Microbial communities in rare earth mining soil after in-situ leaching mining

Interaction effects of different chemical fractions of lanthanum, cerium, and fluorine on the taxonomic composition of soil microbial community

The extensive mining of bastnasite (CeFCO3) has caused pollution of lanthanum (La), cerium (Ce), and fuorine (F) in the surrounding farmland soil, severely threatening the safety of the soil ecosystem. However, the interaction effects of various chemical fractions of La, Ce, and F on the composition of microbial communities are unclear. In our study, high-throughput sequencing was performed based on the pot experiments of four types of combined pollution soils, i.e., La + Ce (LC), Ce + F (CF), La + F (LF), and La + Ce + F (LCF), and the pollution concentration ranges of these three elements of 20-240, 40-450, and 150-900 mg kg-1, respectively. The improved Tessier method was used to investigate the interaction effects of chemical fractions of these elements on the variations in the soil microbial compositions. The result showed the residual form of La (La_RES) displayed restraint on Abditibacteriota, leading to its undetected level in the highest concentration of LC-polluted soils, whereas promoted relative abundance of microbes (Planctomycetota, Elusimicrobiota, Gemmatimonadota, and Rozellomycota) by more than 80%; the exchangeable and organic-bound forms of Ce and F as well as the iron-manganese-bound and residual forms of F were identified as the stress factors for the sensitive bacteria (e.g., WS4, Elusimicrobiota, RCP2-54, and Monoblepharomycota) in CF-polluted soils; in LF-polluted soils, the water-soluble form of La showed the most toxic effect on RCP2-54, Nitrospirota, and FCPU426, leading to decreased relative abundance by more than 80%; while La_RES and iron-manganese-bound form of F were identified as the stress factors for the relative abundance of Nitrospirota, Elusimicrobiota, and GAL15, showing decline of more than 80% in LCF-polluted soils. Our study revealed both inhibition and promotion effects of the element interaction on the growth of microbial communities, providing a certain experimental evidence to support further exploration of the treatment of environmental pollution caused by these elements.

A synthetic bacterial community engineered from Miscanthus floridulus roots enhances ammonia nitrogen removal in ionic rare earth mine tailings

Ammonium sulfate, as the primary leaching agent, has caused significant nitrogen pollution in rare earth elements (REEs) mining areas. Phytoremediation is a promising remediation method, relying on the synergistic relationships between plants and their root-associated microbiome. Nevertheless, harnessing the microbiome to accelerate nitrogen transformation and absorption by plants is challenging. Here, we investigated the composition, activities and culturable fraction of the root bacterial microbiome of the pioneer plant Miscanthus floridulus grown in a REEs tailing soil containing a high ammonia nitrogen (AN) concentration at 344.35 mg kg-1. Based on this, we constructed a simplified synthetic microbial community (SynCom) derived from the roots of M. floridulus, possessing nitrification and denitrification capabilities, to help REEs mine plants efficiently convert pollutant AN into nutrients, thereby enhancing plant growth and AN removal. This SynCom, consisting of 10 bacterial strains, included species of the genera Burkholderia (5) Paraburkholderia (1), Curtobacterium (1), Leifsonia (1) and Sinomonas (2). As a result, this SynCom alone achieved a significant reduction of 24.8% in AN content in tailing soil. When the SynCom inoculated with plants, the reduction in AN was even more significant (32.6%), surpassing the reduction achieved solely by plants (25.5%). Moreover, live SynCom inoculation significantly increased shoot and root biomass by 39.8% and 49.7%, respectively, compared to dead SynCom inoculation. These results indicate that the reduction in AN can be attributed to the SynCom's nitrification and denitrification capabilities, as well as its ability to enhance plant nitrogen absorption by stimulating their growth. Notably, seven nitrifying and denitrifying strains of the SynCom are particularly enriched, suggesting that plant roots selectively recruit nitrogen cycle-related bacteria to accelerate nitrogen transformation and absorption. These results provide a practical solution for harnessing the synergistic relationships between plants and their root microbiome in environmental remediation efforts.

Response of soil fungi to textile dye contamination

This study examines the impact of textile dye contamination on the structure of soil fungal communities near a Shaoxing textile dye factory. We quantified the concentrations of various textile dyes, including anthraquinone azodye and phthalocyanine, which ranged from 20.20 to 140.62 mg kg^-1, 102.01-698.12 mg kg^-1, and 7.78-42.65 mg kg^-1, respectively, within a 1000 m radius of the factory. Our findings indicate that as dye concentration increases, the biodiversity of soil fungi, as measured by the Chao1 index, decreases significantly, highlighting the profound influence of dye contamination on fungal community structure. Additionally, microbial correlation network analysis revealed a reduction in fungal interactions correlating with increased dye concentrations. We also observed that textile dyes suppressed carbon and nitrogen metabolism in fungi while elevating the transcription levels of antioxidant-related genes. Enzymes such as lignin peroxidase (LiP), manganese peroxidase (MnP), laccase (Lac), dye-decolorizing peroxidases (DyPs), and versatile peroxidase (VP) were upregulated in contaminated soils, underscoring the critical role of fungi in dye degradation. These insights contribute to the foundational knowledge required for developing in situ bioremediation technologies for contaminated farmlands.

