Characterization of a bacterial community in an abandoned semiarid lead-zinc mine tailing site

Biochar dose-dependent impacts on soil bacterial and fungal diversity across the globe

Biochar, a widely used material for soil amendment, has been found to offer numerous advantages in improving soil properties and the habitats for soil microorganisms. However, there is still a lack of global perspectives on the influence of various levels of biochar addition on soil microbial diversity and primary components. Thus, in our study, we performed a global meta-analysis of studies to determine how different doses of biochar affect soil total carbon (C), nitrogen (N), pH, alpha- and beta-diversity, and the major phyla of both bacterial and fungal communities. Our results revealed that biochar significantly increased soil pH by 4 %, soil total C and N by 68 % and 22 %, respectively, in which the positive effects increased with biochar doses. Moreover, biochar promoted soil bacterial richness and evenness by 3-8 % at the biochar concentrations of 1-5 % (w/w), while dramatically shifting bacterial beta-diversity at the doses of >2 % (w/w). Specifically, biochar exhibited significantly positive effects on bacterial phyla of Acidobacteria, Bacteroidetes, Gemmatimonadetes, and Proteobacteria, especially Deltaproteobacteria and Gammaproteobacteria, by 4-10 % depending on the concentrations. On the contrary, the bacterial phylum of Verrucomicrobia and fungal phylum of Basidiomycota showed significant negative responses to biochar by -8 % and -24 %, respectively. Therefore, our meta-analysis provides theoretical support for the development of optimized agricultural management practices by emphasizing biochar application dosing.

Actinomycetota bioprospecting from ore-forming environments

Natural products from Actinomycetota have served as inspiration for many clinically relevant therapeutics. Despite early triumphs in natural product discovery, the rate of unearthing new compounds has decreased, necessitating inventive approaches. One promising strategy is to explore environments where survival is challenging. These harsh environments are hypothesized to lead to bacteria developing chemical adaptations (e.g. natural products) to enable their survival. This investigation focuses on ore-forming environments, particularly fluoride mines, which typically have extreme pH, salinity and nutrient scarcity. Herein, we have utilized metagenomics, metabolomics and evolutionary genome mining to dissect the biodiversity and metabolism in these harsh environments. This work has unveiled the promising biosynthetic potential of these bacteria and has demonstrated their ability to produce bioactive secondary metabolites. This research constitutes a pioneering endeavour in bioprospection within fluoride mining regions, providing insights into uncharted microbial ecosystems and their previously unexplored natural products.

Microbial processes with the potential to mobilize As from a circumneutral-pH mixture of flotation and roaster tailings

The Northwest Tailings Containment Area at the inactive Giant Mine (Canada) contains a complex mixture of arsenic-containing substances, including flotation tailings (84.8 wt%; with 0.4 wt% residual S), roaster calcine wastes (14.4 wt% Fe oxides), and arsenic trioxide (0.8 wt%) derived from an electrostatic precipitator as well as As-containing water (21.3 ± 4.1 mg L-1 As) derived from the underground mine workings. In the vadose zone the tailings pore water has a pH of 7.6 and contains elevated metal(loid)s (2.37 ± 5.90 mg L-1 As); mineral oxidizers account for 2.5% of total 16S rRNA reads in solid samples. In the underlying saturated tailings, dissolved Fe and As concentrations increase with depth (up to 72 and 20 mg L-1, respectively), and the mean relative abundance of Fe(III)-reducers is 0.54% of total reads. The potential for As mobilization via both reductive and oxidative (bio)processes should be considered in Giant Mine remediation activities. The current remediation plan includes installation of an engineered cover that incorporates a geosynthetic barrier layer.

Microbial communities from weathered outcrops of a sulfide-rich ultramafic intrusion, and implications for mine waste management

The Duluth Complex (DC) contains sulfide-rich magmatic intrusions that represent one of the largest known economic deposits of copper, nickel, and platinum group elements. Previous work showed that microbial communities associated with experimentally-weathered DC waste rock and tailings were dominated by uncultivated taxa and organisms not typically associated with mine waste. However, those experiments were designed for kinetic testing and do not necessarily represent the conditions expected for long-term environmental weathering. We used 16S rRNA gene methods to characterize the microbial communities present on the surfaces of naturally-weathered and historically disturbed outcrops of DC material. Rock surfaces were dominated by diverse uncultured Ktedonobacteria, Acetobacteria, and Actinobacteria, with abundant algae and other phototrophs. These communities were distinct from microbial assemblages from experimentally-weathered DC rocks, suggesting different energy and nutrient resources in environmental samples. Sulfide mineral incubations performed with and without algae showed that photosynthetic microorganisms could have an inhibitory effect on autotrophic populations, resulting in slightly lower sulfate release and differences in dominant microorganisms. The microbial assemblages from these weathered outcrops show how communities develop during weathering of sulfide-rich DC rocks and represent baseline data that could evaluate the effectiveness of future reclamation of waste produced by large-scale mining operations.

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.

Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region

Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen (NH4+-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.

Plant growth-promoting and heavy metal-resistant Priestia and Bacillus strains associated with pioneer plants from mine tailings

Open mine tailings dams are extreme artificial environments containing sizeable potentially toxic elements (PTEs), including heavy metals (HMs), transition metals, and metalloids. Furthermore, these tailings have nutritional deficiencies, including assimilable phosphorus sources, organic carbon, and combined nitrogen, preventing plant colonization. Bacteria, that colonize these environments, have mechanisms to tolerate the selective pressures of PTEs. In this work, several Priestia megaterium (formerly Bacillus megaterium), Bacillus mojavensis, and Bacillus subtilis strains were isolated from bulk tailings, anthills, rhizosphere, and endosphere of pioneer plants from abandoned mine tailings in Zacatecas, Mexico. Bacillus spp. tolerated moderate HMs concentrations, produced siderophores and indole-3-acetic acid (IAA), solubilized phosphates, and reduced acetylene in the presence of HMs. The strains harbored different PIB-type ATPase genes encoding for efflux pumps and Cation Diffusion Facilitator (CDF) genes. Moreover, nifH and nifD nitrogenase genes were detected in P. megaterium and B. mojavensis genomic DNA. They showed similarity with sequences of the beta-Proteobacteria species, which may represent likely horizontal transfer events. These Bacillus species precede the colonization of mine tailings by plants. Their phenotypic and genotypic features could be essential in the natural recovery of the sites by reducing the oxidative stress of HMs, fixing nitrogen, solubilizing phosphate, and accumulating organic carbon. These traits of the strains reflect the adaptations of Bacillus species to the mine tailings environment and could contribute to the success of phytoremediation efforts.

