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

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.

A combined bibliometric and sustainable approach of phytostabilization towards eco-restoration of coal mine overburden dumps

Extraction of coal through opencast mining leads to the buildup of heaps of overburden (OB) material, which poses a significant risk to production safety and environmental stability. A systematic bibliometric analysis to identify research trends and gaps, and evaluate the impact of studies and authors in the field related to coal OB phytostabilization was conducted. Key issues associated with coal extraction include land degradation, surface and groundwater contamination, slope instability, erosion and biodiversity loss. Handling coal OB material intensifies such issues, initiating additional environmental and physical challenges. The conventional approach such as topsoiling for OB restoration fails to restore essential soil properties crucial for sustainable vegetation cover. Phytostabilization approach involves establishing a self-sustaining plant cover over OB dump surfaces emerges as a viable strategy for OB restoration. This method enhanced by the supplement of organic amendments boosts the restoration of OB dumps by improving rhizosphere properties conducive to plant growth and contaminant uptake. Criteria essential for plant selection in phytostabilization are critically evaluated. Native plant species adapted to local climatic and ecological conditions are identified as key agents in stabilizing contaminants, reducing soil erosion, and enhancing ecosystem functions. Applicable case studies of successful phytostabilization of coal mines using native plants, offering practical recommendations for species selection in coal mine reclamation projects are provided. This review contributes to sustainable approaches for mitigating the environmental consequences of coal mining and facilitates the ecological recovery of degraded landscapes.

Influence of conditioner and straw on the herbaceous plant-based phytoremediation copper tailings: a field trial at Liujiagou tailings pond, China

A field trial was performed to carry out an enhanced phytoremediation technique for multi-metal contaminated copper tailings by Sudan grass (Sorghum Sudanese), ryegrass (Lolium perenne L.), and Bermuda grass (Cynodon dactylon), using conditioner (TH-LZ01) and straw combination into composite amendments as soil amendments, aimed to obtain the maximum of phytoremediation effect. The results showed that compared with untreated herbaceous plants, the application of conditioner and straw planted with herbaceous plants reduced the pH and conductivity and increased the organic matter and water content of the copper tailings to different degrees. With the addition of conditioner and straw, the DTPA-Cd, DTPA-Cu, DTPA-Pb, and DTPA-Zn contents in the copper tailings showed a decreasing trend compared with the untreated group. The herbaceous plants were promoted to reduce the percentage contents of acid soluble fractions Cd, Cu, Pb, and Zn and to increase the percentage contents of reducible, oxidizable, and residual fractions heavy metals (Cd, Cu, Pb, and Zn) in the copper tailings to different degrees. The contents of Cd, Cu, Pb, and Zn in the underground part of herbaceous plants were higher than those in the aboveground part, and the contents of Cd, Cu, Pb, and Zn in the aboveground part and underground part decreased after adding conditioner and straw, which indicated that the conditioner and straw inhibited the transport of heavy metals in the plant. Furthermore, the principal component analysis showed that the application of conditioner and straw with planting ryegrass had more potential for improving the physicochemical properties of copper tailings and reducing heavy metal toxicity, followed by Bermuda grass and Sudan grass.

Extraction of heavy metals from copper tailings by ryegrass (Lolium perenne L.) with the assistance of degradable chelating agents

