Ecological restoration alters microbial communities in mine tailings profiles

Soil Microbial Responses to Varying Environmental Conditions in a Copper Belt Region of Africa: Phytoremediation Perspectives

The mining industry in the copper belt region of Africa was initiated in the early 1900s, with copper being the main ore extracted to date. The main objectives of the present study are (1) to characterize the microbial structure, abundance, and diversity in different ecological conditions in the cupriferous city of Lubumbashi and (2) to assess the metal phytoextraction potential of Leucaena leucocephala, a main plant species used in tailing. Four ecologically different sites were selected. They include a residential area (site 1), an agricultural dry field (site 2), and an agricultural wetland (site 3), all located within the vicinity of a copper/cobalt mining plant. A remediated tailing was also added as a highly stressed area (site 4). As expected, the highest levels of copper and cobalt among the sites studied were found at the remediated tailing, with 9447 mg/kg and 2228 mg/kg for copper and cobalt, respectively. The levels of these metals at the other sites were low, varying from 41 mg/kg to 579 mg/kg for copper and from 4 mg/kg to 110 mg/kg for cobalt. Interestingly, this study revealed that the Leucaena leucocephala grown on the remediated sites is a copper/cobalt excluder species as it accumulates soil bioavailable metals from the rhizosphere in its roots. Amplicon sequence analysis showed significant differences among the sites in bacterial and fungal composition and abundance. Site-specific genera were identified. Acidibacter was the most abundant bacterial genus in the residential and remediated tailing sites, with 11.1% and 4.4%, respectively. Bacillus was predominant in both dry (19.3%) and wet agricultural lands (4.8%). For fungi, Fusarium exhibited the highest proportion of the fungal genera at all the sites, with a relative abundance ranging from 15.6% to 20.3%. Shannon diversity entropy indices were high and similar, ranging from 8.3 to 9 for bacteria and 7.0 and 7.4 for fungi. Β diversity analysis confirmed the closeness of the four sites regardless of the environmental conditions. This lack of differences in the microbial community diversity and structures among the sites suggests microbial resilience and physiological adaptations.

The scientific landscape of phytoremediation of tailings: a bibliometric and scientometric analysis

This article seeks to evaluate the scientific landscape of the phytoremediation of mine tailings through a series of bibliometric and scientometric techniques. Phytoremediation has emerged as a sustainable approach to remediate metal-contaminated mine waste areas. A scientometric analysis of 913 publications indexed in Web of Science from 1999 to 2023 was conducted using CiteSpace. The results reveal an expanding, interdisciplinary field with environmental sciences as the core category. Keyword analysis of 561 nodes and 2,825 links shows a focus on plant-metal interactions, microbial partnerships, bioavailability, and field validation. Co-citation analysis of 1,032 nodes and 2,944 links identifies seminal works on native species, plant-microbe interactions, and amendments. Temporal mapping of 15 co-citation clusters indicates a progression from early risk assessments and native plant inquiries to integrated biological systems, economic feasibility, and sustainability considerations. Recent trends emphasize multidimensional factors influencing adoption, such as plant-soil-microbe interactions, organic amendments, and field-scale performance evaluation. The findings demonstrate an intensifying translation of phytoremediation from scientific novelty to engineering practice. This quantitative and qualitative analysis of research trends aids in understanding the development of phytoremediation for mine tailings. The results provide valuable insights for researchers and practitioners in this evolving field.

The roles of rare and abundant microbial species in the primary succession of biological soil crusts are differentiated in metal tailings ponds with different states

Tailings ponds formed by long-term accumulation of mineral processing waste have become a global environmental problem. Even worse, tailings ponds are often simply abandoned or landfilled after they cease to be used. This allows pollution to persist and continue to spread in the environment. The significance of primary succession mediated by biological soil crusts for tailings pond remediation has been illustrated by previous studies. However, the process of primary succession may not be the same at different stages during the lifetime of tailings ponds. Therefore, we investigated the environmental differences and the successional characteristics of microbial communities in the primary successional stage of tailings ponds at three different states. The results showed that the primary succession process positively changed the environment of tailings ponds in any state of tailings ponds. The primary successional stage determined the environmental quality more than the state of the tailings pond. In the recently abandoned tailings ponds, abundant species were more subjected to heavy metal stress, while rare species were mainly limited by nutrient content. We found that as the succession progressed, rare species gradually acquired their own community space and became more responsive to environmental stresses. Rare species played an important role in microbial keystone species groups.

Prairie restoration promotes the abundance and diversity of mutualistic arbuscular mycorrhizal fungi

Predicting how biological communities assemble in restored ecosystems can assist in conservation efforts, but most research has focused on plants, with relatively little attention paid to soil microbial organisms that plants interact with. Arbuscular mycorrhizal (AM) fungi are an ecologically significant functional group of soil microbes that form mutualistic symbioses with plants and could therefore respond positively to plant community restoration. To evaluate the effects of plant community restoration on AM fungi, we compared AM fungal abundance, species richness, and community composition of five annually cultivated, conventionally managed agricultural fields with paired adjacent retired agricultural fields that had undergone prairie restoration 5-9 years prior to sampling. We hypothesized that restoration stimulates AM fungal abundance and species richness, particularly for disturbance-sensitive taxa, and that gains of new taxa would not displace AM fungal species present prior to restoration due to legacy effects. AM fungal abundance was quantified by measuring soil spore density and root colonization. AM fungal species richness and community composition were determined in soils and plant roots using DNA high-throughput sequencing. Soil spore density was 2.3 times higher in restored prairies compared to agricultural fields, but AM fungal root colonization did not differ between land use types. AM fungal species richness was 2.7 and 1.4 times higher in restored prairies versus agricultural fields for soil and roots, respectively. The abundance of Glomeraceae, a disturbance-tolerant family, decreased by 25% from agricultural to restored prairie soils but did not differ in plant roots. The abundance of Claroideoglomeraceae and Diversisporaceae, both disturbance-sensitive families, was 4.6 and 3.2 times higher in restored prairie versus agricultural soils, respectively. Species turnover was higher than expected relative to a null model, indicating that AM fungal species were gained by replacement. Our findings demonstrate that restoration can promote a relatively rapid increase in the abundance and diversity of soil microbial communities that had been degraded by decades of intensive land use, and community compositional change can be predicted by the disturbance tolerance of soil microbial taxonomic and functional groups.