Zinc and cadmium change the metabolic activities and vegetable cellulose degradation of Bacillus cellulasensis in vegetable soils

Bacillus cellulasensis Zn-B isolated from vegetable soil was highly adaptable to Zinc (Zn) and Cadmium (Cd). Cd, but not Zn, adversely affected the total protein spectrum and functional groups of Bacillus cellulasensis Zn-B. Up to 31 metabolic pathways and 216 metabolites of Bacillus cellulasensis Zn-B were significantly changed by Zn and Cd (Zn&Cd). Some metabolic pathways and metabolites related to functional groups of sulfhydryl (-SH) and amine (-NH-) metabolism were enhanced by Zn&Cd addition. The cellulase activity of Bacillus cellulasensis Zn-B was up to 8.58 U mL^-1, increased to 10.77 U mL^-1 in Bacillus cellulasensis Zn-B + 300 mg L^-1 Zn, and maintained at 6.13 U mL^-1 in Bacillus cellulasensis Zn-B + 50 mg L^-1 Cd. The vegetables' cellulose content was decreased by 25.05-52.37% and 40.28-70.70% under the action of Bacillus cellulasensis Zn-B and Bacillus cellulasensis Zn-B + 300 mg L^-1 Zn. Those results demonstrated that Zn could significantly enhance cellulase activity and biodegradability of Bacillus cellulasensis Zn-B to vegetable cellulose. Bacillus cellulasensis Zn-B can survive in vegetable soil accumulated with Zn&Cd. The tolerance concentration and adsorption capacity of Bacillus cellulasensis Zn-B to Zn were up to 300 mg L^-1 and 56.85%, indicating that Bacillus cellulasensis Zn-B acting as a thermostability biological agent had an essential advantage in accelerating the degradation of discarded vegetables by Zn and were beneficial to maintain organic matter content of vegetable soil.

Characterization of ectomycorrhizal fungal communities associated with tree species on an iron tailings deposit undergoing restoration

Vegetation restoration is an effective method to improve the ecological environment of mine tailings, which has a profound impact on the potential ecological functions of soil fungal communities; yet, little is known about its beneficial effect on soil ectomycorrhizal fungal community. In this study, the responses of soil characteristics and soil ectomycorrhizal fungal community diversity and structure to different revegetation, as well as the contribution of soil factors to soil ectomycorrhizal community were investigated in Liaoning Province, China. As we anticipated, the presence of vegetation significantly improved most soil properties we studied. What's more, compared to Korean pine (Pinus koraiensis Sieb. et Zucc.), Chinese poplar (Populus simonii Carr), and black locust (Robinia pseudoacacia L) could better improve soil total carbon, total nitrogen, total phosphorus, and available phosphorus. In addition, soil ectomycorrhizal fungal community diversity in black locust was greater than Korean pine and Populus simonii. Nonmetric multidimensional scaling analyses indicated that soil ectomycorrhizal community significantly differed depending on different revegetation types. Thus, these results indicated that black locust could be a suitable species for the revegetation of iron mine tailings. The study provided theoretical basis for ecological restoration of iron mine tailings using local plant species.

Physical, Chemical, and Microbiological Characterization of Kettara Mine Tailings, Morocco

The mining industry is of major importance to Morocco’s economy. However, the abandoned pyritic mines are a source of potentially toxic elements that can cause the disruption of the surrounding ecosystems, constituting a huge threat to wellbeing and human health. The present study aimed to analyze the physical and chemical characteristics of different types of tailings and to investigate the microbial populations of acidophilic bacteria involved in the oxidation of pyrite. Coarse and fine tailings collected from different zones of the mine (dike and pond) at two different depths (oxidized and non-oxidized residues) were analyzed for their pH, electrical conductivity, total organic carbon, total nitrogen, available P, major elements, and pseudo-total metal concentrations. The abundance of acidophilic bacteria was determined, and some acidophilic bacterial strains were isolated and tested for their metal tolerance. Tailings showed a pH ≈ 2, very low nutritional content, and high concentrations of Cu, As, Zn, and Pb, which were higher in the non-oxidized samples. The microbial counts of iron- and sulfur-oxidizing bacteria were higher than heterotrophic bacteria, with the highest numbers detected in the oxidized fine tailings. The five acidophilic bacteria isolated from the tailings were affiliated to genera Alicyclobacillus and Sulfobacillus, commonly found in this kind of environment.

Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Assessment of the Transfer of Trace Metals to Spontaneous Plants on Abandoned Pyrrhotite Mine: Potential Application for Phytostabilization of Phosphate Wastes

The abandoned Kettara pyrrhotite mine (Marrakech region, Morocco) is a real source of acid mine drainage (AMD) and heavy metal pollution from previous mining operations-which has spread, particularly because of wind erosion. A store-and-release cover system made of phosphate wastes was built on the site for preventing AMD. To ensure the integrity of this cover and its durability, it is desirable to revegetate it (phytostabilization) with plants adapted to the edaphoclimatic conditions of the region. In this paper, a study was carried out on the spontaneous vegetation around the phosphate cover in order to consider the selection of plants to promote the stabilization of the Kettara mine tailings pond. Nine species of native plants with their rhizospheric soils growing in agricultural soils and tailings from the Kettara mine were collected, and metals (As, Cd, Co, Cu, Pb, Zn, Ni, Cr) were analyzed. The soil analysis showed that the tailings contained high concentrations of Cu (177.64 mg/kg) and Pb (116.80 mg/kg) and that the agricultural soil contained high concentrations of As (25.07 mg/kg) and Cu (251.96 mg/kg) exceeding the toxicity level (Cu > 100 mg/kg, Pb > 100 mg/kg, As > 20 mg/kg). The plant analysis showed low trace metal accumulation in Scolymus hispanicus, Festuca ovina, Cleome brachycarpa, Carlina involucrata and Peganum harmala. These species had a bioconcentration factor (BCF) greater than 1 and a translocation factor (TF) less than 1, demonstrating a high tolerance to trace metals. Therefore, they are good candidates for use in the phytoremediation of the Kettara mine tailings. These species could also potentially be used for the phytostabilization of the phosphate waste cover of the Kettara mine, thus completing the rehabilitation process of this area.

Identification of a novel heavy metal resistant Ralstonia strain and its growth response to cadmium exposure

A novel Ralstonia Bcul-1 strain was isolated from soil samples that was closest to Ralstonia pickettii. Broad-spectrum resistance was identified to a group of heavy metal ions and tolerance to concentrations of Cd²⁺ up to 400 mg L^-1. Low concentrations of heavy metal ions did not have distinctive impact on heavy metal resistance genes and appeared to induce greater expression. Under exposure to Cd²⁺, cell wall components were significantly enhanced, and some proteins were also simultaneously expressed allowing the bacteria to adapt to the high Cd²⁺ living environment. The maximum removal rate of Cd²⁺ by the Ralstonia Bcul-1 strain was 78.97% in the culture medium supplemented with 100 mg L^-1 Cd²⁺. Ralstonia Bcul-1 was able to survive and grow in a low nutrient and cadmium contaminated (0.42 mg kg^-1) vegetable soil, and the cadmium removal rate was up to 65.76% in 9th growth. Ralstonia Bcul-1 mixed with biochar could maintain sustainable growth of this strain in the soil up to 75 d and the adsorption efficiency of cadmium increased by 16.23-40.80% as compared to biochar application alone. Results from this work suggests that Ralstonia Bcul-1 is an ideal candidate for bioremediation of nutrient deficient heavy metal contaminated soil.