Heavy metal contamination is an urgent ecological governance problem in mining areas. In order to seek for a green and environmentally friendly reagent with better plant restoration effect to solve the problem of low efficiency in plant restoration in heavy metal pollution soil. In this study, we evaluated the effects of three biodegradable chelating agents, namely citric acid (CA), fulvic acid (FA) and polyaspartic acid (PASP), on the physicochemical properties of copper tailings, growth of ryegrass (Lolium perenne L.) and heavy metal accumulation therein. The results showed that the chelating agent application improved the physicochemical properties of copper tailings, increased the biomass of ryegrass and enriched more Cu and Cd in copper tailings. In the control group, the main existing forms of Cu and Cd were oxidizable state, followed by residual, weak acid soluble and reducible states. After the CA, FA or PASP application, Cu and Cd were converted from the residual and oxidizable states to the reducible and weak acid soluble states, whose bioavailability in copper tailings were thus enhanced. Besides, the chelating agent incorporation improved the Cu and Cd extraction efficiencies of ryegrass from copper tailings, as manifested by increased root and stem contents of Cu and Cd by 30.29-103.42%, 11.43-74.29%, 2.98-110.98% and 11.11-111.11%, respectively, in comparison with the control group. In the presence of multiple heavy metals, CA, FA or PASP showed selectivity regarding the ryegrass extraction of heavy metals from copper tailings. PCA analysis revealed that the CA-4 and PASP-7 treatment had great remediation potentials against Cu and Cd in copper tailings, respectively, as manifested by increases in Cu and Cd contents in ryegrass by 90.98% and 74.29% compared to the CK group.

Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis

SUMMARY

Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.

Compost-assisted revegetation of highly phytotoxic sulfidic tailings with Medicago sativa L. plants grown from the seed to seedpod stage under greenhouse experimental mesocosms conditions

The revegetation of highly phytotoxic sulfidic tailings is a challenging task which may often be successfully accomplished only following the addition of soil amendments. This study evaluated the use of green compost at increasing rates (10, 25 and 50% v/v) for the revegetation of extremely acidic sulfidic tailings of the North Mathiatis mine, Cyprus, with the use of alfalfa (Medicago sativa L.) plants, under greenhouse conditions. Alfalfa seeds were successfully germinated in tailings amended either with 25% or 50% (v/v) compost (52 and 85%, respectively). Plants managed to complete their life cycle and produce seeds only in the tailings amended with 50% (v/v) compost, since plants grown in tailings amended with lower rates of compost (i.e., 10 or 25% v/v) showed severe symptoms of phytotoxicity and eventually died. The amendment of tailings with 50% (v/v) green compost resulted in increased pH values, water holding capacity and organic content levels, soil respiration rates, as well as changes in soil elemental composition compared with tailings alone treatment, which in turn facilitated the growth and development of alfalfa plants during the whole experimental period (140 days). Plants managed to reach the late seedpod growth stage, indicating their potential regeneration and continual existence to the amended tailings, simultaneously uncovering the development of favorable conditions in the rhizosphere for the successful revegetation of studied tailings.

Different effects of taproot and fibrous root crops on pore structure and microbial network in reclaimed soil

Understanding the effects of plant roots on the pore structure and microbial community of soil is crucial to recovery and improve soil productivity in mining areas. This study aims to assess the impact of taproot (TR) and fibrous root (FR) crops on the physicochemical properties, pore structure, and microbial communities and networks in reclaimed mine soil. Results showed that reclamation positively influenced pore structure and microbial diversity. Tillage with TR and FR crops significantly increased porosity, total pore volume, and area of mining soil (p < 0.05). Compared with TR, FR produced more macropores, mesopores, and micropores. In addition, the module group, average degree, density, and connectivity of microbial network in FR cultivated soil were higher than those in TR cultivated soil. The microbial network map showed that FR had more keystone taxa than TR, and mainly consisted of Acidobacteria and Proteobacteria. In the FR microbial network, Rhizobiales, Betaproteobacteria, and Acidobacteria_Gp11 play critical roles as module hubs and Noviherbaspirillum and Zavarzinella as connectors. Furthermore, most of the key microbes were significantly correlated (p < 0.05) with the total pore area and probably tended to live in pores >75 μm and 0.1-5 μm in size. Therefore, FR crops were more effective than TR crops in improving pore structure and enhancing the development of microbial network in reclaimed soil.

Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome

Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.

