from the pile are almost the same on the temporal scale.

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In the western USA, one legacy of historic mining is drainage of acidic, metal-rich water generated by exposure to oxygen of sulfide minerals in mine workings, referred to as acid mine drainage (AMD). Streams receiving AMD and natural acid rock drainage (ARD) have a low pH, high dissolved metal concentrations, and extensive streambed oxide deposits. Recently, enhanced ARD generation in the Snake River watershed in the Rocky Mountains has been shown to be associated with warmer summer air temperatures, which has been attributed to expanding weathering fronts that promote oxidation due to earlier drying of shallow soils. In mountain watersheds where complex orogeny disseminated minerals throughout the landscape, weathering processes may also mobilize rare earth elements (REEs). We report that in the Snake River REEs are currently distributed in streams at concentrations ranging from 1 to 100 µg/L. Further, analysis of archived sample indicates that REE increases over time are also associated with increased summer air temperatures. In downstream reaches where the Snake River discharges into a water supply reservoir, colloidal and particulate metal oxides are abundant and sorptive processes may influence REE speciation. We also show that REEs accumulate in benthic invertebrates at concentrations comparable to toxic metals associated with ARD.

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Prediction of drainage quantity and quality is critical to reduce the environmental risks associated with weathering mine waste rock. Reactive transport models can be effective tools to understand and disentangle the processes underlying waste-rock weathering and drainage, but their validity and applicability can be impaired by poor parametrization and the non-uniqueness conundrum. Here, a process-based multicomponent reactive transport model is presented to interpret and quantify the processes affecting drainage quantity and quality from 15 waste- rock experiments from the Antamina mine, Peru. The deployed uniform flow formulation and consistent set of geochemical rate equations could be calibrated almost exclusively with measured bulk waste-rock properties in experiments ranging from 2 kg to 6500 tons in size. The quantitative agreement between simulated dynamics and the observed drainage records, for systems with a variety of rock lithologies and over a wide range of pH, supports the proposed selection of processes. The controls of important physicochemical processes and feedbacks such as secondary mineral precipitation, surface passivation, oxygen limitations, were confirmed through sensitivity analyses. Our work shows that reactive transport models with a consistent formulation and evidence-based parametrization can be used to explain waste-rock drainage dynamics across laboratory to field scales.

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In heap bioleaching and waste-rock dumps, complex microbial communities exist in the flowing and interstitial liquid phases and mineral surface-associated biofilms, often embedded in extracellular polymeric substances (EPS). Microbial activity in the interstitial phase and mineral ore surface facilitates mineral degradation, resulting in either metal recovery or acidic, metal -bearing drainage from sulfidic waste-rock. Determining microbial presence and activity through microorganisms leaving the heap or dump has severe limitations. Hence, increasingly the ore-bed is sampled to quantify and characterise this. Here, methods for cell detachment and quantification, microbial activity measurement on the mineral surface and evaluation of EPS, quantitatively and biochemically, were refined and validated to assess microbial presence, using mineral coated beads in continuous flow-through columns. Number of wash steps required were assessed over increasing colonisation times over 30 days. Microbial cells colonising the mineral surface, pre- and post-washing were visualised by scanning electron microscopy (SEM) and their activity quantified by isothermal microcalorimetry (IMC). Using IMC, detachment and enumeration of detached cells, we demonstrated that 6-8 washes provided a reliable estimation of mineral-associated microorganisms, with less than 10% of cells or microbial activity associated with the surface following treatment. This allowed consolidated refinement of the protocol using traditional detachment method, SEM and IMC to provide correlative data. Extraction of EPS in a complete flow-through system is reported for the first time and the biochemical composition was similar to those reported under batch bioleaching conditions.

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High throughput sequencing data collected from acid rock drainage (ARD) communities can reveal the active taxonomic and functional diversity of these extreme environments, which can be exploited for bioremediation, pharmaceutical, and industrial applications. Here, we report a seasonal comparison of a microbiome and transcriptome in Ely Brook (EB-90M), a confluence of clean water and upstream tributaries that drains the Ely Copper Mine Superfund site in Vershire, VT, USA. Nucleic acids were extracted from EB-90M water and sediment followed by shotgun sequencing using the Illumina NextSeq platform. Approximately 575,933 contigs with a total length of 1.54 Gbp were generated. Contigs of at least a size of 3264 (N50) or greater represented 50% of the sequences and the longest contig was 488,568 bp in length. Using Centrifuge against the NCBI "nt" database 141 phyla, including candidate phyla, were detected. Roughly 380,000 contigs were assembled and ∼1,000,000 DNA and ∼550,000 cDNA sequences were identified and functionally annotated using the Prokka pipeline. Most expressed KEGG-annotated microbial genes were involved in amino acid metabolism and several KEGG pathways were differentially expressed between seasons. Biosynthetic gene clusters involved in secondary metabolism as well as metal- and antibiotic-resistance genes were annotated, some of which were differentially expressed, colocalized, and coexpressed. These data can be used to show how ecological stimuli, such as seasonal variations and metal concentrations, affect the ARD microbiome and select taxa to produce novel natural products. The data reported herein is supporting information for the research article "Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site" by Giddings et al. [1].