Microbial diversity and activity assessment in a 100-year-old lead mine

Mining activities frequently leave a legacy of residues that remain in the area for long periods causing the pollution of surroundings. We studied on a 100 year-old mine, the behavior of potentially toxic elements (PTEs) and their ecotoxicological impact on activity and diversity of microorganisms. The PTEs contamination assessment allowed the classification of the materials as highly (reference- and contaminated-samples) and very highly polluted (illegal spill of olive mill wastes (OMW), tailings, and dumps). OMW presented the lowest enzymatic activities while tailings and dumps had low dehydrogenase and arylsulfatase activities. All the α-diversity indices studied were negatively impacted in dumps. Tailings had lower Chao1 and PD whole tree values as compared to those of reference-samples. β-diversity analysis showed similar bacterial community composition for reference- and contaminated-samples, significantly differing from that of tailings and dumps. The relative abundance of Gemmatimonadetes, Bacteroidetes, and Verrucomicrobia was lower in OMW, tailings, and dumps as compared to reference-samples. Fifty-seven operational taxonomic units were selected as responsible for the changes observed between samples. This study highlights that assessing the relationship between physicochemical properties and microbial diversity and activity gives clues about ongoing regulating processes that can be helpful for stakeholders to define an appropriate management strategy.

Metagenomics of mine tailing rhizospheric communities and its selection for plant establishment towards bioremediation

Mining operations often generate tailing dams that contain toxic residues and are a source of contamination when left unconfined. The establishment of a plant community over the tailings has been proposed as a containment strategy known as phytostabilization. Previously, we described naturally occurring mine tailing colonizing plants such as Acacia farnesiana, Brickellia coulteri, Baccharis sarothroides, and Gnaphalium leucocephalum without finding local adaptation. We explored the rhizosphere microbes as contributors in plant establishment and described both the culturable and in situ diversity of rhizospheric bacteria using the 16S rRNA gene and metagenomic shotgun sequencing. We built a synthetic community (SC) of culturable rhizosphere bacteria from the mine tailings. The SC was then the foundation for a serial passes experiment grown in plant-derived nutrient sources, selecting for heavy metals tolerance, community cooperation, and competition. The outcome of the serial passes was named the 'final synthetic community' (FSC). Overall, diversity decreased from in situ uncultivable microbes from roots (399 bacteria genera) to the cultivated communities (291 genera), the SC (94 genera), and the lowest diversity was in the FSC (43 genera). Metagenomic diversity clustered into 94,245 protein families, where we found plant growth promotion-related genes such as the csgBAC and entCEBAH, coded in a metagenome-assembled genome named Kosakonia sp. Nacozari. Finally, we used the FSC to inoculate mine tailing colonizing plants in a greenhouse experiment. The plants with the FSC inocula observed higher relative plant growth rates in sterile substrates. The FSC presents promising features that might make it useful for phytostabilization tailored strategies.

Co-application of a biosolids product and biochar to two coarse-textured pasture soils influenced microbial N cycling genes and potential for N leaching

Co-application of biochar and biosolids to soil has potential to mitigate N leaching due to physical and chemical properties of biochar. Changes in N cycling pathways in soil induced by co-application of biological amendments could further mitigate N loss, but this is largely unexplored. The aim of this study was to determine whether co-application of a biochar and a modified biosolids product to three pasture soils differing in texture could alter the relative abundance of N cycling genes in soil sown with subterranean clover. The biosolids product contained lime and clay and increased subterranean clover shoot biomass in parallel with increases in soil pH and soil nitrate. Its co-application with biochar similarly increased plant growth and soil pH with a marked reduction in nitrate in two coarse textured soils but not in a clayey soil. While application of the biosolids product altered in silico predicted N cycling functional genes, there was no additional change when applied to soil in combination with biochar. This supports the conclusion that co-application of the biochar and biosolids product used here has potential to mitigate loss of N in coarse textured soils due to N adsoption by the biochar and independently of microbial N pathways.

Revegetation approach and plant identity unequally affect structure, ecological network and function of soil microbial community in a highly acidified mine tailings pond

Owing to its sustainability and low cost, direct revegetation (DR) has been considered a promising alternative to capped revegetation (CR) for dealing with the serious environmental problem derived from various types of mine wastelands that are widespread in the world. However, a direct comparison of the performance of these two revegetation approaches for reclamation of extremely acidic mine wastelands and the underlying mechanisms is still lacking. To bridge this critical knowledge gap, we established 5000 m² of vegetation on a highly acidified (pH < 3) Pb/Zn mine tailings pond employing both CR and DR schemes (2500 m² for each scheme). We then profiled the structure, ecological network and function of soil microbial communities associated with two dominant plant species of the vegetations via high-throughput sequencing. Our results showed that CR and DR achieved a vegetation coverage of 59.7% and 90.5% within two years, respectively. This pattern was accompanied by higher concentrations of plant nutrients and lower acidification potentials in topsoils of the rhizospheres of the vegetation established by DR compared to those of CR. Revegetation approach, rather than plant identity, mostly affected the structure, ecological network and function of soil microbial community in the mine tailings pond. Rhizosphere soils of the vegetation established by DR generally had higher microbial diversity, higher relative abundances of dominant microbial phyla (e.g. Nitrospirae) that can aid plant uptake of nutrients, more complicated microbial interactive networks and more microbial genes responsible for nutrient cycling than those by CR. As the first report on a direct comparison of CR and DR schemes for reclamation of an extremely acidic mine wasteland, our study has important implications for not only the understanding of microbial ecology in revegetated mine wastelands but also the further development of sustainable revegetation schemes.

Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit

Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit regardless of vegetation density, showing a greater relative abundance of Hypocrea sp. Tailings deposit fungal communities were distinct from those found in boreal forest soils. Alder rhizosphere had greater relative abundances of Hypocrea sp. and Thelephora sp., while birch rhizosphere were more often associated with Mollisia sp. Our results indicate that, with increasing vegetation density on the mine site, the bacterial communities associated with the individual deciduous or coniferous species studied were increasingly similar to the bacterial communities found in the adjacent forest. In order to properly assess and restore disturbed sites, it is important to characterize and understand the plant-microbe associations that occur since they likely improve plant fitness in these harsh environments.