The effect of biogeochemical redox oscillations on arsenic release from legacy mine tailings

Exposed and un-remediated metal(loid)-bearing mine tailings are susceptible to wind and water erosion that disperses toxic elements into the surrounding environment. Compost-assisted phytostabilization has been successfully applied to legacy tailings as an inexpensive, eco-friendly, and sustainable landscape rehabilitation that provides vegetative cover and subsurface scaffolding to inhibit offsite transport of contaminant laden particles. The possibility of augmented metal(loid) mobility from subsurface redox reactions driven by irrigation and organic amendments is known and arsenic (As) is of particular concern because of its high affinity for adsorption to reducible ferric (oxyhydr)oxide surface sites. However, the biogeochemical transformation of As in mine tailings during multiple redox oscillations has not yet been addressed. In the present study, a redox-stat reactor was used to control oscillations between 7 d oxic and 7 d anoxic half-cycles over a three-month period in mine tailings with and without amendment of compost-derived organic matter (OM) solution. Aqueous and solid phase analyses during and after redox oscillations by mass spectrometry and synchrotron X-ray absorption spectroscopy revealed that soluble OM addition stimulated pyrite oxidation, which resulted in accelerated acidification and increased aqueous sulfate activity. Soluble OM in the reactor solution significantly increased mobilization of As under anoxic half-cycles primarily through reductive dissolution of ferrihydrite. Microbially-mediated As reduction was also observed in compost treatments, which increased partitioning to the aqueous phase due to the lower affinity of As(III) for complexation on ferric surface sites, e.g. ferrihydrite. Oxic half-cycles showed As repartitioned to the solid phase concurrent with precipitation of ferrihydrite and jarosite. Multiple redox oscillations increased the crystallinity of Fe minerals in the Treatment reactors with compost solution due to the reductive dissolution of ferrihydrite and precipitation of jarosite. The release of As from tailings gradually decreased after repeated redox oscillations. The high sulfate, ferrous iron, and hydronium activity promoted the precipitation of jarosite, which sequestered arsenic. Our results indicated that redox oscillations under compost-assisted phytostabilization can promote As release that diminishes over time, which should inform remediation assessment and environmental risk assessment of mine site compost-assisted phytostabilization.

Vanadium mobilization and redistribution during mineral transformation of vanadium-titanium magnetite tailings with different weathering degrees

Due to the long-term open stockpile, the release of vanadium (V) from V-containing tailings will cause continuous V pollution in the mining area. Previous studies on the concentration and speciation of V primarily focused on surface tailings at a regional scale. However, the mobilization and redistribution of V within the tailing profile during the mineral transformation of tailings remain unclear. Herein, a series of concentrations of V(V) (0-200 mg L-1) solutions were added to the vanadium‑titanium magnetite tailings at different depths separately to simulate the redistribution of dissolved V released from tailings in the solid phase of tailings. During the 56-day incubation, the concentrations of aqueous V in the surface tailings were significantly lower than those in the deep tailings under the same level of V(V) treatment, indicating that the shallow tailings had a stronger immobilization capacity for V than the deep tailings. Morphological analysis and color overlays of the elements demonstrated that most of V was immobilized into the tailings and adsorbed or precipitated by the Fe (hydr)oxides in the tailings in 200 mg L-1 V(V) treatment. This portion of V mainly occurred in acid-soluble and reducible fractions in the tailings after a 7-day incubation, accounting for >71.7 % of the total V. However, these two factions of V with high bioavailability were gradually mineralized over time and transferred to residual V, which is difficult to move and has low bioavailability. Mineral phase analysis revealed that additional V(V) favored the formation of melanovanadite (Ca2V8O20·10H2O) and chromium vanadium oxide (Cr2V4O13) in the tailings. This study reveals that the dissolved V influenced the fractionation and redistribution of solid-phase V during tailing weathering, improving the understanding of the geochemical processes of V in tailing profiles and providing important guidance for the management of V-containing tailings.