Rare earth elements redistribution in mine tailings soil: A comparative study of sunlit and shady slopes after in-situ leaching

The in-situ leaching of rare earth minerals results in ecological differences between sunlit and shady slopes, which may be related to differences in the distribution REEs in the associated soil matrices. Studies of REEs mine tailings in Southern China indicated higher total concentrations of REEs on sunlit slopes compared to shady ones. Specifically, the exchangeable REEs fraction (F1-REEs) was higher on the shady slopes, whereas the Fe/Mn oxides bound REEs fraction (F3-REEs) was higher on the sunlit slopes. In addition, light REE (LREE) concentrations were lower at lower elevations. With the exception of the Ce fraction which remained stable, this indicated a change in all REEs distributions, moving from F1-REEs towards the residual fraction. Hierarchical cluster and principal component analysis revealed a strong correlation between F3-REEs, organic matter bound REEs (F4-REEs), and LREEs, and a positive association of F3-REEs with sunlight exposure. Partial Least Squares Path Modeling analysis suggested that OM promoted the conversion of LREEs to F3 and F4-REEs in soil driven by sunlight exposure. Additionally, as the Feo/Fed ratio decreased, more LREEs were converted to F3. This study suggests that sunlight and elevation both play a critical role in the geochemical dynamics of REEs in in-situ tailings, advocating for environmental evaluations to be undertaken in order to accurately understand the ecological impacts of rare earth mining.

Interactive effects of ammonium sulfate and lead on alfalfa in rare earth tailings: Physiological responses and toxicity thresholds

Ion-adsorption rare earth ore contains significant levels of leaching agents and heavy metals, leading to substantial co-contamination. This presents significant challenges for ecological rehabilitation, yet there is limited understanding of the toxicity thresholds associated with the co-contamination of ammonium sulfate (AS) and lead (Pb) on pioneer plants. Here, we investigated the toxicity thresholds of various aspects of alfalfa, including growth, ultrastructural changes, metabolism, antioxidant system response, and Pb accumulation. The results indicated that the co-contamination of AS-Pb decreased the dry weight of shoot and root by 26 %-77 % and 18 %-92 %, respectively, leading to irregular root cell morphology and nucleus disintegration. The high concentration and combined exposures to AS and Pb induced oxidative stress on alfalfa, which stimulated the defense of the antioxidative system and resulted in an increase in proline levels and a decrease in soluble sugars. Structural equation modeling analysis and integrated biomarker response elucidated that the soluble sugars, proline, and POD were the key physiological indicators of alfalfa under stresses and indicated that co-exposure induced more severe oxidative stress in alfalfa. The toxicity thresholds under single exposure were 496 (EC5), 566 (EC10), 719 (EC25), 940 (EC50) mg kg-1 for AS and 505 (EC5), 539 (EC10), 605 (EC25), 678 (EC50) mg kg-1 for Pb. This study showed that AS-Pb pollution notably influenced plant growth performance and had negative impacts on the growth processes, metabolite levels, and the antioxidant system in plants. Our findings contribute to a theoretical foundation and research necessity for evaluating ecological risks in mining areas and assessing the suitability of ecological restoration strategies.

Comprehensive assessment of the microbial community structure in a typical lead-zinc mine soil

Understanding the microbial community structure in soil contaminated with heavy metals (HMs) is a precondition to conduct bioremediation in mine soil. Samples were collected from a typical lead-zinc (Pb-Zn) mine to assess the microbial community structure of the HMs concentrated in the soil. The goal was to analyze the bacterial and fungal community structures and their interactions using the 16S rRNA genes and internal transcribed spacer high-throughput sequencing. Analyses at different sampling sites showed that contamination with HMs significantly reduced the bacterial richness and diversity but increased that of the fungi. The predominant bacteria genera of Acidobacteriales, Gaiellales, Anaerolineaceae, Sulfurifustis, and Gemmatimonadaceae, and predominant fungal genera of Sordariomycetes, Talaromyces, and Mortierella were assumed as HM resistant genera in Pb-Zn mining area. The pH effect on the bacterial and fungal communities was opposite to those of Cd, Pb, and Zn. This study offers comprehensive outlooks for bacterial and fungal community structures upon multiple HM stresses in the soil around a typical Pb-Zn mine area.

Comparison of microbial communities in unleached and leached ionic rare earth mines

The leaching of ionic rare earth elements has caused serious environmental pollution and ecological damage. Microorganisms play a crucial role in soil ecosystems and are one of the most important components of these systems. However, there are fewer studies related to the changes that occur in microbial community structure and diversity before and after leaching in ionic rare earth mines. In this study, Illumina high-throughput sequencing was used to examine the diversity and composition of soil microorganisms on the summit, hillside, and foot valley surfaces of unleached and leached mines after in situ leaching. The results showed that microbial diversity and abundance in the surface soil of the unleached mine were higher than those in the leached mine, and leaching had a significant impact on the microbial community of mining soil. pH was the main factor affecting the microbial community. Proteobacteria, Actinobacteriota, and Chloroflexi were phyla that showed high abundance in the soil. Network analysis showed that microbial interactions can improve microbial adaptation and stability in harsh environments. PICRUSt2 predictions indicate functional changes and linkages in soil microbial communities.

Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater

Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.

Comparative analysis of endophytic fungal communities in bamboo species Phyllostachys edulis, Bambusa rigida, and Pleioblastus amarus

Fungal endophytes in plant leaf mesophyll form mutually beneficial associations through carbon assimilation, synthesis of biologically active chemicals, and enhancement of aesthetic and nutritional value. Here, we compared community structure, diversity, and richness of endophytic fungi in the leaves of three bamboo species, including Phyllostachys edulis (MZ), Bambusa rigida (KZ), and Pleioblastus amarus (YT) via high-throughput Illumina sequencing. In total, 1070 operational taxonomic units (OTUs) were retrieved and classified into 7 phylum, 27 classes, 82 orders, 185 families, 310 genus, and 448 species. Dominant genera were Cladosporium, Trichomerium, Hannaella, Ascomycota, Sporobolomyces, Camptophora and Strelitziana. The highest fungal diversity was observed in Pleioblastus amarus, followed by Bambusa rigida, and Phyllostachys edulis. Comparatively, monopodial species Ph. edulis and sympodial B. rigida, mixed P. amarus revealed the highest richness of endophytic fungi. We retrieved a few biocontrol agents, Sarocladium and Paraconiothyrium, and unique Sporobolomyces, Camptophora, and Strelitziana genera. FUNGuild analysis revealed the surrounding environment (The annual average temperature is between 15 and 25 °C, and the relative humidity of the air is above 83% all year round) as a source of fungal accumulation in bamboo leaves and their pathogenic nature. Our results provide precise knowledge for better managing bamboo forests and pave the way for isolating secondary metabolites and potential bioactive compounds.

Heap leaching of ion adsorption rare earth ores and REEs recovery from leachate with lixiviant regeneration

In this work, semi-industrial scale heap leaching of 200 t ion adsorption rare earth ores (IRE-ore) and rare earth elements (REEs) recovery from lixivium was first conducted. Biosynthetic citrate/(Na)3Cit, a typical microbial metabolite, was chosen as the lixiviant to conduct heap leaching. Subsequently, an organic precipitation method was proposed, which used oxalic acid to effectively recover REEs and reduce the production cost by lixiviant regeneration. The results showed that the heap leaching efficiency of REEs reached 98 % with a lixiviant concentration of 50 mmol/L and a solid-liquid ratio of 1:2. The lixiviant can be regenerated during the precipitation process, with REE yields and impurity aluminum yields of 94.5 % and 7.4 %, respectively. The residual solution can then be cyclically used as a new lixiviant after simple adjustment. High-quality rare earth concentrates with a rare earth oxide (REO) content of 96 % can be finally obtained after roasting. This work provides an eco-friendly alternative for IRE-ore extraction to solve the environmental issues caused by traditional technology. The results proved feasibility and provided a foundation for in situ (bio)leaching processes in further industrial tests and production.

Exploitation alters microbial community and its co-occurrence patterns in ionic rare earth mining sites

The exploitation of ion-adsorption rare earth elements (REEs) deposits results in serious ecological and environmental problems, which has attracted much attention. However, the influences of exploitation on the prokaryotic communities and their complex interactions remain poorly understood. In the present study, bacterial and archaeal communities, as well as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), in and around REEs mining area were investigated through high throughput sequencing and quantitative polymerase chain reaction (qPCR). Our results indicated that mining soil was characterized by poor soil structure, nutrient deficiency, and high concentrations of residual REEs. Oligotrophic bacteria (e.g., Chloroflexi and Acidobacteriota) were dominant in unexploited soil and mining soil, while copiotrophic bacteria (Proteobacteria and Actinobacteriota) were more abundant in surrounding soil. Nutrient was the key factor affecting microbial variation and abundance in mining soil. The bacterial community was more sensitive to REEs, while the archaeal communities were relatively stable. As the key members for ammonia oxidation, AOA outnumbered AOB in all the soil types, and the former was significantly influenced by pH, nutrients, and TREEs in mining soil. The microbial co-occurrence network analysis demonstrated that exploitation significantly influenced topological properties, decreased the complexity, and resulted in a much unstable network, leading to a more fragile microbial ecosystem in mining areas. Notably, the abundance of keystone taxa decreased after exploitation, and oligotrophic groups (Chloroflexi) replaced copiotrophic groups (Proteobacteria and Actinobacteriota) as the key to rebuilt a co-occurrence network, suggesting potentially important roles in maintaining network stability. The current results are of great significance to the ecological risk assessment of REEs exploitation.