Environmental drivers of shifts on microbial traits in sites disturbed by a large-scale tailing dam collapse

This study aimed to assess the most affected traits related to microbial ecophysiology and activity and investigate its relationships with environmental drivers in mine tailings spilled from the Fundão dam at disturbed sites across Gualaxo do Norte river, Minas Gerais, Brazil. The mine tailings are characterized by increased pH value, silt percentage, and bulk density, while clay percentage, organic carbon (C_org), total nitrogen (Nt), and moisture contents are reduced. Microbial biomass, enzymatic activities (arylsulfatase, β-1,4-glucosidase, acid and alkaline phosphatases), and the total microbial activity potential (FDA hydrolysis) were generally lower in tailings compared to undisturbed reference soil (Und). Enzyme-based indexes (GMea, WMean, and IBRv2) showed microbial communities with significantly lower degradative efficacy in the tailings than Und in all sites (R² ≥ 0.94, p < 0.001). Non-metric multidimensional scaling and distance-based redundancy analysis revealed that microbial communities exhibited significant differentiation (R² adjusted = 0.73, p = 0.0001) between mine tailings and Und over the different studied sites, which was strongly influenced by changes on physicochemical properties (pH, C_org and Nt contents, the predominance of small-sized particles of silt, and bulk density) and the presence of Se, Cr, Fe, and Ni, even at low concentrations. Our study suggests that the physicochemical properties and the presence of low bioavailable concentrations of heavy metals in dam tailings promote shifts on microbial communities through reductions in the C storage and biogeochemical cycling of nutrients by these communities compared to those in undisturbed reference soils surrounding and, therefore, has negative implications for the ecosystem functioning.

The importance of edaphic niches functionality for the sustainability of phytomanagement in semiarid mining impacted ecosystems

Mining activities on metal sulphide ores are considered one of the most environmentally damaging anthropogenic activities worldwide, mainly due to the production of metal(loid)- enriched tailings. The objective of the work was to elucidate which factors, including edaphic, vegetation and microbiological aspects, determine soil functionality in the phytomagement of mine tailings piles in semiarid areas. For this purpose, a field study was conducted using a transect experimental design in a former mining area located in southern Spain. Soil characteristics, including edaphic parameters, bacterial and fungal compositions, were determined. The variation in edaphic parameters (pH, electrical conductivity, organic carbon, particle size distribution, etc) through the deterioration transect caused a decrease in plant and microbial diversities, as well as in microbial productivity measured by enzymatic activities. Variation in bacterial relative abundances through the transect was better explained by soil fertility related factors, such as organic matter, pH, salinity, enzymatic activities or microbial biomass (which in turn were related to the presence of plants), than by metals concentrations. The presence of vegetation at the tailings allowed the transition from lithotrophic bacterial orders which dominated in bare tailings areas (e.g. Acidimicrobiales, Chromatiales) to organotrophic oriented orders (e.g. Cytophagales, Actinomycetales). Vegetated patches at the tailings pile and its borders shared some organotrophic bacteria with control forest samples (e.g. Rhizobiales), indicating that natural plant mediated successional processes might stimulate biogeochemical cycles similar to those occurring at non-polluted systems. This functionality of the impacted sites, which include unfavourable edaphic conditions, should be taken into account in the phytomanagement of mine tailings, since it may support its long-term sustainability. Unlike bacteria, variations in fungal relative abundances through the transect were not clearly explained by soil parameters or the presence of plants. Other factors related to spatial distribution or the type of organic substrates may be more determinant in the case of fungi.

Isolation and characterization of an acid and metal tolerant Enterobacter cloacae NZS strain from former mining lake in Selangor, Malaysia

Background

Metal polluted environments have been found to harbor acid and metal tolerant bacterial communities. Metal oxidizing bacteria in particular are industrially important microorganisms that can be utilized for potential applications in biomining and bioremediation. However, some well-characterized strains are not readily culturable as they are obligate and fastidious chemolithotrophs requiring special techniques for their cultivation. Hence, this study was aimed at isolating, identifying, and characterizing indigenous metal tolerant heterotroph(s) from abandoned mines that can potentially be used for biomining or bioremediation processes in the future.

Results

Seventeen bacteria from former mining lakes were isolated and identified using 16S rRNA. Minimal inhibition concentration (MIC) and growth study of isolated bacteria carried out in Luria-Bertani media containing three different metals ions, zinc (II), copper (II), and iron (II), showed that a particular isolate termed Enterobacter cloacae NZS was found to exhibit better growth and tolerance for copper (up to 90 mM), zinc (up to 200 mM), and iron (up to 170 mM). Growth of the strain was notably well in the presence of iron (II). Compared to all the isolates, only E. cloacae NZS was able to be enumerated at pH lower than 5 while other strains were culturable only at pH 7. Its capability in iron (II) oxidation was preliminary assessed based on the pH, cell count, glucose consumption, and amount of iron oxidized throughout incubation in 9K media. E. cloacae NZS strain was found to be capable of oxidizing iron (II) supplied in 9K media to iron (III).

Conclusion

As preliminary investigation showed that E. cloacae NZS was able to oxidize iron (II) in 9K media at pH2, further optimization on the strain, medium, and culture conditions in future may be able to provide a better insight on this strain to be possibly used as an iron oxidizer for various applications.

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention

Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.

New Soil, Old Plants, and Ubiquitous Microbes: Evaluating the Potential of Incipient Basaltic Soil to Support Native Plant Growth and Influence Belowground Soil Microbial Community Composition

The plant–microbe–soil nexus is critical in maintaining biogeochemical balance of the biosphere. However, soil loss and land degradation are occurring at alarmingly high rates, with soil loss exceeding soil formation rates. This necessitates evaluating marginal soils for their capacity to support and sustain plant growth. In a greenhouse study, we evaluated the capacity of marginal incipient basaltic parent material to support native plant growth and the associated variation in soil microbial community dynamics. Three plant species, native to the Southwestern Arizona-Sonora region, were tested with three soil treatments, including basaltic parent material, parent material amended with 20% compost, and potting soil. The parent material with and without compost supported 15%, 40%, and 70% germination of Common Bean (Phaseolus vulgaris L. ‘Tarahumara Norteño’), Mesquite (Prosopis pubescens Benth), and Panic Grass (Panicum Sonorum Beal), respectively, though germination was lower than in the potting soil. Plant growth was also sustained over the 30 day period, with plants in parent material (with and without amendment) reaching 50% height compared to those in the potting soil. A 16S rRNA gene amplicon sequencing approach showed Proteobacteria to be the most abundant phyla in both parent material and potting soil, followed by Actinobacteria. The potting soil showed Gammaproteobacteria (19.6%) to be the second most abundant class, but its abundance was reduced in the soil + plants treatment (5.6%–9.6%). Within the basalt soil type, Alphaproteobacteria (42.7%) and Actinobacteria (16.3%) had a higher abundance in the evaluated bean plant species. Microbial community composition had strong correlations with soil characteristics, but not plant attributes within a given soil material. Predictive functional potential capacity of the communities revealed chemoheterotrophy as the most abundant metabolism within the parent material, while photoheterotrophy and anoxygenic photoautotrophy were prevalent in the potting soil. These results show that marginal incipient basaltic soil, both with and without compost amendments, can support native plant species growth, and non-linear associations may exist between plant–marginal soil–microbial interactions.

Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings

Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.

Performance of a Geosynthetic-Clay-Liner Cover System at a Cu/Zn Mine Tailings Impoundment

The abandoned Kam Kotia Mine (Canada) is undergoing remediation. A geosynthetic-clay-liner (GCL) cover system was installed in the Northern Impounded Tailings (NIT) area in 2008 to isolate acid-generating tailings from water and oxygen and to mitigate sulfide oxidation. The cover system includes a vegetated uppermost soil layer underlain by a granular protective layer (sand), a clay moisture-retaining layer, a GCL, a granular capillary-break material (cushion sand), and a crushed waste rock-capillary break layer installed above the tailings. The goal of this study was to characterize the microbiology of the covered tailings to assess the performance of the cover system for mitigating sulfide bio-oxidation. Tailings beneath the GCL were characterized by high sulfur and low carbon content. The bulk pH of the tailings pore water was circumneutral (∼5.5 to 7.3). Total genomic DNA was extracted from 36 samples recovered from the constituent layers of the cover system and the underlying tailings and was analyzed in triplicates using high-throughput amplicon sequencing of 16S rRNA genes. Iron-oxidizing, sulfur-oxidizing, sulfate-reducing, and aerobic heterotrophic microorganisms were enumerated by use of most probable number enumeration, which identified heterotrophs as the most numerous group of culturable microorganisms throughout the depth profile. Low relative abundances and viable counts of microorganisms that catalyze transformations of iron and sulfur in the covered tailings, compared to previous studies on unreclaimed tailings, indicate that sulfide oxidation rates have decreased due to the presence of the GCL. Characterization of the microbial community can provide a sensitive indicator for assessing the performance of remediation systems.IMPORTANCE Mining activities are accompanied by significant environmental and financial liabilities, including the release of acid mine drainage (AMD). AMD is caused by accelerated chemical and biological oxidation of sulfide minerals in mine wastes and is characterized by low pH and high concentrations of sulfate and metal(loid)s. Microorganisms assume important roles in the catalysis of redox reactions. Our research elucidates linkages among the biogeochemistry of mine wastes and remediation systems and microbial community and activity. This study assesses the performance and utility of geosynthetic-clay-liner cover systems for management of acid-generating mine wastes. Analyses of the microbial communities in tailings isolated beneath an engineered cover system provide a better understanding of the complex biogeochemical processes involved in the redox cycling of key elements, contribute to the remediation of mine wastes, and provide a valuable tool for assessment of the effectiveness of the remediation system.

The dynamic development of bacterial community following long-term weathering of bauxite residue

Bauxite residue is the industrial waste generated from alumina production and commonly deposited in impoundments. These sites are bare of vegetation due to the extreme high salinity and alkalinity, as well as lack of nutrients. However, long term weathering processes could improve residue properties to support the plant establishment. Here we investigate the development of bacterial communities and the geochemical drivers in bauxite residue, using Illumina high-throughput sequencing technology. Long term weathering reduced the pH in bauxite residue and increased its nutrients content. The bacterial community also significantly developed during long term weathering processes. Taxonomic analysis revealed that natural weathering processes encouraged the populations of Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes, whereas reducing the populations of Firmicutes and Actinobacteria. Redundancy analysis (RDA) indicated that total organic carbon (TOC) was the dominant factors affecting microbial structure. The results have demonstrated that natural weathering processes improved the soil development on the abandoned bauxite residue disposal areas, which also increased our understanding of the correlation between microbial variation and residue properties during natural weathering processes in Bauxite residue disposal areas.

Acidithiobacillus ferrianus sp. nov.: an ancestral extremely acidophilic and facultatively anaerobic chemolithoautotroph

Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidi-thiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98–99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. Strain MG is proposed as a novel species, Acidithiobacillus ferrianus sp. nov. The type strain is MG^T (= DSM 107098^T = JCM 33084^T). Similar strains have been found as isolates or indicated by cloned 16S rRNA genes from several mineral sulfide mine sites.

Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.

Bacterial influence on storage and mobilisation of metals in iron-rich mine tailings from the Salobo mine, Brazil

In this study we investigated the potential effects of promoting bacterial activity on tailings from the Salobo iron-oxide copper‑gold (IOCG) mine, Brazil. In particular we focussed on (1) the potential for mobilising additional Cu and (2) the effects of long-term storage on other metals. Unlike typical sulphide-ore tailings, the pH of the Salobo tailings is circumneutral and these tailings are dominated by Fe-bearing silicates and magnetite, with minor micrometre-scale encapsulated Cu-bearing sulphides. While these tailings do not produce acid mine drainage, an endemic strain of Acidithiobacillus ferrooxidans was isolated from the mine site. These bacteria were used in laboratory column leaching experiments of tailings material, which ran for up to 395 days, without the addition of ferrous iron. Bacteria-tailings interactions were typically maintained at a pH > 5, due to silicate-mediated pH buffering. This was eventually overcome after ~200 days by regular addition of acidic (pH 2.2) nutrient solution, as well as growth and acid generation by bacteria. Copper dissolution was not significantly enhanced by bacterial activity compared to abiotic control experiments while pH was >5. However, as the experiments were progressively acidified, additional Cu was mobilised in the biotic systems. The mineral alteration reactions produced abundant ferrihydrite precipitates within the tailings, which was enhanced by bacterial activity as the pH decreased. Adsorption of metal cations to these precipitates ensured that effluent solutions had only low levels (<0.5 mg/l) of dissolved trace metals such as As, Co, Pb, Zn, Se, Ni and Cr. These adsorption processes will strongly inhibit metal leaching from the tailings during long-term storage, as long as the iron oxidising bacteria are producing the requisite excess of ferrihydrite and the pH is >5. This case study shows that bacterially-mediated silicate weathering, in Fe(II)-bearing silicate rich tailings with only minor sulphides and Acidithiobacillus ferrooxidans can enhance the environmental stability of the tailings.