Aerobic composting with sauerkraut fermentation waste water: Increasing the stability and complexity of bacterial community and changing bacterial community assembly processes

Aerobic composting renders the sauerkraut fermentation waste water harmless while adding soluble nutrients. Unravelling the bacterial community assembly processes, changes in community robustness and community cohesion and the relationship between them under composting treatment of sauerkraut fermentation waste water is an interesting topic. Sauerkraut fermentation waste water was used for composting, which increased bacterial linkages, community robustness, competitive behaviour during warming periods and cooperative behaviour during cooling periods, and the control of community assembly processes shifts from deterministic processes (variable selection) to stochastic processes (decentralised limitation). At the same time, the influence of community robustness and community cohesion on community assembly processes was increased. Community cohesion and robustness were significantly correlated with community function. These results indicate that community robustness and community cohesion are critical for the biological handling of hazardous substances.

Effect of composite amendments on physicochemical properties of copper tailings repaired by herbaceous plants

Phytoremediation is considered to be the most environmentally friendly green restoration technology for dealing with mine waste. Adding amendments can improve the substrate environment for plant growth and enhance remediation efficiency. Herbaceous plants have become the preferred species for vegetation restoration in abandoned mines because of their fast greening and simple management. After 8 weeks of pot experiments in the early stage, it was shown that the plant height and fresh weight of the plants treated with 5% conditioner and 0.5% straw (C₂S₂) were significantly higher than those of other treatments. Considering that, in this paper, to explore the effect of composite amendments on physicochemical properties of copper tailings repaired by herbaceous plants, the untreated copper tailings were employed as the control group, whereas copper tailings repaired by ryegrass (Lolium perenne L.), vetiver grass (Chrysopogon zizanioides L.), and tall fescue (Festuca arundinacea) with or without conditioners and straw combination into the compound amendments were taken separately as the test group. After 6 months of planting, the pH, electrical conductivity, water content, available potassium, organic matter, total nitrogen, and available phosphorus in the main physical and chemical properties of copper tailings in each experimental area were analyzed. The results showed that the electrical conductivity, organic matter, and total nitrogen content of copper tailings were improved to a certain extent by planting plants without treatment. Meanwhile, compared with the control group, all indexes of planting plants showed an upward trend after adding composite amendments. Among them, pH, water content, and available potassium content of copper tailings were enhanced more obviously. Furthermore, as discovered from the gray correlation analysis results, vetiver grass planted with composite amendments has the best comprehensive effect of improving the physicochemical properties of copper tailings, followed by tall fescue and ryegrass.

Isolation and Genome Analysis of an Amoeba-Associated Bacterium Dyella terrae Strain Ely Copper Mine From Acid Rock Drainage in Vermont, United States

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

Soil microbial community and abiotic soil properties influence Zn and Cd hyperaccumulation differently in Arabidopsis halleri

Soil contamination with trace metal(loid) elements (TME) is a global concern. This has focused interest on TME-tolerant plants, some of which can hyperaccumulate extraordinary amounts of TME into above-ground tissues, for potential treatment of these soils. However, intra-species variability in TME hyperaccumulation is not yet sufficiently understood to fully harness this potential. Particularly, little is known about the rhizosphere microbial communities associated with hyperaccumulating plants and whether or not they facilitate TME uptake. The aim of this study is to characterize the diversity and structure of Arabidopsis halleri rhizosphere-influenced and background (i.e., non-Arabidopsis) soil microbial communities in four plant populations with contrasting Zn and Cd hyperaccumulation traits, two each from contaminated and uncontaminated sites. Microbial community properties were assessed along with geographic location, climate, abiotic soil properties, and plant parameters to explain variation in Zn and Cd hyperaccumulation. Site type (TME-contaminated vs. uncontaminated) and location explained 44% of bacterial/archaeal and 28% of fungal community variability. A linear discriminant effect size (LEfSe) analysis identified a greater number of taxa defining rhizosphere microbial communities than associated background soils. Further, in TME-contaminated soils, the number of rhizosphere-defining taxa was 6-fold greater than in the background soils. In contrast, the corresponding ratio for uncontaminated sites, was 3 and 1.6 for bacteria/archaea and fungi, respectively. The variables analyzed explained 71% and 76% of the variance in Zn and Cd hyperaccumulation, respectively; however, each hyperaccumulation pattern was associated with different variables. A. halleri rhizosphere fungal richness and diversity associated most strongly with Zn hyperaccumulation, whereas soil Cd and Zn bioavailability had the strongest associations with Cd hyperaccumulation. Our results indicate strong associations between A. halleri TME hyperaccumulation and rhizosphere microbial community properties, a finding that needs to be further explored to optimize phytoremediation technology that is based on hyperaccumulation.