Metallophore Activity toward the Rare Earth Elements by Bacteria Isolated from Acid Mine Drainage Due to Coal Mining

The field of microbe-metal interactions has been gaining significant attention. While the direct impact of metal oxyanions on bacteria has been investigated, significantly less attention has been placed on the ability of certain microbes to 'collect' such metal ions via secreted proteins. Many bacteria possess low-weight molecules called siderophores, which collect Fe from the environment to be brought back to the cell. However, some appear to have additional roles, including binding other metals, termed 'metallophores'. Microbes can remove/sequester these from their surroundings, but the breadth of those that can be removed is still unknown. Using the Chromeazurol S assay, we identified eight isolates, most belonging to the genus Pseudomonas, possessing siderophore activity, mainly from sites impacted by coal mine drainage, also possessing a metallophore activity toward the rare earth elements that does not appear to be related to ionic radii or previously reported EC50 concentrations for E. coli. We found the strength of metallophore activity towards these elements was as follows: Pr > Sc > Eu > Tm > Tb > Er > Yb > Ce > Lu > Sm > Ho > La > Nd > Dy > Gd > Y. This is the first study to investigate such activity and indicates bacteria may provide a means of removal/recovery of these critical elements.

Removal of ammonia nitrogen from residual ammonium leaching solution by heterotrophic nitrification-aerobic denitrification process

The aftermath of mining weathered crust elution-deposited rare earth ore produces a large amount of residual ammonium leaching solution, which causes ammonia and nitrogen pollution to the mine site. Recently, denitrification by heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria has attracted much attention. However, limited studies exist regarding the denitrification process of HN-AD bacteria. In this study, we combined four strains of HN-AD bacteria, Pseudomonas fulva K3, Pseudomonas mosselii K17, Klebsiella oxytoca A12, and Enterobacter hormaechei A16, obtained from rare earth element leaching sites, to select the best microbial consortium for ammonia nitrogen removal. We designed an ammonia removal process applicable to HN-AD bacteria to directly remove ammonia nitrogen from acidic leaching solutions. The experimental results demonstrated that the most efficient microbial consortium for ammonia nitrogen removal to be K3 + K17 + A16, with a removal efficiency of 89.68% for 8 h. In this process, considering the influencing factors of the ammonia removal process, the larger the influent flow rate and influent ammonia nitrogen concentration, the greater the ammonia nitrogen accumulation and pH decrease in the reactor. In consecutive multi-batch experiments, the ammonia removal process was used to remove ammonia nitrogen, at concentrations of 100-600 mg/L, from the simulated leaching solution at pH 4-7, whereby the effluent ammonia nitrogen concentration was lower than 15 mg/L. The results demonstrate that the ammonia removal process is highly feasible and stable. These findings will provide new ideas for the application of HN-AD bacteria and new methods for the removal of ammonia nitrogen from acidic leaching solutions.

Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils

Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.

Pollution caused by mining reshaped the structure and function of bacterial communities in China's largest ion-adsorption rare earth mine watershed

Ion-adsorption rare earth mining results in the production of high levels of nitrogen, multiple metals, and strong acidic mine drainage (AMD), the impacts of which on microbial assembly and ecological functions remain unclear. To address this knowledge gap, we collected river sediments from the watershed of China's largest ion-adsorption rare earth mine and analyzed the bacterial community's structure, function, and assembly mechanisms. Results showed that bacterial community assembly was weakly affected by spatial dispersion, and dispersal limitation and homogeneous selection were the dominant ecological processes, with the latter increasing with pollution gradients. Bacterial alpha diversity decreased with pollution, which was mainly influenced by lead (Pb), pH, rare earth elements (REEs), and electrical conductivity (EC). However, bacteria developed survival strategies (i.e., enhanced acid tolerance and interspecific competition) to adapt to extreme environments, sustaining species diversity and community stability. Community structure and function showed a consistent response to the polluted environment (r = 0.662, P = 0.001). Enhanced environmental selection reshaped key microbial-mediated biogeochemical processes in the mining area, in particular weakening the potential for microbial denitrification. These findings provide new insights into the ecological response of microbes to compound pollution and offer theoretical support for proposing effective remediation and management strategies for polluted areas.

Ecological insight into antibiotic resistome of ion-adsorption rare earth mining soils from south China by metagenomic analysis

Antibiotic resistome has led to growing global threat to public health. Rare earth elements play important roles in modern society and mining activity for them has caused serious impact on soil ecosystems. However, antibiotic resistome in, especially, ion-adsorption rare earth-related soils is still poorly understood. In this work, soils were collected from ion-adsorption rare earth mining areas and adjacent regions of south China and metagenomic analysis was employed for profile, driving factors and ecological assembly of antibiotic resistome in the soils. Results show prevalence of antibiotic resistance genes conferring resistance to tetracycline/fluoroquinolone (adeF), peptide (bcrA), aminoglycoside (rpsL), tetracycline (tet(A)) and mupirocin (mupB) in ion-adsorption rare earth mining soils. Profile of antibiotic resistome is accompanied by its driving factors, i.e., physicochemical properties (La, Ce, Pr, Nd and Y of rare earth elements in 12.50-487.90 mg kg^-1), taxonomy (Proteobacteria, Actinobacteria) and mobile genetic elements (MGEs, plasmid pYP1, Transposase_20). Variation partitioning analysis and partial least-squares-path modeling demonstrate that taxonomy is the most important individual contributor and pose most direct/indirect effect to antibiotic resistome. Further, null model analysis reveals stochastic processes as dominant ecological assembly of antibiotic resistome. This work advances our knowledge on antibiotic resistome with emphasis on ecological assembly in ion-adsorption rare earth-related soils for ARGs mitigation, mining management and mine restoration.