Effect of Re-acidification on Buffalo Grass Rhizosphere and Bulk Microbial Communities During Phytostabilization of Metalliferous Mine Tailings

Phytostabilized highly acidic, pyritic mine tailings are susceptible to re-acidification over time despite initial addition of neutralizing amendments. Studies examining plant-associated microbial dynamics during re-acidification of phytostabilized regions are sparse. To address this, we characterized the rhizosphere and bulk bacterial communities of buffalo grass used in the phytostabilization of metalliferous, pyritic mine tailings undergoing re-acidification at the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, AZ. Plant-associated substrates representing a broad pH range (2.35-7.76) were sampled to (1) compare the microbial diversity and community composition of rhizosphere and bulk compartments across a pH gradient, and (2) characterize how re-acidification affects the abundance and activity of the most abundant plant growth-promoting bacteria (PGPB; including N2-fixing) versus acid-generating bacteria (AGB; including Fe-cycling/S-oxidizing). Results indicated that a shift in microbial diversity and community composition occurred at around pH 4. At higher pH (>4) the species richness and community composition of the rhizosphere and bulk compartments were similar, and PGPB, such as Pseudomonas, Arthrobacter, Devosia, Phyllobacterium, Sinorhizobium, and Hyphomicrobium, were present and active in both compartments with minimal presence of AGB. In comparison, at lower pH (<4) the rhizosphere had a significantly higher number of species than the bulk (p < 0.05) and the compartments had significantly different community composition (unweighted UniFrac; PERMANOVA, p < 0.05). Whereas some PGPB persisted in the rhizosphere at lower pH, including Arthrobacter and Devosia, they were absent from the bulk. Meanwhile, AGB dominated in both compartments; the most abundant were the Fe-oxidizer Leptospirillum and Fe-reducers Acidibacter and Acidiphilium, and the most active was the Fe-reducer Aciditerrimonas. This predominance of AGB at lower pH, and even their minimal presence at higher pH, contributes to acidifying conditions and poses a significant threat to sustainable plant establishment. These findings have implications for phytostabilization field site management and suggest re-application of compost or an alternate buffering material may be required in regions susceptible to re-acidification to maintain a beneficial bacterial community conducive to long-term plant establishment.

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced "iron mound" sediments

Fe(III)-rich deposits referred to as “iron mounds” develop when Fe(II)-rich acid mine drainage (AMD) emerges at the terrestrial surface, and aeration of the fluids induces oxidation of Fe(II), with subsequent precipitation of Fe(III) phases. As Fe(III) phases accumulate in these systems, O₂ gradients may develop in the sediments and influence the distributions and extents of aerobic and anaerobic microbiological Fe metabolism, and in turn the solubility of Fe. To determine how intrusion of O₂ into iron mound sediments influences microbial community composition and Fe metabolism, we incubated samples of these sediments in a column format. O₂ was only supplied through the top of the columns, and microbiological, geochemical, and electrochemical changes at discrete depths were determined with time. Despite the development of dramatic gradients in dissolved Fe(II) concentrations, indicating Fe(II) oxidation in shallower portions and Fe(III) reduction in the deeper portions, microbial communities varied little with depth, suggesting the metabolic versatility of organisms in the sediments with respect to Fe metabolism. Additionally, the availability of O₂ in shallow portions of the sediments influenced Fe metabolism in deeper, O₂-free sediments. Total potential (E_H + self-potential) measurements at discrete depths in the columns indicated that Fe transformations and electron transfer processes were occurring through the sediments and could explain the impact of O₂ on Fe metabolism past where it penetrates into the sediments. This work shows that O₂ availability (or lack of it) minimally influences microbial communities, but influences microbial activities beyond its penetration depth in AMD-derived Fe(III) rich sediments. Our results indicate that O₂ can modulate Fe redox state and solubility in larger volumes of iron mound sediments than only those directly exposed to O₂.

Acid mine drainage affects the diversity and metal resistance gene profile of sediment bacterial community along a river

Acid mine drainage (AMD) is one of the most hazardous byproducts of some types of mining. However, research on how AMD affects the bacterial community structure of downstream riverine ecosystems and the distribution of metal resistance genes (MRGs) along pollution gradient is limited. Comprehensive geochemical and high-throughput next-generation sequencing analyses can be integrated to characterize spatial distributions and MRG profiles of sediment bacteria communities along the AMD-contaminated Hengshi River. We found that (1) diversities of bacterial communities significantly and gradually increased along the river with decreasing contamination, suggesting community composition reflected changes in geochemical conditions; (2) relative abundances of phyla Proteobacteria and genus Halomonas and Planococcaceae that function in metal reduction decreased along the AMD gradient; (3) low levels of sediment salinity, sulfate, aquatic lead (Pb), and cadmium (Cd) were negatively correlated with bacterial diversity despite pH was in a positive manner with diversity; and (4) arsenic (As) and copper (Cu) resistance genes corresponded to sediment concentrations of As and Cu, respectively. Altogether, our findings offer initial insight into the distribution patterns of sediment bacterial community structure, diversity and MRGs along a lotic ecosystem contaminated by AMD, and the factors that affect them.

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

To enrich the understanding of the complex environmental system of soil and microorganisms in gold tailings, we studied the effects of environmental factors on the microbial community diversity in gold mine tailing soil in Beijing, and the strains screened from the soil with serious mercury (Hg) pollution. The results showed that microbial diversity and community composition varied among sites, and at varying depths, soil microbes were significantly affected by soil environmental factors such as lead (Pb), Hg, pH, and total organic carbon (TOC). Pb and Hg negatively affected soil microbial diversity, and less-polluted soil showed increased microbial diversities and complex community structure. Community composition analysis showed that Firmicutes, Proteobacteria and Actinobacteria were the dominant microorganisms. Moreover, Hg-resistant bacterial species isolated from soil samples were identified as Pseudomonas plecoglossicida with a high Hg tolerance efficiency. This study is important in understanding the microbial diversity and function in gold mine tailing soils and can widen the application for bioremediation process.

Initiation of soil formation in weathered sulfidic Cu-Pb-Zn tailings under subtropical and semi-arid climatic conditions

Field evidence has been scarce about soil (or technosol) formation and direct phytostabilization of base metal mine tailings under field conditions. The present study evaluated key attributes of soil formation in weathered and neutral Cu-Pb-Zn tailings subject to organic amendment (WC: woodchips) and colonization of pioneer native plant species (mixed native woody and grass plant species) in a 2.5-year field trial under subtropical and semi-arid climatic conditions. Key soil indicators of engineered soil formation process were characterized, including organic carbon fractions, aggregation, microbial community and key enzymatic activities. The majority (64-87%) of the OC was stabilized in microaggregate or organo-mineral complexes in the amended tailings. The levels of OC and water soluble OC were elevated by 2-3 folds across the treatments, with the highest level in the treatment of WC and plant colonization (WC+P). Specifically, the WC+P treatment increased the proportion of water stable macroaggregates. Plants further contributed to the N rich organic matter in the tailings, favouring organo-mineral interactions and organic stabilization. Besides, the plants played a major role in boosting microbial biomass and activities in the treated tailings. WC and plants enhanced the contents of organic carbon (OC) associated with aggregates (e.g., physically protected OC), formation of water-stable aggregates (e.g., micro and macroaggregates), chemical buffering capacity (e.g., cation exchange capacity). Microbial community and enzymatic activities were also stimulated in the amended tailings. The present results showed that the formation of functional technosol was initiated in the eco-engineered and weathered Cu-Pb-Zn tailings under field conditions for direct phytostabilization.