Functional and Taxonomic Effects of Organic Amendments on the Restoration of Semiarid Quarry Soils

The application of organic amendments to mining soils has been shown to be a successful method of restoration, improving key physicochemical soil properties. However, there is a lack of a clear understanding of the soil bacterial community taxonomic and functional changes that are brought about by these treatments. We present further metagenomic sequencing (MGS) profiling of the effects of different restoration treatments applied to degraded, arid quarry soils in southern Spain which had previously been profiled only with 16S rRNA gene (16S) and physicochemical analyses. Both taxonomic and functional MGS profiles showed clear separation of organic treatment amendments from control samples, and although taxonomic differences were quite clear, functional redundancy was higher than expected and the majority of the latter signal came from the aggregation of minor (<0.1%) community differences. Significant taxonomic differences were seen with the presumably less-biased MGS-for example, the phylum Actinobacteria and the two genera Chloracidobacterium (Acidobacteria) and Paenibacillus (Firmicutes) were determined to be major players by the MGS and this was consistent with their potential functional roles. The former phylum was much less present, and the latter two genera were either minor components or not detected in the 16S data. Mapping of reads to MetaCyc/BioCyc categories showed overall slightly higher biosynthesis and degradation capabilities in all treatments versus control soils, with sewage amendments showing highest values and vegetable-based amendments being at intermediate levels, matching higher nutrient levels, respiration rates, enzyme activities, and bacterial biomass previously observed in the treated soils. IMPORTANCE The restoration of soils impacted by human activities poses specific challenges regarding the reestablishment of functional microbial communities which will further support the reintroduction of plant species. Organic fertilizers, originating from either treated sewage or vegetable wastes, have shown promise in restoration experiments; however, we still do not have a clear understanding of the functional and taxonomic changes that occur during these treatments. We used metagenomics to profile restoration treatments applied to degraded, arid quarry soils in southern Spain. We found that the assortments of individual functions and taxa within each soil could clearly identify treatments, while at the same time they demonstrated high functional redundancy. Functions grouped into higher pathways tended to match physicochemical measurements made on the same soils. In contrast, significant taxonomic differences were seen when the treatments were previously studied with a single marker gene, highlighting the advantage of metagenomic analysis for complex soil communities.

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

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

Effects of hydroxyl, carboxyl, and amino functionalized carbon nanotubes on the functional diversity of microbial community in riverine sediment

Nowadays, more and more attention is focused on the environmental harm brought by the wide production and use of carbon nanotubes. In this study, the metabolic function of sediment microbial community was investigated after unfunctionalized or functionalized multi-walled carbon nanotubes (MWCNTs) were incorporated. The surface functional groups on the studied functionalized MWCNTs in this work were hydroxyl, carboxyl, and amino, respectively. The metabolic functional diversity was determined by Biolog EcoPlates after one-month exposure to MWCNTs. Incorporating 0.5 wt% amino functionalized MWCNTs significantly decreased the microbial activity and diversity, and all types of MWCNTs caused great inhibition on the microbial metabolism at the dosage of 2.0 wt%. The sediment microbes preferred polymers and amino acids. Principal component and similarity analysis indicated that the microbial carbon metabolism was more affected by the MWCNT dosage compared with the functionalization, and 2.0 wt% amino functionalized MWCNTs made the greatest difference in metabolic function of sediment microbial community. These consequences may help to assess the environmental risks of MWCNTs from the aspect of ecological relevance of sediment microbial community.

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.