Pronounced temporal changes in soil microbial community and nitrogen transformation caused by benzalkonium chloride

As one typical cationic disinfectant, quaternary ammonium compounds (QACs) were approved for surface disinfection in the coronavirus disease 2019 pandemic and then unintentionally or intentionally released into the surrounding environment. Concerningly, it is still unclear how the soil microbial community succession happens and the nitrogen (N) cycling processes alter when exposed to QACs. In this study, one common QAC (benzalkonium chloride (BAC) was selected as the target contaminant, and its effects on the temporal changes in soil microbial community structure and nitrogen transformation processes were determined by qPCR and 16S rRNA sequencing-based methods. The results showed that the aerobic microbial degradation of BAC in the two different soils followed first-order kinetics with a half-life (4.92 vs. 17.33 days) highly dependent on the properties of the soil. BAC activated the abundance of N fixation gene (nifH) and nitrification genes (AOA and AOB) in the soil and inhibited that of denitrification gene (narG). BAC exposure resulted in the decrease of the alpha diversity of soil microbial community and the enrichment of Crenarchaeota and Proteobacteria. This study demonstrates that BAC degradation is accompanied by changes in soil microbial community structure and N transformation capacity.

Trade-offs between fertilizer-N availability and Cd pollution potential under crop straw incorporation by 15 N stable isotopes in rice

Application of crop residues and chemical nitrogen (N) fertilizer is a conventional practice for achieving high yield in a rice system. However, the fallacious combination of N fertilizers with crop straw not only significantly reduces the N use efficiencies (NUEs) but also leads to serious environmental problems. The present study employed five treatments including no N fertilization and no straw incorporation (ck), N fertilization incorporation only (S0), N fertilization with 40% straw (S₄₀), N fertilization with 60% straw (S₆₀), and N fertilization with 100% straw (S₁₀₀) to improve N use efficiency as well as reduced Cd distribution in rice. The crop yields were largely enhanced by fertilization ranging from 13 to 52% over the straw addition treatments. Compared with ck, N fertilizer input significantly decreased soil pH, while DOC contents were raised in response to straw amendment, reaching the highest in S₆₀ and S₁₀₀ treatments, respectively. Moreover, straw addition substantially impacted the Cd accumulation and altered the bacterial community structure. The soil NH₄⁺-N concentration under S₀ performed the maximum in yellow soil, while the minimum in black soil compared to straw-incorporated pots. In addition, the soil NO₃^--N concentration in straw-incorporated plots tended to be higher than that in straw-removed plots in both soils, indicating that crop straw triggering the N mineralization was associated with native soil N condition. Furthermore, the NUE increased with ¹⁵ N uptake in the plant, and the residual ¹⁵ N in soil was increased by 26.8% with straw addition across four straw application rates. Overall, our study highlights the trade-offs between straw incorporation with N fertilizer in eliminating potential Cd toxicity, increasing fertilizer-N use efficiencies and help to provide a feasible agricultural management.

Activating soil nitrification by co-application of peanut straw biochar and organic fertilizer in a rare earth mining soil

The intensive mining activities to extract rare earth elements from ion-adsorption rare earth deposits have introduced massive amounts of ammonium into the tailing soils in southern China. Compared to the ubiquitous soil nitrification in cropland, forest, and grassland soils, however, there is no feasible strategy to alleviate the ammonium contamination in tailing soil. Herein, the feasibility to remove ammonium by adding ammonium adsorbents (e.g., biochar, activated carbon, and zeolite), alkaline materials, and organic fertilizer to the rare earth mining soil was explored. The amendment of rice straw biochar, activated carbon, or zeolite in combination with CaCO₃ and organic fertilizer showed no significant effect on ammonium removal due to their limited capacity to elevate soil pH. However, the co-application of peanut straw biochar (PSBC), CaCO₃, and organic fertilizer activated both the ammonia volatilization and soil nitrification processes. Specifically, the three components functioned as follows: organic fertilizer supplied active ammonia-oxidizing bacteria (AOB); PSBC stimulated AOB proliferation by elevating soil pH above 7.75; CaCO₃ ameliorated soil acidity and reduced the lag time for activating soil nitrification. The soil ammonium removal and nitrate accumulation rates were positively correlated to the acid neutralization capacity of PSBC prepared at 400 °C-800 °C. The qPCR and microbial community analysis results indicated that Nitrosomonas europaea was the dominant AOB that was responsible for enhanced soil nitrification. Our findings pave the way for developing cost-effective strategies to remediate ammonium contamination in rare earth mining soils.