Impact of Ecological Restoration on the Physicochemical Properties and Bacterial Communities in Alpine Mining Area Soils

Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04-8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm-1 in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30-27.98 cmol·kg-1) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg-1 over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai-Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems.

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.

Insights on the assembly processes and drivers of soil microbial communities in different depth layers in an abandoned polymetallic mining district

Soil microbes, which play crucial roles in maintaining soil functions and restoring degraded lands, are impacted by heavy metal pollution. This study investigated the vertical distribution of bacterial communities along the soil profiles across four types of areas (heavy metal pollution level: tailings heap area > phytoremediation area > natural restoration area > original forest area) in an abandoned polymetallic mining district by 16S rRNA sequencing, and aimed to disentangle the assembly mechanisms and key drivers of the vertical variation in bacterial community structure. Bacterial diversity and composition were found to vary remarkably between the depth layers in all types of areas, with heterogeneous selection dominated the vertical distribution pattern of soil bacterial communities. Pearson correlation analysis and partial Mantel test revealed that soil nutrients mainly shaped the vertical distribution of bacterial microbiota along soil profiles in the original forest and natural restoration areas. Ni, As, and bioavailable As were the key drivers regulating the vertical variation of bacterial assemblages in the phytoremediation area, whereas Pb, pH, soil organic carbon, and available nitrogen were crucial drivers in the tailings heap area. These findings reveal the predominant assembly mechanisms and drivers governing the vertical distribution of soil bacterial microbiota and indicate the efficiency of phytoremediation and ecological restoration on ameliorating edaphic micro-ecosystems in heavy metal-contaminated areas.

Phytoremediation strategies for heavy metal-contaminated soil by selecting native plants near mining areas in Inner Mongolia

Phytoremediation technology, as an eco-friendly and cost-effective approach, is widely used to restore soil contaminated by heavy metal(loid)s. However, the adaptability and absorption capacity of plants to multiple elements are the crucial factors affecting the application of phytoremediation in mining areas. In this study, dominant native plant species and their paired soils were collected near a lead-zinc mine in Inner Mongolia, to assess the ecological risk of heavy metal(loid)s and phytoremediation potential. The results showed that Cd and As were the dominant soil pollutants, with levels of 90.91% and 100%, respectively, exceeding the risk intervention values for soil contamination of agricultural land. The rates of Pb, Cu, and Zn exceeding the risk screening values were 69.70%, 60.61%, and 96.97%, respectively. Extremely high ecological risk of heavy metal(loid)s was observed in this area. The ability of native plants accumulating heavy metals varied among species. The bioconcentration factor (BCF) varied from 0.14 to 2.59 for Cd, 0.02 to 0.45 for As, 0.06 to 0.76 for Pb, 0.05 to 2.69 for Cr, 0.15 to 1.00 for Cu, and 0.22 to 4.10 for Zn. Chinese Cinquefoil Herb (Potentilla chinensis Ser.) showed the potential to accumulate multiple toxic elements based on the biomass, shoot content, translocation factor (TF), BCF, and metal extraction rate (MER), while, other species showed the potential to accumulate single toxic element: goosefoot (Chenopodium album L.), Lespedeza daurica (Laxm.) Schindl. and peashrubs (Caragana korshinskii Kom.), Herba Artemisiae Scopariae (Artemisia capillaris Thunb.), alfalfa (Medicago sativa L.), and Moldavian Dragonhead (Dracocephalum moldavica L.) for Cd, As, Cr, Cu, and Zn, respectively. Furthermore, wild leek (Allium ramosum L.), cogongrass (Imperata cylindrica (L.) Beauv.), fringed sagebrush (Artemisia frigida Willd.), and field bindweed (Convolvulus arvensis L.) were selected for phytostabilization of specific elements, considering the heavy metal contents in the roots and low TF values. This study provides a reference for selecting appropriate species for the remediation of heavy metal-contaminated soils in certain mining areas.

Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia

Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.

Past, present and future trends in the remediation of heavy-metal contaminated soil - Remediation techniques applied in real soil-contamination events

Most worldwide policy frameworks, including the United Nations Sustainable Development Goals, highlight soil as a key non-renewable natural resource which should be rigorously preserved to achieve long-term global sustainability. Although some soil is naturally enriched with heavy metals (HMs), a series of anthropogenic activities are known to contribute to their redistribution, which may entail potentially harmful environmental and/or human health effects if certain concentrations are exceeded. If this occurs, the implementation of rehabilitation strategies is highly recommended. Although there are many publications dealing with the elimination of HMs using different methodologies, most of those works have been done in laboratories and there are not many comprehensive reviews about the results obtained under field conditions. Throughout this review, we examine the different methodologies that have been used in real scenarios and, based on representative case studies, we present the evolution and outcomes of the remediation strategies applied in real soil-contamination events where legacies of past metal mining activities or mine spills have posed a serious threat for soil conservation. So far, the best efficiencies at field-scale have been reported when using combined strategies such as physical containment and assisted-phytoremediation. We have also introduced the emerging problem of the heavy metal contamination of agricultural soils and the different strategies implemented to tackle this problem. Although remediation techniques used in real scenarios have not changed much in the last decades, there are also encouraging facts for the advances in this field. Thus, a growing number of mining companies publicise in their webpages their soil remediation strategies and efforts; moreover, the number of scientific publications about innovative highly-efficient and environmental-friendly methods is also increasing. In any case, better cooperation between scientists and other soil-related stakeholders is still required to improve remediation performance.

Active tailings disturb the surrounding vegetation soil fungal community: Diversity, assembly process and co-occurrence patterns

Soil fungi play an important role in the soil biogeochemical cycle and are important biological indicators for the ecological remediation of mine tailings contaminated sites, therefore understanding the characteristics of soil fungal communities is a key aspect of pollution remediation. However, the influence of biological factors on the characteristics of fungal community diversity; assembly mechanisms and co-occurrence patterns of fungal community along environmental gradients around tailings are not well understood. In this study, soil samples from forest, agriculture and grass around tailings were collected to reveal the assembly mechanisms and co-occurrence patterns of soil fungal community and to quantify the contribution of abiotic and biotic factors to fungal diversity. The results suggest that vegetation types and Cu concentration together drive the distribution of fungal diversity. We found that Exophiala has potential as a biomarker species indicative of restoration progress. Increased environmental stress accelerates the process of changing fungal community assemblages from stochastic to deterministic, while also allowing fungal communities tend to resist tailings-induced environmental stresses through species coexistence. Together, this study provides new insights into the influence of biological factors on fungal community diversity, as well as revealing mechanisms of fungal community assembly and co-occurrence patterns, which are important for understanding the maintenance mechanisms of fungal community diversity and ecological remediation of tailings-contaminated soils.

