Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids

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

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

Fe/S oxidation-coupled arsenic speciation transformation mediated by AMD enrichment culture under different pH conditions

Arsenic (As) speciation transformation in acid mine drainage (AMD) is comprehensively affected by biological and abiotic factors, such as microbially mediated Fe/S redox reactions and changes in environmental conditions (pH and oxidation-reduction potential). However, their combined impacts on arsenic speciation transformation remain poorly studied. Therefore, we explored arsenic transformation and immobilization during pyrite dissolution mediated by AMD enrichment culture under different acidic pH conditions. The results for incubation and mineralogical transformation of solid residues show that in the presence of AMD enrichment culture, pH 2.0, 2.5, and 3.0 are more conducive to the formation of jarosites and ferric arsenate, which could immobilize high quantities of dissolved arsenic by adsorption and coprecipitation. The pH conditions significantly affect the initial adsorption of microbial cells to the minerals and the evolution of microbial community structure, further influencing the biodissolution of pyrite and the release and oxidation process of Fe/S. The results of Fe/S/As speciation transformation of the solid residues show that the transformation of Fe, S, and As in solution is mainly regulated by pH and potential values, which imposed significantly different effects on the formation of secondary minerals and thus arsenic oxidation and immobilization. The above results indicated that arsenic transformation is closely related to the Fe/S oxidation associated with pyrite bio-oxidation, and this correlation is critically regulated by the pH conditions of the system.

Microbiology of a multi-layer biosolid/desulfurized tailings cover on a mill tailings impoundment

The Strathcona Waste Water Treatment System (SWWTS; Sudbury, ON, Canada) has received mill tailings from Ni/Cu ore processing from 1970 to present. Demonstration-scale, multi-layer cover systems were installed on selected tailings deposition cells at the SWWTS. The cover systems are comprised of an upper layer of organic carbon-rich material, composed of a layer biosolids fertilizer along with composted municipal food and yard waste, then a layer of desulfurized, fine-grained tailings. Organic carbon components used in these covers promote microbial communities that consume O₂, thus decreasing sulfide oxidation rates in the underlying tailings. The aim of this study was to investigate the microbiology of the cover systems and the underlying tailings, using a combination of culture-dependent (most probable number) and culture-independent (16S rRNA gene amplicon sequencing) techniques, and assess the impact of the organic component of the cover system four to six years after implementation. Most tailings samples were characterized by circumneutral bulk pH and low concentrations of dissolved metals. The presence of the organic cover resulted in elevated counts of sulfate-reducers (by two orders of magnitude, compared to control samples) immediately below the organic cover, as well as an increased abundance of heterotrophic species (∼10⁸ cells g^-1) at greater depth (∼4 m) in the tailings profile. Mineral-oxidizing microorganisms were also present in the tailings, with neutrophilic sulfur-oxidizers dominating the samples (mean ∼10⁶ cells g^-1). Relative abundances of sulfur- and/or iron-oxidizers determined by sequencing ranged from 0.5 to 18.3% of total reads (mean ∼5.6% in amended tailings) and indicated the presence of local microenvironments with ongoing sulfide oxidation. This work provides a detailed characterization of the microbiology of a tailings impoundment with an organic cover, highlighting the opportunities associated with monitoring microbial processes in such remediation systems.

Biosolids towards Back-To-Earth alternative concept (BEA) for environmental sustainability: a review

Biosolids are a nutrient-rich stable substance obtained during wastewater treatment process. With amplifying population and industrial development, upsurge of biosolid generation is also speculated. Biosolids are endowed with essential plant nutrient (macro- and micro-nutrients) which qualifies them to be used as soil amendment and in turn dwindles the use of chemical fertilizers. The characteristics of biosolid depends on the nature of the treatment process. In this regard, it would be possible to recycle certain nutrients from the agricultural use of biosolids and could be a sustainable solution to the management of this waste. Biosolids may therefore serve as a key tool for farm utilization. It improves the soil health through nutrient supply and promotes the plant growth. Furthermore, they are slow-release fertilizer and hence, restrains from groundwater contamination. This review, in a nutshell, unravels the influence of biosolids on land application, its effect on soil properties, agricultural and horticultural crops, environmental ramification of biosolids in restoring the degraded land and carbon sequestration.