Molecular Characterization of Distinct Fungal Communities in the Soil of a Rare Earth Mining Area

The exploitation of ion-absorbed rare earth elements (REEs) has caused serious ecological destruction and environmental pollution. Effects on soil fungal structure and diversity exerted by mining activities are usually ignored, although fungus is one of the most important components in soil ecosystems. In the present research, quantitative polymerase chain reaction (qPCR) and high-throughput Illumina MiSeq sequencing were conducted to characterize fungal community composition and structure in soil of a rare earth mining area after in situ leaching. Statistical analyses, network, and FUNGuild were used to conduct in-depth analyses. Ascomycota, Basidiomycota, and Glomeromycota were the most abundant phyla in the mining soils. Fungal community structures were stable after leaching practice, but nutrition contents (organic matter, TC, and TN) significantly and positively contributed to fungal abundances and diversities. Saprotrophs in phyla Ascomycota and Basidiomycota were the dominant fungal trophic mode, and they played critical roles in nutrient cycling, transformation processes, and reducing REE toxicity. Symbiotrophs of phyla Glomeromycota contributed to soil aggregation and slowing down nutrient losses after in situ leaching practice. In addition, fungi could regulate the interactions between species to resist the harsh environment of REE toxicity or ammonium caused by in situ leaching practice.

Enhanced terrestrial Fe(II) mobilization identified through a novel mechanism of microbially driven cave formation in Fe(III)-rich rocks

Most cave formation requires mass separation from a host rock in a process that operates outward from permeable pathways to create the cave void. Given the poor solubility of Fe(III) phases, such processes are insufficient to account for the significant iron formation caves (IFCs) seen in Brazilian banded iron formations (BIF) and associated rock. In this study we demonstrate that microbially-mediated reductive Fe(III) dissolution is solubilizing the poorly soluble Fe(III) phases to soluble Fe(II) in the anoxic zone behind cave walls. The resultant Fe(III)-depleted material (termed sub muros) is unable to maintain the structural integrity of the walls and repeated rounds of wall collapse lead to formation of the cave void in an active, measurable process. This mechanism may move significant quantities of Fe(II) into ground water and may help to explain the mechanism of BIF dissolution and REE enrichment in the generation of canga. The role of Fe(III) reducing microorganism and mass separation behind the walls (outward-in, rather than inward-out) is not only a novel mechanism of speleogenesis, but it also may identify a previously overlooked source of continental Fe that may have contributed to Archaean BIF formation.

Recovering rare earth elements via immobilized red algae from ammonium-rich wastewater

Biotreatment of acidic rare earth mining wastewater via acidophilic living organisms is a promising approach owing to their high tolerance to high concentrations of rare earth elements (REEs); however, simultaneous removal of both REEs and ammonium is generally hindered since most acidophilic organisms are positively charged. Accordingly, immobilization of acidophilic Galdieria sulphuraria (G. sulphuraria) by calcium alginate to improve its affinity to positively charged REEs has been used for simultaneous bioremoval of REEs and ammonium. The results indicate that 97.19%, 96.19%, and 98.87% of La, Y, and Sm, respectively, are removed by G. sulphuraria beads (GS-BDs). The adsorption of REEs by calcium alginate beads (BDs) and GS-BDs is well fitted by both pseudo first-order (PFO) and pseudo second-order (PSO) kinetic models, implying that adsorption of REEs involves both physical adsorption caused by affinity of functional groups such as -COO- and -OH and chemical adsorption based on ion exchange of Ca²⁺ with REEs. Notably, GS-BDs exhibit high tolerance to La, Y, and Sm with maximum removal efficiencies of 97.9%, 96.6%, and 99.1%, respectively. Furthermore, the ammonium removal efficiency of GS-BDs is higher than that of free G. sulphuraria cells at an initial ammonium concentration of 100 mg L^-1, while the efficiency decreases when initial concentration of ammonium is higher than 150 mg L^-1. Last, small size of GS-BDs favors ammonium removal because of their lower mass transfer resistance. This study achieves simultaneous removal of REEs and ammonium from acidic mining drainage, providing a potential strategy for biotreatment of REE tailing wastewater.

Isolation and Nitrogen Removal Efficiency of the Heterotrophic Nitrifying-Aerobic Denitrifying Strain K17 From a Rare Earth Element Leaching Site

K17, an indigenous and heterotrophic nitrifying-aerobic denitrifying bacterium, was isolated from the soil of a weathered crust elution-deposited rare earth ore leaching site in Longnan County, China. Strain K17 was identified as Pseudomonas mosselii. In this study, the morphological characteristics of strain K17 were observed and the optimal ammonia nitrogen removal conditions for the strain were studied using a single-factor experiment. Key enzyme activities were determined, and we also explored the ammonia nitrogen removal process of strain K17 on simulated leaching liquor of the rare earth element leaching site. Based on the determination of ammonia nitrogen removal and enzyme activity, it was found that strain K17 has both heterotrophic nitrifying and aerobic denitrifying activities. In addition, single-factor experiments revealed that the most appropriate carbon source for strain K17 was sodium citrate with a C/N ratio of 10 and an initial NH₄⁺-N concentration of 100 mg/l. Furthermore, the optimal initial pH and rotation speed were 7 and 165 r/min, respectively. Under optimal conditions, the ammonia nitrogen removal efficiency of strain K17 was greater than 95%. As an indigenous bacterium, strain K17 has great potential for treating residual ammonium leaching solutions from rare earth element leaching sites.