Arsenic and iron speciation and mobilization during phytostabilization of pyritic mine tailings

Particulate and dissolved metal(loid) release from mine tailings is of concern in (semi-) arid environments where tailings can remain barren of vegetation for decades and, therefore, become highly susceptible to dispersion by wind and water. Erosive weathering of metalliferous tailings can lead to arsenic contamination of adjacent ecosystems and increased risk to public health. Management via phytostabilization with the establishment of a vegetative cap using organic amendments to enhance plant growth has been employed to reduce both physical erosion and leaching. However, prior research suggests that addition of organic matter into the oxic weathering zone of sulfide tailings has the potential to promote the mobilization of arsenate. Therefore, the objective of the current work was to assess the impacts of phytostabilization on the molecular-scale mechanisms controlling arsenic speciation and lability. These impacts, which remain poorly understood, limit our ability to mitigate environmental and human health risks. Here we report on subsurface biogeochemical transformations of arsenic and iron from a three-year phytostabilization field study conducted at a Superfund site in Arizona, USA. Legacy pyritic tailings at this site contain up to 3 g kg^-1 arsenic originating from arsenopyrite that has undergone oxidation to form arsenate-ferrihydrite complexes in the top 1 m. Tailings were amended in the top 20 cm with 100, 150, or 200 g kg^-1 (300-600 T ha^-1) of composted organic matter and seeded with native halotolerant plant species. Treatments and an unamended control received irrigation of 360 ± 30 mm y^-1 in addition to 250 ± 160 mm y^-1 of precipitation. Cores to 1 m depth were collected annually for three years and sectioned into 20 cm increments for analysis by synchrotron iron and arsenic X-ray absorption spectroscopy (XAS) coupled with quantitative wet chemical and mass balance methods. Results revealed that > 80% of arsenic exists in ammonium oxalate-extractable and non-extractable phases, including dominantly ferrihydrite and jarosite. Arsenic release during arsenopyrite oxidation resulted in both downward translocation and As^(V) attenuation by stable Fe^(III)(oxyhydr)oxide and Fe^(III) (hydroxy)sulfate minerals over time, highlighting the need for sampling at multiple depths and time points for accurate interpretation of arsenic speciation, lability, and translocation in weathering profiles. Less than 1% of total arsenic was highly-labile, i.e. water-extractable, from all treatments, depths, and years, and more than 99% of arsenate released by arsenopyrite weathering was attenuated by association with secondary minerals. Although downward translocation of both arsenic and iron was detected during phytostabilization by temporal enrichment analysis, a similar trend was measured for the uncomposted control, indicating that organic amendment associated with phytostabilization practices did not significantly increase arsenic mobilization over non-amended controls.

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

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

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

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.

Response of microbial communities and interactions to thallium in contaminated sediments near a pyrite mining area

Thallium (Tl) is a well-recognized hazardous heavy metal with very high toxicity. It is usually concentrated in sulfide minerals, such as pyrite (FeS₂), sphalerite (ZnS), chalcopyrite (CuS) and galena (PbS). Here, this study was carried out to investigate the indigenous microbial communities via 16S rRNA gene sequence analysis in typical surface sediments with various levels of Tl pollution (1.8-16.1 mg/kg) due to acid mine drainage from an active Tl-containing pyrite mining site in South China. It was found with more than 50 phyla from the domain Bacteria and 1 phyla from the domain Archaea. Sequences assigned to the genera Ferroplasma, Leptospirillum, Ferrovum, Metallibacterium, Acidithiobacillus, and Sulfuriferula manifested high relative abundances in all sequencing libraries from the relatively high Tl contamination. Canonical correspondence analysis further uncovered that the overall microbial community in this area was dominantly structured by the geochemical fractionation of Tl and geochemical parameters such as pH and Eh. Spearman's rank correlation analysis indicated a strong positive correlation between acidophilic Fe-metabolizing species and Tl_total, Tl_oxi, and Tl_res. The findings clarify potential roles of such phylotypes in the biogeochemical cycling of Tl, which may facilitate the development of in-situ bioremediation technology for Tl-contaminated sediments.