Semiarid bunchgrasses accumulate molybdenum on alkaline copper mine tailings: assessing phytostabilization in the greenhouse

Phytostabilization is the use of plants and soil amendments to physically stabilize and remediate contaminated mine wastes and to control wind and water erosion in semiarid environments. The aim of this study was to evaluate two native bunchgrass species’ (Pseudoroegneria spicata and Festuca campestris) biomass accumulation and metals uptake response to locally available soil amendments (compost, wood ash and wood chips) to determine their suitability for phytostabilization at an alkaline copper mine tailings site in British Columbia, Canada. In the greenhouse, bunchgrasses important as forage for livestock and wildlife were grown in tailings with various ash–compost–wood chip combinations and evaluated using a randomized complete block design with 13 treatments and 10 replicates. Plants were harvested after 90 d, and tissues were analyzed for root and shoot biomass. Tissue samples (n = 3) from three treatment subsets (ash, compost, blend) were selected for elemental analysis. Biomass increased with increasing compost applications, and the response was greatest for P. spicata. Shoot molybdenum exceeded the maximum tolerable level for cattle and was significantly higher when grasses were grown on the ash treatment (183–202 mg kg−1) compared to the others (19.7–58.3 mg kg−1). Translocation and root bioconcentration factors were highest on the ash treatment (2.53–12.5 and 1.75–7.96, respectively) compared to the other treatments (0.41–3.43 and 1.47–4.79, respectively) and indicate that both species are ‘accumulators.’ The findings suggest that these bunchgrasses were not ideal candidates for phytostabilization due to high shoot tissue molybdenum accumulation, but provide important considerations for mine restoration in semiarid grassland systems.

Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

Characterizations of heavy metal contamination, microbial community, and resistance genes in a tailing of the largest copper mine in China

Copper mine tailings are causing great environmental concern nowadays due to their high contents of heavy metals. These hazards may release to air, water, and soil, posing great threat to the living organisms in the surroundings. In the present work, we profiled the heavy metal contents, microbiome and resistome of a mine tailing in Dexing Copper Mine, which is the largest open-pit copper mine in China. A total of 39.75 Gb clean data was generated by metagenomics sequencing and taxonomy analysis revealed Actinobacteria, Proteobacteria, Acidobacteria, Euryarchaeota, and Nitrospirae as the most abundant phylum in this tailing. In general, 76 heavy metal resistance genes (HMRGs) and 194 antimicrobial resistance genes (ARGs) were identified with merA and rpoB2 as the most abundant HMRG and ARG, respectively. We also compared the differences of heavy metal concentrations among the six sampling sites in the same tailing and found that significant differences exited in copper and zinc. Hierarchical cluster analysis showed that the samples from the six sampling sites were clustering in two groups based on heavy metal concentrations. Accordingly, clustering based on microbial composition and relative abundances of resistance genes exhibited the same clustering pattern, indicating a possible shaping influence of heavy metals on the microbiome and resistome in this tailing. Our work presented heavy metal contents, microbial composition and resistance genes in a copper mine tailing of the largest copper mine in China, and these data will of great use in the surveillance, maintenance, and remediation of this tailing.