Microorganisms Accelerate REE Mineralization in Supergene Environments

Exogenic deposits are an important source of rare earth elements (REEs), especially heavy REEs (HREEs). It is generally accepted that microorganisms are able to dissolve minerals and mobilize elements in supergene environments. However, little is known about the roles of microorganisms in the formation of exogenic deposits such as regolith-hosted REE deposits that are of HREE enrichment and provide over 90% of global HREE demand. In this study, we characterized the microbial community composition and diversity along a complete weathering profile drilled from a regolith-hosted REE deposit in Southeastern China and report the striking contributions of microorganisms to the enrichment of REEs and fractionation between HREEs and light REEs (LREEs). Our results provide evidence that the variations in REE contents are correlated with microbial community along the profile. Both fungi and bacteria contributed to the accumulation of REEs, whereas bacteria played a key role in the fractionation between HREEs and LREEs. Taking advantage of bacteria strains isolated from the profile, Gram-positive bacteria affiliated with Bacillus and Micrococcus preferentially adsorbed HREEs, and teichoic acids in the cell wall served as the main sites for HREE adsorption, leading to an enrichment of HREEs in the deposit. The present study provides the first database of microbial community in regolith-hosted REE deposits. These findings not only elucidate the crucial contribution of fungi and bacteria in the supergene REE mineralization but also provide insights into efficient utilization of mineral resources via a biological pathway.

IMPORTANCE Understanding the role of microorganisms in the formation of regolith-hosted rare earth element (REE) deposits is beneficial for improving the metallogenic theory and deposit exploitation, given that such deposits absolutely exist in subtropical regions with strong microbial activities. Little is known of the microbial community composition and its contribution to REE mineralization in this kind of deposit. Using a combination of high-throughput sequencing, batch adsorption experiments, and spectroscopic characterization, the functional microorganisms contributing to REE enrichment and fractionation are disclosed. For bacteria, the surface carboxyl and phosphate groups are active sites for REE adsorption, while teichoic acids in the cell walls of G⁺ bacteria lead to REE fractionation. The above-mentioned findings not only unravel the importance of microorganisms in the formation of supergene REE deposits but also provide experimental evidence for the bioutilization of REE resources.

The enrichment of rare earth from magnesium salt leaching solution of ion-adsorbed type deposit: A waste-free process for removing impurities

Due to the complex composition of ion-adsorbed type rare earth ore leaching solution, there are challenges in the process of rare earth (RE) separation, such as large RE loss rate, low product purity, radioactive residue and so on. In this article, 8-hydroxyquinoline modified silica gel (HQ-SiO₂) and 2,2'-(1,4-phenylenebis(oxy)) dioctanoic acid (PPBOA) were used to form an efficient process for impurities removal and RE enrichment. Solid phase extraction successfully intercepted 96.7% of the radioactive element thorium. The concentration of aluminium was reduced to 2.14 ppm by frank chromatography. Rare earth elements were enriched from 336.35 mg/L to 237.75 g/L by extraction-precipitation, that is, the enrichment multiple reached more than 700 and the proportion of RE was increased from 21.85% to 96.62%. The loss rate of RE was controlled below 1.59%. Moreover, the magnesium salt leaching solution could be recycled for the leaching of RE ores. Although some liquid waste need to be treated in the processes of HQ-SiO₂ production and regeneration, the integrated process helps to decrease volatile organic solvent, acid-base consumption, wastewater and waste residue. It is an environment-friendly RE enrichment and impurity removal process, which shows application potential in the production field of ion-adsorbed type rare earth mineral products.

Simultaneous partial nitrification, anammox, and denitrification in an upflow microaerobic membrane bioreactor treating middle concentration of ammonia nitrogen wastewater with low COD/TN ratio