Woody plants have the advantages in the phytoremediation process of manganese ore with the help of microorganisms

The serious ecological damage caused by mining activities cannot be ignored. The use of an environmentally friendly restoration method to rebuild the vegetation and soil environment in the mining area has attracted more and more attention. This paper aims to study soil quality as well as vegetation characteristics of four woody species including Pinus massoniana (P. massoniana), Broussonetia papyrifera (B. papyrifera), Koelreuteria paniculata (K. paniculata), Osmanthus fragrans (O. fragrans), and two herbaceous species including Setaria viridis (S. viridis) and Cynodon dactylon (C. dactylon). In addition, we further clarified the effects of B. papyrifera and K. paniculata on soil nutrients and microbial communities after restoration. The results showed that the vegetation restoration area had better soil quality and plant community diversity, and the woody plants restoration effect were better. Compared with slag, B. papyrifera and K. paniculata remediation could improve soil pH and mitigate heavy metal contamination in mining areas, but was not effective in enhancing Soil Organic Matter (SOM), Total Nitrogen (TN), Total Potassium (TK) and Total Phosphorus (TP). In addition, the abundance and diversity of soil bacterial communities were increased. Of all the study sites, Proteobacteria had the greatest dominance. Vegetation restoration resulted in an increase in the relative abundance of Acidobacteria, while a decrease in Actinobacteria, Cyanobacteria and Firmicutes. With the restoration of vegetation, the increase of pH, the change of TN, SOM, TK, TP and the mitigation of Manganese (Mn) pollution were the main reasons affecting the soil microbial community. This study has great significance for understanding the ecological changes in the mining area after artificially mediated vegetation restoration, including changes in soil environment, plant community and microbial community, and woody plants will be more encouraged for the restoration of manganese mining areas.

Comparison of Soil Bacterial Communities under Canopies of Pinus tabulaeformis and Populus euramericana in a Reclaimed Waste Dump

To compare the effects of different remediation tree species on soil bacterial communities and provide a theoretical basis for the selection of ecosystem function promotion strategies after vegetation restoration, the characteristic changes in soil bacterial communities after Pinus tabulaeformis and Populus euramericana reclamation were explored using high-throughput sequencing and molecular ecological network methods. The results showed that: (1) With the increase in reclamation years, the reclaimed soil properties were close to the control group, and the soil properties of Pinus tabulaeformis were closer to the control group than those of P. euramericana. (2) The dominant bacteria under the canopies of P. tabulaeformis and P. euramericana was the same. Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Bacteroidetes, and Cyanobacteria were the dominant bacteria in the restored soil, accounting for more than 95% of the total abundance. The average values of the Shannon diversity index, Simpson diversity index, Chao 1 richness estimator, and abundance-based coverage estimator of the bacterial community in the P. euramericana reclaimed soil were higher than those in the P. tabulaeformis reclaimed soil. The influence of reclamation years on the bacterial community of samples is greater than that of species types. (3) The results of ecological network construction showed that the total number of nodes, total number of connections, and average connectivity of the soil bacterial network under P. euramericana reclamation were greater than those under P. tabulaeformis reclamation. The bacterial molecular ecological network under P. euramericana was more abundant. (4) Among the dominant bacteria, the relative abundance of Actinobacteria was negatively correlated with soil pH, soil total nitrogen content, and the activities of urease, invertase, and alkaline phosphatase, while the relative abundance of Proteobacteria and Bacteroidetes was positively correlated with these environmental factors. The relationship between the soil bacterial community of P. tabulaeformis and P. euramericana and the environmental factors is not completely the same, and even the interaction between some environmental factors and bacteria is opposite.

Effects of composite materials and revegetation on soil nutrients, chemical and microbial properties in rare earth tailings

The mining of ionic rare earth elements in Ganzhou left large area of barren tailings with severe vegetation destruction in pressing needs of remediation. However, the remediating effects of soil additives combined with revegetation on the preservation of nutrients in the tailings and microbial communities were rarely studied. For this purpose, pilot experiments were implemented in a field, with the control group (CK) only cultivating plants without adding materials, and three treatments including peanut straw biochar composite (T1), phosphorus‑magnesium composite (T2) and modified zeolite composite (T3) along with the cultivation of Medicago sativa L., Paspalum vaginatum Sw. and Lolium perenne L. Soil pH and organic matter in CK significantly decreased from 4.90 to 4.17 and from 6.62 g/kg to 3.87 g/kg after six months, respectively (p ≤ 0.05), while all the treatments could effectively buffer soil acidification (over 5.74) and delay the loss of soil organic matter. Soil cation exchange capacity was still below the detection limit in all the groups except T2. The results of rainfall runoff monitoring indicated that compared with CK, only T2 could significantly reduce the runoff loss of soil NO₃^- and SO₄^2- by 45.61 %-75.78 % and 64.03 %-76.12 %, respectively (p ≤ 0.05). Compared with CK, the bacterial diversity in T2 and T3 significantly increased 21.18 % and 28.15 %, respectively (p ≤ 0.05), while T1 didn't change the bacterial or fungal diversity (p > 0.05). Co-occurrence network analysis showed that compared with CK, the whole microbial communities interacted more closely in the three treatments. Functional prediction of the microbial communities revealed all the treatments were dominated by carbon transforming bacteria and saprotrophic fungi except T2. This study demonstrated that the composite materials combined with revegetation couldn't retain soil nitrogen compounds and sulfate in rare earth tailings in the long term.