Diversity of Metal-Resistant and Tensoactive-Producing Culturable Heterotrophic Bacteria Isolated from a Copper Mine in Brazilian Amazonia

Bacterial extracellular polymeric substances (EPSs) present diverse properties of biotechnological interest, such as surface modification, metal adsorption and hydrophobic substances solubilization through surface tension reduction. Thus, there is a growing demand for new producing strains and structurally variable biomolecules with different properties. One approach for scanning this biodiversity consists of exploring environments under selective pressures. The aim of this study was to evaluate the composition of culturable heterotrophic bacterial communities from five different sites from a copper mine in the Amazon biome by an enrichment technique to obtain metal resistant bacteria (lead, arsenic, cadmium, copper and zinc) capable of producing EPSs. The bacterial densities at the sites varied from 2.42 × 103 to 1.34 × 108 NMP mL-1 and the 77 bacterial isolates obtained were classified in four divisions, β-Proteobacteria (16.88%), γ-Proteobacteria (7.29%), Firmicutes (61%) and Actinobacteria (12.98%). Bacillus, Alcaligenes, and Lysinibacillus were the most dominant among the 16 observed genera, but the relative frequency of each varied according to the sample and the metal used in the enrichment culture. 58% of the bacterial strains (45) could produce EPSs. From these, 33 strains showed emulsifying activity (E24), and 9 of them reached values higher than 49%. Only Actinomyces viscosus E3.Pb5 and Bacillus subtilis group E3.As2 reduced the medium surface tension to values lower than 35 mN m-1. It was possible to confirm the high presence of bacteria capable of producing EPSs with tensoactive properties in Amazon copper mines and the evolutionary pressure exerted by the heavy metals during enrichment. These molecules can be tested as an alternative for use in processes that involve the removal of metals, such as the bioremediation of contaminated environments.

Review: mine tailings in an African tropical environment-mechanisms for the bioavailability of heavy metals in soils

Heavy metals are of environmental significance due to their effect on human health and the ecosystem. One of the major exposure pathways of Heavy metals for humans is through food crops. It is postulated in the literature that when crops are grown in soils which have excessive concentrations of heavy metals, they may absorb elevated levels of these elements thereby endangering consumers. However, due to land scarcity, especially in urban areas of Africa, potentially contaminated land around industrial dumps such as tailings is cultivated with food crops. The lack of regulation for land-usage on or near to mine tailings has not helped this situation. Moreover, most countries in tropical Africa have not defined guideline values for heavy metals in soils for various land uses, and even where such limits exist, they are based on total soil concentrations. However, the risk of uptake of heavy metals by crops or any soil organisms is determined by the bioavailable portion and not the total soil concentration. Therefore, defining bioavailable levels of heavy metals becomes very important in HM risk assessment, but methods used must be specific for particular soil types depending on the dominant sorption phases. Geochemical speciation modelling has proved to be a valuable tool in risk assessment of heavy metal-contaminated soils. Among the notable ones is WHAM (Windermere Humic Aqueous Model). But just like most other geochemical models, it was developed and adapted on temperate soils, and because major controlling variables in soils such as SOM, temperature, redox potential and mineralogy differ between temperate and tropical soils, its predictions on tropical soils may be poor. Validation and adaptation of such models for tropical soils are thus imperative before such they can be used. The latest versions (VI and VII) of WHAM are among the few that consider binding to all major binding phases. WHAM VI and VII are assemblages of three sub-models which describe binding to organic matter, (hydr)oxides of Fe, Al and Mn and clays. They predict free ion concentration, total dissolved ion concentration and organic and inorganic metal ion complexes, in soils, which are all important components for bioavailability and leaching to groundwater ways. Both WHAM VI and VII have been applied in a good number of soils studies with reported promising results. However, all these studies have been on temperate soils and have not been tried on any typical tropical soils. Nonetheless, since WHAM VII considers binding to all major binding phases, including those which are dominant in tropical soils, it would be a valuable tool in risk assessment of heavy metals in tropical soils. A discussion of the contamination of soils with heavy metals, their subsequent bioavailability to crops that are grown in these soils and the methods used to determine various bioavailable phases of heavy metals are presented in this review, with an emphasis on prospective modelling techniques for tropical soils.