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China

To unravel the ecological function played by pioneer plants in the practical restoration of mine tailings, it is vital to explore changes of soil characteristics and microbial communities in rhizosphere and bulk soil following the adaptation and survival of plants. In the present study, the diversity and structure of rhizospheric bacterial communities of three pioneer plants in copper mine tailings were investigated by Illumina MiSeq sequencing, and the effects of pioneer plants on soil properties were also evaluated. Significant soil improvement was detected in rhizospheric samples, and Alnus cremastogyne showed higher total organic matter, total nitrogen, and available phosphorus than two other herbaceous plants. Microbial diversity indices in rhizosphere and bulk soil of reclaimed tailings were significantly higher than bare tailings, even the soil properties of bulk soil in reclaimed tailings were not significantly different from those of bare tailings. A detailed taxonomic composition analysis demonstrated that Alphaproteobacteria and Deltaproteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes showed significantly higher relative abundance in rhizosphere and bulk soil. In contrast, Gammaproteobacteria and Firmicutes were abundant in bare tailings, in which Bacillus, Pseudomonas, and Lactococcus made up the majority of the bacterial community (63.04%). Many species within known heavy metal resistance and nutrient regulatory microorganism were identified in reclaimed tailings, and were more abundant among rhizospheric microbes. Hierarchical clustering and principal coordinate analysis (PCoA) analysis demonstrated that the bacterial profiles in the rhizosphere clustered strictly together according to plant types, and were distinguishable from bulk soil. However, we also identified a large shared OTUs that occurred repeatedly and was unaffected by highly diverse soil properties in rhizosphere and bulk samples. Redundancy analysis indicated that water content and Cu and As concentrations were the main environmental regulators of microbial composition. These results suggest that the interactive effect of pioneer plants and harsh soil environmental conditions remodel the specific bacterial communities in rhizosphere and bulk soil in mine tailings. And A. cremastogyne might be approximate candidate for phytoremediation of mine tailings for better soil amelioration effect and relative higher diversity of bacterial community in rhizosphere.

Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions

Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes.

The geomicrobiology of mining environments

As the global population increases, so does the demand for minerals and energy resources. Demand for some of the major global commodities is currently growing at rates of: copper – 1.6% p.a.1; iron ore: 1.4% p.a.2; aluminium – 5% p.a.3; rare earth elements – 7% p.a.4, driven not only by population growth in China, India, and Africa, but also by increasing urbanisation and industrialisation globally. Technological advances in renewable energy production and storage, construction materials, transport, and computing could see demand for some of these resources spike by 2600% over the next 25 years under the most extreme demand scenarios5. Coupled with declining ore grades, this demand means that the global extent of mining environments is set to increase dramatically. Land disturbance attributed to mining was estimated to be 400 000 km2 in 20076, with projected rates of increase of 10 000 km2 per year7. This will increase the worldwide extent of mining environments from around 500 000 km2 at present to 1 330 000 km2 by 2100, larger than the combined land area of New South Wales and Victoria (1 050 000 km2), making them a globally important habitat for the hardiest of microbial life. The extreme geochemical and physical conditions prevalent in mining environments present great opportunities for discovery of novel microbial species and functions, as well as exciting challenges for microbiologists to apply their understanding to solve complex remediation problems.

Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites

Derelict mines pose potential risks to environmental health. Several factors such as soil structure, organic matter, and nutrient content are the greatly affected qualities in mined soils. Soil microbial communities are an important element for successful reclamation because of their major role in nutrient cycling, plant establishment, geochemical transformations, and soil formation. Yet, microorganisms generally remain an undervalued asset in mined sites. The microbial diversity in derelict mine sites consists of diverse species belonging to four key phyla: Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes. The activity of plant symbiotic microorganisms including root-colonizing rhizobacteria and ectomycorrhizal fungi of existing vegetation in the mined sites is very high since most of these microbes are extremophiles. This review outlines the importance of microorganisms to soil health and the rehabilitation of derelict mines and how microbial activity and diversity can be exploited to better plan the soil rehabilitation. Besides highlighting the major breakthroughs in the application of microorganisms for mined site reclamation, we provide a critical view on plant-microbiome interactions to improve revegetation at the mined sites. Also, the need has been emphasized for deciphering the molecular mechanisms of adaptation and resistance of rhizosphere and non-rhizosphere microbes in abandoned mine sites, understanding their role in remediation, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.

Bacterial Rhizoplane Colonization Patterns of Buchloe dactyloides Growing in Metalliferous Mine Tailings Reflect Plant Status and Biogeochemical Conditions

Plant establishment during phytostabilization of legacy mine tailings in semiarid regions is challenging due to low pH, low organic carbon, low nutrients, and high toxic metal(loid) concentrations. Plant-associated bacterial communities are particularly important under these harsh conditions because of their beneficial services to plants. We hypothesize that bacterial colonization profiles on rhizoplane surfaces reflect deterministic processes that are governed by plant health and the root environment. The aim of this study was to identify associations between bacterial colonization patterns on buffalo grass (Buchloe dactyloides) rhizoplanes and both plant status (leaf chlorophyll and plant cover) and substrate biogeochemistry (pH, electrical conductivity, total organic carbon, total nitrogen, and rhizosphere microbial community). Buffalo grass plants from mesocosm- and field-scale phytostabilization trials conducted with tailings from the Iron King Mine and Humboldt Smelter Superfund Site in Dewey-Humboldt, Arizona, were analyzed. These tailings are extremely acidic and have arsenic and lead concentrations of 2-4 g kg^-1 substrate. Bacterial communities on rhizoplanes and in rhizosphere-associated substrate were characterized using fluorescence in situ hybridization and 16S rRNA gene amplicon sequencing, respectively. The results indicated that the metabolic status of rhizoplane bacterial colonizers is significantly related to plant health. Principal component analysis revealed that root-surface Alphaproteobacteria relative abundance was associated most strongly with substrate pH and Gammaproteobacteria relative abundance associated strongly with substrate pH and plant cover. These factors also affected the phylogenetic profiles of the associated rhizosphere communities. In summary, rhizoplane bacterial colonization patterns are plant specific and influenced by plant status and rhizosphere biogeochemical conditions.

Understanding the variation of microbial community in heavy metals contaminated soil using high throughput sequencing

To improve the understanding of bacterial community in heavy metals contaminated soils, we studied the effects of environmental factors on the bacterial community structure in contaminated fields located in Shaanxi Province of China. Our results showed that microbial community structure varied among sites, and it was significantly affected by soil environmental factors such as pH, soil organic matter (SOM), Cd, Pb and Zn. In addition, Spearman's rank-order correlation indicated heavy metal sensitive (Ralstonia, Gemmatimona, Rhodanobacter and Mizugakiibacter) and tolerant (unidentified-Nitrospiraceae, Blastocatella and unidentified-Acidobacteria) microbial groups. Our findings are crucial to understanding microbial diversity in heavy metal polluted soils of China and can be used to evaluate microbial communities for scientific applications such as bioremediation projects.

Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA

The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste.IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits.

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.

Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India

Mine tailings from copper mines are considered as one of the sources of highly hazardous acid mine drainage (AMD) due to bio-oxidation of its sulfidic constituents. This study was designed to understand microbial community composition and potential for acid generation using samples from mine tailings of Malanjkhand copper project (MCP), India through 16S rRNA gene based amplicon sequencing approach (targeting V4 region). Three tailings samples (T1, T2 and T3) with varied physiochemical properties selected for the study revealed distinct microbial assemblages. Sample (T3) with most extreme nature (pH < 2.0) harbored Proteobacteria, Actinobacteria, Chloroflexi while the samples (T1 and T3) with slightly moderate nature (pH < 4.0 and > 3.0) exhibited abundance of Proteobacteria, Fimicutes, Actinobacteria and/or Nitrospirae. Metagenomic sequences are available under the BioProject ID PRJNA361456.

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco)

In Morocco, pollution caused by closed mines continues to be a serious threat to the environment, like the generation of acid mine drainage. Mine drainage is produced by environmental and microbial oxidation of sulfur minerals originating from mine wastes. The fundamental role of microbial communities is well known, like implication of Fe-oxidizing and to a lesser extent S-oxidizing microorganism in bioleaching. However, the structure of the microbial communities varies a lot from one site to another, like diversity depends on many factors such as mineralogy, concentration of metals and metalloids or pH, etc. In this study, prokaryotic communities in the pyrrhotite-rich tailings of Kettara mine were characterized using the Illumina sequencing. In-depth phylogenetic analysis revealed a total of 12 phyla of bacteria and 1 phyla of Archaea. The majority of sequences belonged to the phylum of Proteobacteria and Firmicutes with a predominance of Bacillus, Pseudomonas or Corynebacterium genera. Many microbial populations are implicated in the iron, sulfur and arsenic cycles, like Acidiferrobacter, Leptospirillum, or Alicyclobacillus in Fe; Acidiferrobacter and Sulfobacillus in S; and Bacillus or Pseudomonas in As. This is one of the first description of prokaryotic communities in pyrrhotite-rich mine tailings using high-throughput sequencing.

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

To solve the competition problem of acidophilic bacteria and sulfate-reducing bacteria in the practical application of mine tailing bioremediation, research into the mechanisms of using different nutrients to adjust the microbial community was conducted. Competition experiments involving acidophilic bacteria and sulfate-reducing bacteria were performed by supplementing the media with yeast extract, tryptone, lactate, and glucose. The physiochemical properties were determined, and the microbial community structure and biomass were investigated using MiSeq sequencing and qRT-PCR, respectively. Four nutrients had different remediation mechanisms and yielded different remediation effects. Yeast extract and tryptone (more than 1.6 g/L) promoted sulfate-reducing bacteria and inhibited acidophilic bacteria. Lactate inhibited both sulfate-reducing and acidophilic bacteria. Glucose promoted acidophilic bacteria more than sulfate-reducing bacteria. Yeast extract was the best choice for adjusting the microbial community and bioremediation, followed by tryptone. Lactate kept the physiochemical properties stable or made slight improvements; however, glucose was not suitable for mine tailing remediation. Different nutrients had significant effects on the abundance of the second enzyme of the sulfate-reducing pathway (p < 0.05), which is the rate-limiting step of sulfate-reducing pathways. Nutrients changed the remediation effects effectively by adjusting the microbial community and the abundance of the sulfate-reducing rate-limiting enzyme.

Ammonia-Oligotrophic and Diazotrophic Heavy Metal-Resistant Serratia liquefaciens Strains from Pioneer Plants and Mine Tailings

Mine tailings are man-made environments characterized by low levels of organic carbon and assimilable nitrogen, as well as moderate concentrations of heavy metals. For the introduction of nitrogen into these environments, a key role is played by ammonia-oligotrophic/diazotrophic heavy metal-resistant guilds. In mine tailings from Zacatecas, Mexico, Serratia liquefaciens was the dominant heterotrophic culturable species isolated in N-free media from bulk mine tailings as well as the rhizosphere, roots, and aerial parts of pioneer plants. S. liquefaciens strains proved to be a meta-population with high intraspecific genetic diversity and a potential to respond to these extreme conditions. The phenotypic and genotypic features of these strains reveal the potential adaptation of S. liquefaciens to oligotrophic and nitrogen-limited mine tailings with high concentrations of heavy metals. These features include ammonia-oligotrophic growth, nitrogen fixation, siderophore and indoleacetic acid production, phosphate solubilization, biofilm formation, moderate tolerance to heavy metals under conditions of diverse nitrogen availability, and the presence of zntA, amtB, and nifH genes. The acetylene reduction assay suggests low nitrogen-fixing activity. The nifH gene was harbored in a plasmid of ∼60 kb and probably was acquired by a horizontal gene transfer event from Klebsiella variicola.

Vegetation successfully prevents oxidization of sulfide minerals in mine tailings

The oxidization of metal sulfide in tailings causes acid mine drainage. However, it remains unclear whether vegetation prevents the oxidization of metal sulfides. The oxidization characteristics and microbial indices of the tailings in the presence of various plant species were investigated to explore the effects of vegetation on the oxidization of sulfide minerals in tailings. The pH, reducing sulfur, free iron oxides (Fed), chemical oxygen consumption (COC) and biological oxygen consumption (BOC) were measured. Key iron- and sulfur-oxidizing bacteria (Acidithiobacillus spp., Leptospirillum spp. and Thiobacillus spp.) were quantified using real-time PCR. The results indicate that vegetation growing on tailings can effectively prevent the oxidization of sulfide minerals in tailings. A higher pH and reducing-sulfur content and lower Fed were observed in the 0-30 cm depth interval in the presence of vegetation compared to bare tailings (BT). The COC gradually decreased with depth in all of the soil profiles; specifically, the COC rapidly decreased in the 10-20 cm interval in the presence of vegetation but gradually decreased in the BT profiles. Imperata cylindrica (IC) and Chrysopogon zizanoides (CZ) profiles contained the highest BOC in the 10-20 cm interval. The abundance of key iron- and sulfur-oxidizing bacteria in the vegetated tailings were significantly lower than in the BT; in particular, IC was associated with the lowest iron- and sulfur-oxidizing bacterial abundance. In conclusion, vegetation successfully prevented the oxidization of sulfide minerals in the tailings, and Imperata cylindrica is the most effective in reducing the number of iron- and sulfur-oxidizing bacteria and helped to prevent the oxidization of sulfide minerals in the long term.