Short-Term Vegetation Restoration Enhances the Complexity of Soil Fungal Network and Decreased the Complexity of Bacterial Network

Different vegetation restoration methods may affect the soil’s physicochemical properties and microbial communities. However, it is not known how the microbial network’s complexity of the bacterial and fungal communities respond to short-term vegetation restoration. We conducted a short-term ecological restoration experiment to reveal the response of the soil’s microbial community and microbial network’s stability to initial vegetation restoration during the restoration of the degraded grassland ecosystem. The two restoration methods (sowing alfalfa (Medicago sativa, AF) and smooth brome (Bromus inermis, SB)) had no significant effect on the alpha diversity of the fungal community, but the SB significantly increased the alpha diversity of the soil surface bacterial community (p < 0.01). The results of NMDS showed that the soil’s fungal and bacterial communities were altered by a short-term vegetation restoration, and they showed that the available phosphorus (AP), available potassium (AK), and nitrate nitrogen (nitrate-N) were closely related to changes in bacterial and fungal communities. Moreover, a short-term vegetation restoration significantly increased the complexity and stability of fungi ecological networks, but the opposite was the case with the bacteria. Our findings confirm that ecological restoration by sowing may be favorable to the amelioration of soil fungi complexity and stability in the short-term. Such findings may have important implications for soil microbial processes in vegetation recovery.

Synergistic Impacts of Arsenic and Antimony Co-contamination on Diazotrophic Communities

Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N₂ into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s.

Low Frequency of Plants Associated with Symbiotic Nitrogen-Fixers Exhibits High Frequency of Free-Living Nitrogen Fixing Bacteria: A Study in Karst Shrub Ecosystems of Southwest China

Plants associated with symbiotic nitrogen-fixers and soil free-living nitrogen-fixing bacteria are good indicators for detecting the source of nitrogen in natural ecosystems. However, the community composition and diversity of plants associated with symbiotic nitrogen-fixers and soil free-living nitrogen-fixing bacteria in karst shrub ecosystems remain poorly known. The community composition and diversity of soil free-living nitrogen-fixing bacteria and plants, as well as the soil physical–chemical properties were investigated in 21 shrub plots (including different topographies and plant types). The frequency of plants associated with symbiotic nitrogen-fixers was found to be low in the 21 shrub plots. The soil free-living nitrogen-fixing bacterial community structure varied among the 21 shrub soils. Based on a variance partitioning analysis, topography, plant type, and soil pH explained 48.5% of the observed variation in bacterial community structure. Plant type had a predominant effect on community structure, and topography (aspect and ascent) and soil pH had minor effects. A negative correlation between the abundance of the soil free-living nitrogen-fixing bacterial community and the richness index for plants associated with symbiotic nitrogen-fixers was observed. The result of the low frequency of plants associated with symbiotic nitrogen-fixers highlights the importance of sources of fixed nitrogen by soil free-living nitrogen-fixing bacteria in the nitrogen limitation shrub ecosystem of the karst regions.

Variation in the diazotrophic community in a vertical soil profile contaminated with antimony and arsenic

A nitrogen (N) deficiency will usually hinder bioremediation efforts in mining-derived habitats such as occurring in mining regions. Diazotrophs can provide N to support the growth of plants and microorganisms in these environments. However, diazotrophic communities in mining areas have been not studied frequently and are more poorly understood than those in other environments, such as in agricultural soils or in the presence of legumes. The current study compares the differences in depth-resolved diazotrophic community compositions and interactions in two contrasting sites (to depths of 2 m), including a highly contaminated and a moderately contaminated site. Antimony (Sb) and arsenic (As) co-contamination induced a loosely connected biotic interaction, and a selection of deep soils by diazotrophic communities. Multiple lines of evidence, including the enrichment of diazotrophic taxa in the highly contaminated sites, microbe-microbe interactions, environment-microbe interactions, and a machine learning approach (random forests regression), demonstrated that Rhizobium was the keystone taxon within the vertical profile of contaminated soil and was resistant to the Sb and As contaminant fractions. All of these observations suggest that one diazotroph, Rhizobium, may play an important role in N fixation in the examined contaminated sites.

Native plants facilitate vegetation succession on amended and unamended mine tailings

Facilitating the establishment of native pioneer plant species on mine tailings with inherent metal and/or acid tolerance is important to speed up natural succession at minimal cost, especially in remote areas where phytoremediation can be labor intensive. We investigated vegetation community dynamics after ∼48 years of succession along two legacy Ni-Cu mine tailings and waste rock deposits in the Sudbury Basin, Ontario, Canada with and without various site amendments (i.e. liming and fertilization) and planting. Metal/acid tolerant pioneer plants (Betula papyrifera, Populus tremuloides, Pohlia nutans) appeared to facilitate the establishment of less tolerant species. Conifers and nitrogen-fixers less tolerant to site conditions were planted at the fully amended (limed, fertilized, planted) mine tailings site in the 1970s, but conifers were not propagating at the site or facilitating understory succession. The planted nitrogen-fixing leguminous species Lotus corniculatus was, however, associated with increased diversity. These findings have implications for long-term reclamation strategies in acidic mine waste deposits utilizing native species, as primary colonizing tree species are only recently emerging as candidates for phytoremediation. Novelty statement The potential for native species to act as facilitators for vegetation colonization has rarely been investigated on tailings, despite wide use in remediation of less toxic sites. This study provides a retrospective of over 40 years of plant growth following initial treatment of toxic tailings. We observed that regardless of tailings geochemical conditions, acid/metal tolerant pioneer plants were facilitating ecological succession on acidic Ni-Cu mine tailings sites.

The microbial community from the early-plant colonizer (Baccharis linearis) is required for plant establishment on copper mine tailings

Plants must deal with harsh environmental conditions when colonizing abandoned copper mine tailings. We hypothesized that the presence of a native microbial community can improve the colonization of the pioneer plant, Baccharis linearis, in soils from copper mining tailings. Plant growth and microbial community compositions and dynamics were determined in cultivation pots containing material from two abandoned copper mining tailings (Huana and Tambillos) and compared with pots containing fresh tailings or surrounding agricultural soil. Controls without plants or using irradiated microbe-free substrates, were also performed. Results indicated that bacteria (Actinobacteria, Gammaproteobacteria, and Firmicutes groups) and fungi (Glomus genus) are associated with B. linearis and may support plant acclimation, since growth parameters decreased in both irradiated (transiently without microbial community) and fresh tailing substrates (with a significantly different microbial community). Consistently, the composition of the bacterial community from abandoned copper mining tailings was more impacted by plant establishment than by differences in the physicochemical properties of the substrates. Bacteria located at B. linearis rhizoplane were clearly the most distinct bacterial community compared with those of fresh tailings, surrounding soil and non-rhizosphere abandoned tailings substrates. Beta diversity analyses showed that the rhizoplane bacterial community changed mainly through species replacement (turnover) than species loss (nestedness). In contrast, location/geographical conditions were more relevant than interaction with the plants, to explain fungal community differences.