Variations of soil microbial communities accompanied by different vegetation restoration in an open-cut iron mining area

Overexploitation of iron mining in China has caused serious environmental pollution. Therefore, establishing a stable ecological restoration with vegetation in mining areas has gradually aroused people's awareness and obtained extensive concerns. This study aimed to evaluate vegetation restoration with Robinia pseudoacacia (RP), Acer mono (AM) and Pinus koraiensis (PK) in iron mining compared with unrestored area, to investigate the soil environment factors and microbial communities, and to better understand the correlations between soil environment factors and soil microbial communities. Vegetation restoration could reduce soil pH and alleviate soil alkaline, and remarkably increase soil nutrients, especially in RP site. Analysis of 16S rRNA and ITS rRNA gene sequences provided a total of 645,004 and 906, 276 valid sequences clustered into 7091 OTUs and 1689 OTUs at a 0.03 genetic distance for bacteria and fungi, respectively. The predominant bacterial and fungal phyla were Actinobacteria and Ascomycota in studied sites, respectively. Additionally, revegetation significantly increased the relative abundances of Proteobacteria, Gemmatimonadetes, Bacteroidetes and Patescibacteria, and decreased the relative abundance of Actinobacteria. Robinia pseudoacacia harbored the highest soil fungal community diversity, and bacterial Simpson index and Shannon index. Vegetation restoration with RP could clearly shifted soil communities compared to AM and PK. Along with the restoration of vegetation, the remarkable abiotic changes were the accumulation of total C, total N, total P, available P, available N and available K and the decreasing of soil pH, which were the most important factors affecting soil microbial communities. Our results addressed that Robinia pseudoacacia was the best preferable species than AM and PK in improving soil nutrients, soil community diversity and structure in Fe mining, providing a helpful guideline for selection of tree species.

Bacterial Community Structure Recovery in Reclaimed Coal Mined Soil under Two Vegetative Regimes

Coal mining can be deleterious to the soil physical and chemical makeup, but also to the soil microbial community. Effectively, the removal of nearly all organic matter from the upper soil horizons reduces the effectiveness of any soil to support vegetation, and up until recently, microbial community parameters were not considered in the successful reclamation of overburden. Thus, our study proposes to measure the uncultivated bacterial community using 16S ribosomal RNA (rRNA) high-throughput sequencing in a chronosequence of reclaimed overburden in Mississippi. The study sites comprised samplings of pasture and wooded reclamation sites consisting of 1 to 13 yr post reclamation time, as well as reference sites. Overall, the primary driver of bacterial community dynamics was vegetative cover, although time also influenced dynamics. Richness estimations for operational taxonomic units (OTUs) showed that recently reclaimed (∼1 yr) and Pasture sites were more OTU rich with levels of >1400 compared with reference site levels of ∼1000. Diversity levels also followed a similar trend. Community structure typically differed between time points and vegetative cover; however, membership was similar between sites and reference, indicating that new communities still shared some membership from the previous community. Overall, physicochemical properties trended toward more positive for soil health as time progressed, but bacterial community recovery was still not structurally recovered, although richness and diversity values exceeded reference. Overall, this study demonstrated that mine reclamation using pasture and/or wood restoration can reestablish the bacterial community to approximate reference conditions, but vegetation is still the dominating environmental factor dictating microbial community.

Defunct gold mine tailings are natural reservoir for unique bacterial communities revealed by high-throughput sequencing analysis