Impacts and tolerance responses of Coprinus comatus and Pleurotus cornucopiae on cadmium contaminated soil

Large amounts of cadmium (Cd) have been discharged into soil with the rapid development of industry. In this study, we revealed the impacts of Coprinus comatus (C. comatus) and Pleurotus cornucopiae (P. cornucopiae) on soil and the tolerance responses of macrofungi in the presence of Cd by the analysis of soil biochemical properties and macrofungi growth indexes. Results showed that with the cultivation of C. comatus and P. cornucopiae, the HOAc-extractable Cd in soil individually reduced by 9.53% and 11.35%, the activities of soil urease, acid phosphatase, dehydrogenase, and Fluorescein diacetate (FDA) hydrolysis increased by 18.11-101.45%, 8.39-18.24%, 9.37-55.50% and 28.94-41.92%, respectively. Meanwhile, different soil bacterial communities were observed with various macrofungi cultivations. Also, Cd accumulation significantly enhanced the macrofungi antioxidant enzyme activities, which increased by 24.10-45.43%, 30.11-61.53% and 7.03-26.81% for catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) activities in the macrofungi, respectively. Moreover, the enhanced macrofungi endophytic bacterial diversities with Cd existence was firstly observed in the present experiment. These findings revealed the possible Cd resistance mechanisms in macrofungi, suggesting C. comatus and P. cornucopiae were promising ameliorators for Cd contaminated soil.

Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar

Abandoned unrestored mines are an important environmental concern as they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic and unfavorable biotic conditions. However, some pioneer tree species having high levels of genetic diversity, such as balsam poplar (Populus balsamifera), can naturally colonize these sites and initiate plant succession. This suggests that some tree genotypes are likely more suited for acclimation to the conditions of mine wastes. In this study, we selected two contrasting mine waste storage facilities (waste rock from a gold mine and tailings from a molybdenum mine) from the Abitibi region of Quebec (Canada), on which poplars were found to have grown naturally. First, we assessed in situ the impact of vegetation presence on each mine waste type. The presence of balsam poplars improved soil health locally by modifying the physicochemical properties (e.g., higher nutrient content and pH) of the mine wastes and causing an important shift in their bacterial and fungal community compositions, going from lithotrophic communities that dominate mine waste environments to heterotrophic communities involved in nutrient cycling. Next, in a greenhouse experiment we assessed the impact of plant genotype when grown in these mine wastes. Ten genotypes of P. balsamifera were collected locally, found growing either at the mine sites or in the surrounding natural forest. Tree growth was monitored over two growing seasons, after which the effects of genotype-by-environment interactions were assessed by measuring the physicochemical properties of the substrates and the changes in microbial community assembly. Although substrate type was identified as the main driver of rhizosphere microbiome diversity and community structure, a significant effect due to tree genotype was also detected, particularly for bacterial communities. Plant genotype also influenced aboveground tree growth and the physicochemical properties of the substrates. These results highlight the influence of balsam poplar genotype on the soil environment and the potential importance of tree genotype selection in the context of mine waste revegetation.

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.

Changes of root microbial populations of natively grown plants during natural attenuation of V-Ti magnetite tailings

Mine tailings contain dangerously high levels of toxic metals which pose a constant threat to local ecosystems. Few naturally grown native plants can colonize tailings site and the existence of their root-associated microbial populations is poorly understood. The objective of this study was to give further insights into the interactions between native plants and their microbiota during natural attenuation of abandoned V-Ti magnetite mine tailings. In the present work, we first examined the native plants' potential for phytoremediation using plant/soil analytical methods and then investigated the root microbial communities and their inferred functions using 16 S rRNA-based metagenomics. It was found that in V-Ti magnetite mine tailings the two dominant plants Bothriochloa ischaemum and Typha angustifolia were able to increase available nitrogen in the rhizosphere soil by 23.3% and 53.7% respectively. The translocation factors (TF) for both plants indicated that B. ischaemum was able to accumulate Pb (TF = 1.212), while T. angustifolia was an accumulator of Mn (TF = 2.502). The microbial community structure was more complex in the soil associated with T. angustifolia than with B. ischaemum. The presence of both plants significantly reduced the population of Acinetobacter. Specifically, B. ischaemum enriched Massilia, Opitutus and Hydrogenophaga species while T. angustifolia significantly increased rhizobia species. Multivariate analyses revealed that among all tested soil variables Fe and total organic carbon (TOC) could be the key factors in shaping the microbial structure. The putative functional analysis indicated that soil sample of B. ischaemum was abundant with nitrate/nitrite reduction-related functions while that of T. angustifolia was rich in nitrogen fixing functions. The results indicate that these native plants host a diverse range of soil microbes, whose community structure can be shaped by plant types and soil variables. It is also possible that these plants can be used to improve soil nitrogen content and serve as bioaccumulators for Pb or Mn for phytoremediation purposes.

Distribution of antibiotic resistance genes in an agriculturally disturbed lake in China: Their links with microbial communities, antibiotics, and water quality

In this study, six antibiotic resistance genes (ARGs), one mobile genetic element (int1), and their relation with microbial communities, antibiotics, and water quality were investigated in and around of an agriculturally disturbed lake, namely, Lake Honghu. The ARGs and int1 in the research area had a 100 % detection frequency in each sample during two sampling times. The ARGs were higher in the rivers and inlets than in Lake Honghu. Sul1 was the main ARG in this area. Antibiotics, nutrients, and dissolved oxygen were significantly, positively, and negatively correlated with nearly all of the ARGs, respectively. This finding suggests that reducing antibiotics and the eutrophication level could reduce the risk of ARGs. Microbial community shift had the most direct contribution to ARG variation. However, when the indirect effect was considered, environmental factors contributed 34 % to the ARGs' variance, the microbial community contributed 28 %, and their joint effect contributed 27 % to the ARG profiles. The abundance of Firmicutes, Gemmatimonadetes, Proteobacteria, etc. and their positive correlation with ARGs were significant, suggesting that these phyla probably carry ARGs. The study provides a systematic profile of ARG distribution and dissemination in a typical Chinese lake and new ideas to control this emerging contaminant in lakes.