Mine tailing dumps are arguably one of the leading sources of environmental degradation with often both public health and ecologically consequences. The present study investigated the concentration of heavy metals in gold mine tailings, and used high throughput sequencing techniques to determine the microbial community diversity of these tailings using 16S rRNA gene based amplicon sequence analysis. The concentration of detected metals and metalloids followed the order Si > Al > Fe > K > Ca > Mg. The 16S rRNA gene based sequence analysis resulted in a total of 273,398 reads across the five samples, represented among 7 major phyla, 41 classes, 77 orders, 142 families and 247 major genera. Phylum Actinobacteria was the most dominant, followed by Proteobacteria, Firmicutes, Chloroflexi, Cyanobacteria, Bacteroidetes, Acidobacteria and Planctomycetes. Redundancy analysis (RDA) and pairwise correlation analysis positively correlated the distribution of Alphaproteobacteria and Gammaproteobacteria to Al and K; Actinobacteria to Cr and Chloroflexi to Si. Negative correlations were observed in the distribution of Bacteroidetes with respect to As concentrations, Actinobacteria to Al, and Alphaproteobacteria and Gammaproteobacteria to high As and Te content of the soils. Predictive functional analysis showed the presence of putative biosynthetic and degradative pathways across the five sample sites. The study concludes that mine tailing sites harbour diverse and unique microbial assemblages with potentially biotechnologically important genes for biosynthesis and biodegradation.

Bacterial community structure and diversity responses to the direct revegetation of an artisanal zinc smelting slag after 5 years

This comparative field study examined the responses of bacterial community structure and diversity to the revegetation of zinc (Zn) smelting waste slag with eight plant species after 5 years. The microbial community structure of waste slag with and without vegetation was evaluated using high-throughput sequencing. The physiochemical properties of Zn smelting slag after revegetation with eight plant rhizospheres for 5 years were improved compared to those of bulk slag. Revegetation significantly increased the microbial community diversity in plant rhizospheres, and at the phylum level, Proteobacteria, Acidobacteria, and Bacteroidetes were notably more abundant in rhizosphere slags than those in bulk waste slag. Additionally, revegetation increased the relative abundance of plant growth-promoting rhizobacteria such as Flavobacterium, Streptomyces, and Arthrobacter as well as symbiotic N₂ fixers such as Bradyrhizobium. Three dominant native plant species (Arundo donax, Broussonetia papyrifera, and Robinia pseudoacacia) greatly increased the quality of the rhizosphere slags. Canonical correspondence analysis showed that the differences in bacterial community structure between the bulk and rhizosphere slags were explained by slag properties, i.e., pH, available copper (Cu) and lead (Pb), moisture, available nitrogen (N), phosphorus (P), and potassium (K), and organic matter (OM); however, available Zn and cadmium (Cd) contents were the slag parameters that best explained the differences between the rhizosphere communities of the eight plant species. The results suggested that revegetation plays an important role in enhancing bacterial community abundance and diversity in rhizosphere slags and that revegetation may also regulate microbiological properties and diversity mainly through changes in heavy metal bioavailability and physiochemical slag characteristics.

Bacterial communities established in bauxite residues with different restoration histories

Bauxite residue is the alkaline byproduct generated when alumina is extracted from bauxite ores and is commonly deposited in impoundments. These sites represent hostile environments with increased salinity and alkalinity and little prospect of revegetation when left untreated. This study reports the establishment of bacterial communities in bauxite residues with and without restoration amendments (compost and gypsum addition, revegetation) in samples taken in 2009 and 2011 from 0 to 10 cm depth. DNA fingerprint analysis of bacterial communities based on 16S rRNA gene fragments revealed a significant separation of the untreated site and the amended sites in both sampling years. 16S amplicon analysis (454 FLX pyrosequencing) revealed significantly lower alpha diversities in the unamended in comparison to the amended sites and hierarchical clustering separated the unamended site from the amended sites. The taxonomic analysis revealed that the restoration resulted in the accumulation of bacterial populations typical for soils including Acidobacteriaceae, Nitrosomonadaceae, and Caulobacteraceae. In contrast, the unamended site was dominated by taxonomic groups including Beijerinckiaceae, Xanthomonadaceae, Acetobacteraceae, and Chitinophagaceae, repeatedly associated with alkaline salt lakes and sediments. While bacterial communities developed in the initially sterile bauxite residue, only the restoration treatments created diverse soil-like bacterial communities alongside diverse vegetation on the surface.