Response of microbial community composition in soils affected by coal mine exploitation

Surface mining activities, despite their benefits, lead to the deterioration of local and regional environmental quality and play a role in global ecosystem pollution. This research aimed to estimate the culturable microbial population structure at five locations near the opencast coal mine "Kakanj" (Bosnia and Herzegovina) via agar plate and phospholipid fatty acids (PLFA) method and to establish its relationship to the physical and chemical properties of soil. Using the ICP-OES method, the heavy metal pollution of all examined locations (overburden, former grass yard, forest, arable soil, and greenhouse) was observed. Substantial variations among the sites regarding the most expressed indicators of heavy metal pollution were noted; Cr, Pb, Ni, and Cu content ranged from 63.17 to 524.47, 20.57 to 349.47, 139.13 to 2785.67, and 25.97 to 458.73 mg/kg, respectively. In the overburden sample, considerable low microbial activity was detected; the bacterial count was approximately 6- to 18-fold lower in comparison with the other samples. PLFA analysis showed the reduction of microbial diversity, reflected through the prevalence of normal and branched saturated fatty acids, their ratio (ranged from 0.92 to 7.13), and the absence of fungal marker 18:2ω6 fatty acid. The principal component analysis showed a strong negative impact of heavy metals Na and B on main microbial and PLFA profiles. In contrast, stock of main chemical parameters, including Ca, K, Fe, and pH, was positively correlated with the microbial community structure.

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.

Revegetation by sowing reduces soil bacterial and fungal diversity

AIM

The aim of this study was to understand the effects of revegetation on the diversity of bacteria and fungi in soil by sowing a single species and exploring the underlying mechanism.

LOCATION

Beijing, China.

TAXON

Plants and Microbes.

METHODS

In a short-term ecological restoration experiment, one natural recovery treatment and three seed sowing treatments were chosen to assess their effects on the alteration of fungal and bacterial diversity. Plant species richness, abundance, and height were investigated. The diversity of fungi and bacteria was analyzed by high-throughput sequencing technologies. Linear mixed-effects model analysis was used to examine the effects of different restoration methods on biodiversity and ecosystem functions. Pearson's correlation analysis, analysis of covariance, and structural equation modeling (SEM) were used to examine the relationship between biodiversity and environmental factors.

RESULTS

Species richness and the Shannon-Wiener Index (H') of plants in the sown treatments were lower than in the natural recovery treatment, especially with sowing of Medicago sativa L. Similarly, the sum of the observed species and H' of fungi and bacteria significantly decreased in the sown treatments. Moreover, plant density, community coverage, and soil moisture increased markedly, while soil bulk density decreased in the sown treatments. Importantly, SEM showed that sown treatments reduced the diversity of plants through increasing plant density, while it decreased the diversity of fungi and bacteria through decreasing the plant diversity and increasing soil moisture.

MAIN CONCLUSIONS

Our findings confirm that ecological restoration by sowing could improve soil conditions, but may be unfavorable to the amelioration of soil microbial diversity in the short-term. Restoration practitioners should consider long-term studies on the dynamics of biodiversity in the above- and belowground after revegetation by native species to achieve goals related to biodiversity conservation.

Subsoil microbial community responses to air exposure and legume growth depend on soil properties across different depths

Anthropogenic disturbance, such as agricultural and architectural activities, can greatly influence belowground soil microbes, and thus soil formation and nutrient cycling. The objective of this study was to investigate microbial community variation in deep soils affected by strong disturbances. In present study, twelve soil samples were collected from different depths (0–300 cm) and placed onto the surface. We investigated the structure variation of the microbial community down through the soil profiles in response to disturbance originated by legume plants (robinia and clover) cultivation vs. plant-free controls. The high-throughput sequencing of 16S rRNA genes showed that microbial α-diversity decreased with depth, and that growing both plants significantly impacted the diversity in the topsoil. The soil profile was clustered into three layers: I (0–40 cm), II (40–120 cm), and III (120–300 cm); with significantly different taxa found among them. Soil properties explained a large amount of the variation (23.5%) in the microbial community, and distinct factors affected microbial assembly in the different layers, e.g., available potassium in layer I, pH and total nitrogen in layer II, pH and organic matter in layer III. The prediction of metabolic functions and oxygen requirements indicated that the number of aerobic bacteria increased with more air exposure, which may further accelerate the transformation of nitrogen, sulfur, carbon, and pesticides in the soil. The diversity of soil microorganisms followed a depth-decay pattern, but became higher following legume growth and air exposure, with notable abundance variation of several important bacterial species, mainly belonging to Nitrospira, Verrucomicrobia, and Planctomycetes, and soil properties occurring across the soil profiles.

Implications of spatial heterogeneity of tailing material and time scale of vegetation growth processes for the design of phytostabilisation

Phytostabilisation projects for tailing dams depend on processes occurring at spatial scales of 10⁶ m² and at decadal time scales. Most experiments supporting the design and monitoring of such projects have much smaller spatial and time scales. Usually, they are only designed for one single scale. Here, we report the results of three coupled experiments performed at pot, lysimeter and field plot scales using six sampling periodstimes from 3 to 20 months. The work explicitly accounts for the sampling times when evaluating the effects of amendments on the performance of plants grown in tailing substrates. Two treatments with potentially complementary roles were applied: zeolites to decrease availability of Cd, Cu, Pb and Zn and green fertilizer to increase the availability of nutrients. Zeolites have a positive influence on plant development, especially in the early stages. Analyses of the pooled datasets for all sampling times revealed the possibility of predicting plant physiological variables, such as protein concentrations, pigments and oxidative stress enzyme activities, as a function of the factors extracted by principal component analysis from the metal concentrations in plants, phosphorus concentrations in plants, and sampling times. Two potentially general methodological rules were extracted: account for the spatial geochemical variability of tailings, and cover the broadest possible range of time scales by experiments. The proposed experimental methodology can be of general use for the design of tailing dam remediation technologies with improvements involving the set of measured variables and sampling frequency and by carefully relating the costs to the institutional aspects of tailing dam management.

Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification

Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.

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.

Effects of Amendments on Soil Microbial Diversity, Enzyme Activity and Nutrient Accumulation after Assisted Phytostabilization of an Extremely Acidic Metalliferous Mine Soil

Current criteria for successful phytostabilization of metalliferous mine wastelands have paid much attention to soil physico-chemical properties and vegetation characteristics. However, it remains poorly understood as to how the soil microbial community responds to phytostabilization practices. To explore the effects of amendments on the microbial community after assisted phytostabilization of an extremely acidic metalliferous mine soil (pH < 3), a pot experiment was performed in which different amendments and/or combinations including lime, nitrogen-phosphorus-potassium (NPK) compound fertilizer, phosphate fertilizer and river sediment were applied. Our results showed the following: (1) The amendments significantly increased soil microbial activity and biomass C, being 2.6–4.9 and 1.9–4.1 times higher than those in the controls, respectively. (2) The activities of dehydrogenase, cellulase and urease increased by 0.9–7.5, 2.2–6.8 and 6.7–17.9 times while acid phosphatase activity decreased by 58.6%–75.1% after the application of the amendments by comparison with the controls. (3) All the amendments enhanced the nutrient status of the mine soil, with organic matter, total nitrogen and total phosphorus increased by 5.7–7.8, 3.1–6.8 and 1.1–1.9 times, relative to the mine soil. In addition, there were strong positive correlations between soil microbial community parameters and nutrient factors, suggesting that they were likely to be synergistic. From an economic view, the combination of lime (25 t ha−1) and sediment from the Pearl River (30%) was optimal for functional rehabilitation of the microbial community in the extremely acidic metalliferous mine soil studied.

Mine landslide susceptibility assessment using IVM, ANN and SVM models considering the contribution of affecting factors

The fragile ecological environment near mines provide advantageous conditions for the development of landslides. Mine landslide susceptibility mapping is of great importance for mine geo-environment control and restoration planning. In this paper, a total of 493 landslides in Shangli County, China were collected through historical landslide inventory. 16 spectral, geomorphic and hydrological predictive factors, mainly derived from Landsat 8 imagery and Global Digital Elevation Model (ASTER GDEM), were prepared initially for landslide susceptibility assessment. Predictive capability of these factors was evaluated by using the value of variance inflation factor and information gain ratio. Three models, namely artificial neural network (ANN), support vector machine (SVM) and information value model (IVM), were applied to assess the mine landslide sensitivity. The receiver operating characteristic curve (ROC) and rank probability score were used to validate and compare the comprehensive predictive capabilities of three models involving uncertainty. Results showed that ANN model achieved higher prediction capability, proving its advantage of solve nonlinear and complex problems. Comparing the estimated landslide susceptibility map with the ground-truth one, the high-prone area tends to be located in the middle area with multiple fault distributions and the steeply sloped hill.

The bacterial community of Quesnel Lake sediments impacted by a catastrophic mine tailings spill differ in composition from those at undisturbed locations - two years post-spill

The West Basin of Quesnel Lake (British Columbia, Canada) suffered a catastrophic disturbance event in August 2014 when mine tailings and scoured natural material were deposited into the lake’s West Basin due to an impoundment failure at the adjacent Mount Polley copper-gold mine. The deposit covered a significant portion of the West Basin floor with a thick layer of material. Since lake sediments host bacterial communities that play key roles in the geochemical cycling in lacustrine environments, it is important to understand which groups inhabit the newly deposited material and what this implies for the ecological function of the West Basin. Here we report a study conducted two years post-spill, comparing the bacterial communities from sediments of both disturbed and undisturbed sites. Our results show that sediments from disturbed sites differed in physical and chemical properties than those in undisturbed sites (e.g. higher pH, particle size and Cu concentration). Furthermore, bacterial communities from the disturbed sites appeared to be legacy communities from the tailings impoundment, with metabolic potential revolving mainly around the cycling of S and metals, whereas the ones from the undisturbed sites were associated with the cycling of N.

Variance in bacterial communities, potential bacterial carbon sequestration and nitrogen fixation between light and dark conditions under elevated CO2 in mine tailings

This study is the first to show the response of bacterial communities with primary carbon and nitrogen fixers to elevated CO₂ (eCO₂) in light and dark conditions based on 6 months of culture growth. Carbon sequestration and nitrogen fixation were analyzed by ¹³C and ¹⁵N isotope labeling using ¹³C-labeled CO₂ and ¹⁵N-labeled N₂, followed by pyrosequencing and DNA-based stable isotope probing (SIP) to identify carbon fixers and nitrogen fixers. The results indicated that eCO₂ decreased the Chao 1 richness, and the eCO₂-light treatment exhibited the highest Shannon diversity. In addition, eCO₂ (in either light or dark conditions) greatly increased the relative abundances of bacteria belonging to the classes Betaproteobacteria and Alphaproteobacteria. The ¹³C atom % in the mine tailings increased from 1.108 to 1.84 ± 0.11 under light conditions and 1.52 ± 0.17 under dark conditions after 6 months of culture growth. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I-coding gene (cbbL) copy numbers were 164.30-fold and 40.36-fold higher than RubisCO form II-coding gene (cbbM) copy numbers in the heavy fractions with a buoyant density of 1.7388 g·mL^-1 relative to the buoyant density gradients of DNA fractions obtained under eCO₂-light and eCO₂-dark treatment, respectively. The Proteobacteria-like cbbL genes were dominant in the carbon fixers. In addition, the ¹⁵N atom % in the mine tailings increased from 0.366 to 0.454 ± 0.021 in light conditions and 0.437 ± 0.018 in dark conditions. Furthermore, uncultured nitrogen-fixing bacteria were the dominant nitrogen fixers in light conditions, and bacteria harboring the Bradyrhizobium-like nifH and Leptospirillum-like nifH genes were the dominant nitrogen fixers in dark conditions. These first data for a mine tailing ecosystem are inconsistent with those obtained for a range of other ecosystems, in which the effects of CO₂ were limited to several nonphotoautotrophic communities and different nitrogen fixers.

A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining

Microorganisms are useful environmental indicators, able to deliver essential insights to processes regarding mine land rehabilitation. To compare microbial communities from a chronosequence of mine land rehabilitation to pre-disturbance levels from references sites covered by native vegetation, we sampled non-rehabilitated, rehabilitating and reference study sites from the Urucum Massif, Southwestern Brazil. From each study site, three composed soil samples were collected for chemical, physical, and metagenomics analysis. We used a paired-end library sequencing technology (NextSeq 500 Illumina); the reads were assembled using MEGAHIT. Coding DNA sequences (CDS) were identified using Kaiju in combination with non-redundant NCBI BLAST reference sequences containing archaea, bacteria, and viruses. Additionally, a functional classification was performed by EMG v2.3.2. Here, we provide the raw data and assembly (reads and contigs), followed by initial functional and taxonomic analysis, as a base-line for further studies of this kind. Further investigation is needed to fully understand the mechanisms of environmental rehabilitation in tropical regions, inspiring further researchers to explore this collection for hypothesis testing.

The Effects of Different Lead Pollution Levels on Soil Microbial Quantities and Metabolic Function with/without Salix integra Thunb. Planting

Background and Objectives: Salix integra Thunb., a fast-growing woody species, has been used in phytoremediation in recent years. It has the potential to accumulate high amounts of lead (Pb) in its growth, however, its effects on soil microbial community structure and function during its phytoextraction processes are not well understood, especially at different pollution levels. Materials and Methods: In our study, we set unplanted and planted Salix integra in areas with four levels of Pb treatments (0, 500, 1000, and 1500 mg/kg). After six months of planting, the rhizospheric soil, bulk soil, and unplanted soil were collected. Soil properties and microbes participating in nitrogen and phosphorus cycling were measured, following standard methods. Microbial metabolic functions were assessed using a Biolog-ECO microplate. Results: The bacteria (nitrogen-fixing bacteria, ammonifying bacteria, inorganic phosphorus-solubilizing bacteria, and nitrosobacteria) all increased in the 500 mg/kg treatment and decreased in the 1500 mg/kg treatment compared with the 0 mg/kg treatment, especially in rhizospheric soil. The microbial metabolisms decreased along with the increase of Pb levels, with the exception of the rhizospheric soil with a 500 mg/kg treatment. The metabolic patterns were relative to the pollution levels. The utilization of carbohydrates was decreased, and of amino acids or fatty acids was increased, in the 500 mg/kg treatment, while the opposite occurred in the 1500 mg/kg treatment. The values of soil properties, microbial quantities, and metabolic activities were higher in rhizospheric than bulk soil, while the differences between bulk and unplanted soil were different among the different Pb treatments. The soil properties had little effect on the microbial quantities and metabolic activities. Conclusions: S. integra planting and Pb levels had an interactive effect on the microbial community. In general, S. integra planting promoted microbial quantities and metabolic activity in rhizospheric soil. Lower Pb pollution increased microbial quantities and promoted the utilization of amino acids or fatty acids, while higher Pb concentrations decreased microbial quantities and metabolic activities, and promoted the utilization of carbohydrates.

Extreme Geochemical Conditions and Dispersal Limitation Retard Primary Succession of Microbial Communities in Gold Tailings

Microbial community succession in tailings materials is poorly understood at present, and likely to be substantially different from similar processes in natural primary successional environments due to the unusual geochemical properties of tailings and the isolated design of tailings storage facilities. This is the first study to evaluate processes of primary succession in microbial communities colonizing unamended tailings, and compare the relative importance of stochastic (predominantly dust-borne dispersal) and deterministic (strong selection pressures from extreme geochemical properties) processes in governing community assembly rates and trajectories to those observed in natural environments. Dispersal-based recruitment required > 6 months to shift microbial community composition in unamended, field-weathered gold tailings; and in the absence of targeted inoculants, recruitment was dominated by salt- and alkali-tolerant species. In addition, cell numbers were less than 10⁶ cells/g tailings until > 6 months after deposition. Laboratory experiments simulating microbial cell addition via dust revealed that high (>6 months' equivalent) dust addition rates were required to effect stabilization of microbial cell counts in tailings. In field-weathered tailings, topsoil addition during rehabilitation works exerted a double effect, acting as a microbial inoculant and correcting geochemical properties of tailings. However, microbial communities in rehabilitated tailings remained compositionally distinct from those of reference soils in surrounding environments. pH, water extractable Mg, and water extractable Fe emerged as major controls on microbial community composition in the field-weathered gold tailings. Overall, this study highlights the need for application of targeted microbial inoculants to accelerate rates of microbial community succession in tailings, which are limited primarily by slow dispersal due to physical and spatial isolation of tailings facilities from inoculant sources; and for geochemical properties of tailings to be amended to moderate values to encourage microbial community diversification and succession.

Glucose-induced changes in the bacterial communities of mine tailings at different acidification stages

Ecological restoration technologies applied to tailings can influence the associated bacterial communities. However, it is unknown if the shifts in these bacterial communities are caused by increased organic carbon. Glucose-induced respiration and high-throughput sequencing were used to assess the microbial activity and bacterial communities, respectively. Glucose addition increased the microbial activity, and glucose + ammonium nitrate addition resulted in slightly higher CO₂ emission than did glucose addition alone, suggesting that carbon and nitrogen limited microbial community growth. In neutral pH tailings, the bacterial taxa that increased by glucose addition were assigned to the phyla Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Planctomycetes. However, the bacterial taxa that increased by glucose addition in acidic tailings only belonged to the phylum Actinobacteria (maximum increase of 43.78%). In addition, the abundances of the total nitrogen-fixing genera and of the genus Arthrobacter (representing approximately 97.89% of the total nitrogen-fixing genera) increased by glucose addition in acidic tailings (maximum increase of 46.98%). In contrast, the relative abundances of the total iron- and (or) sulfur-oxidizing bacteria decreased (maximum decrease of 10.41%) in response to the addition of glucose. These findings indicate that the addition of organic carbon is beneficial to the development of bacterial communities in mine tailings.

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.

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.

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.