The rapid start-up and operating characteristics of simultaneous partial nitrification, anammox, and denitrification (SNAD) process was investigated using synthetic wastewater with a low C/N ratio (COD: NH₄⁺-N = 200 mg/L: 200 mg/L) in a novel upflow microaerobic membrane bioreactor (UMMBR). The average removal efficiencies of COD, NH₄⁺-N, and TN in the stable phase were 89%, 96%, and 86%, respectively. Carmine granule, which coexisted with sludge floc, appeared on day 83. The high sludge concentration (12.9-17.2 g/L) and the upflow mode of the UMMBR could establish some anaerobicregions for anammox process. The anammox bacteria and short-cut denitrification (NO₂^-→N₂) bacteria with activities of 4.46 mg NH₄⁺-N/gVSS·h and 2.57 mg NO₂^--N/gVSS·h contributed TN removal of 39% and 61% on day 129, respectively. High-throughput sequencing analysis revealed that the ammonia-oxidizing archaea (AOA, 49.45% in granule and 17.05% in sludge floc) and ammonia-oxidizing bacterial (AOB, 1.30% in sludge floc) dominated the nitrifying microbial community. Candidatus Jettenia (47.14%) and Denitratisoma (10.92%) mainly existed in granule with positive correlations. Some heterotrophic bacteria (OLB13, SJA-15, 1-20, SBR1031, and SJA-28) in sludge floc benefited system stability and sludge activity and protected Candidatus Jettenia from adverse environments.

Di(2-ethylhexyl) phthalate and dibutyl phthalate have a negative competitive effect on the nitrification of black soil

Di (2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) are the most widely used plasticizers for agricultural mulching films and one of the most common organic pollutants in black soil. However, little is known about the effect of these two contaminants on nitrification in black soil. This study investigated the changes of 20 mg/kg DEHP and DBP on the diversity of nitrification microbial communities, the abundance of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) related genes, and the activities of key enzymes involved in nitrification. During ammonia oxidation, DEHP and DBP had uncompetitive inhibition of urease, reducing the copy number of amoA gene, and microorganisms (Azoarcus, Streptomyces and Caulobacter) would use inorganic nitrogen as a nitrogen source for physiological growth. During nitrite oxidation, the copy number of nxrA gene also reduced, and the relative abundance of chemoautotrophic nitrifying bacteria (Nitrosomonas and Nitrobacter) decreased. Moreover, the path analysis results showed that DEHP and DBP mainly directly or indirectly affect AOB and NOB through three ways. These results help better understand the ecotoxicological effects of DEHP and DBP on AOB and NOB in black soil.

Microbial characteristics of the leachate contaminated soil of an informal landfill site

Because informal landfills are not constructed in a regulated manner, they will inevitably become a source of leachate pollution to the surrounding environment over time. Microbes are an important part of the soil system, playing a vital role in maintaining the normal functionality of soil. This study investigated the microbial composition and co-occurrence pattern in the leachate contaminated soil of an informal landfill site. The landfill leachate underwent horizontal and vertical migration through the contaminated soil, resulting in significant differences in the microbial compositions of horizontal surface soil (CS) and vertical subsurface soil (DS and ES) compared to uncontaminated soil (S). The microbial diversity of CS, DS, and ES was lower than that of S. Due to the migration of landfill leachate, the microbial composition of the surface soil was substantially changed. The dominant phyla in S included Proteobacteria (26.88%), Chloroflexi (23.68%), Actinobacteroita (17.36%), and Acidobacteroita (16.86%), but in contaminated soils, Firmicutes (35.27-86.68%) were the dominant bacteria. A network analysis indicated that Bacilli, Clostridia, and Thermacetogeniazai of the Firmicutes were the keystone taxa and played a vital role in maintaining the stability of the soil ecosystem. A functional annotation of prokaryotic taxa (FAPROTAX) analysis showed that the microbes involved in the C-, N-, and S-cycles in contaminated soil were significantly different to those in uncontaminated soil. The proportion of (aerobic)-chemoheterotrophy and cellulolysis functional communities in contaminated soils was significantly reduced, while there was an increase in functional communities, such as anammox and denitrification, which are not conducive to soil nitrogen fixation. This negatively affected the maintenance of normal soil ecological functions. This study identified the microbial characteristics in leachate contaminated soil and the results will be beneficial for the remediation of contaminated soil in informal landfill sites.

Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene

Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g^-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.

Multiple factors influence bacterial community diversity and composition in soils with rare earth element and heavy metal co-contamination

The effects of long-term rare earth element (REE) and heavy metal (HM) contamination on soil bacterial communities remains poorly understood. In this study, soil samples co-contaminated with REEs and HMs were collected from a rare-earth tailing dam. The bacterial community composition and diversity were analyzed through Illumina high-throughput sequencing with 16S rRNA gene amplicons. Bacterial community richness and diversity were lower in the co-contaminated soils than in the uncontaminated soils, with clearly different bacterial community compositions. The results showed that total organic carbon and available potassium were the most important factors affecting bacterial community richness and diversity, followed by the REE and HM contents. Although the canonical correspondence analysis results showed that an REE alone had no obvious effects on bacterial community structures, we found that the combined effects of soil physicochemical properties and REE and HM contents regulated bacterial community structure and composition. The effects of REEs and HMs on bacterial communities were similar, whereas their combined contributions were greater than the individual effects of REEs or HMs. Some bacterial taxa were worth noting. These specifically included the plant growth-promoting bacteria Exiguobacterium (sensitive to REEs and HMs) and oligotrophic microorganisms with metal tolerance (prevalent in contaminated soil); moreover, relative abundance of JTB255-Marine Benthic Group, Rhodobacteraceae, Erythrobacter, and Truepera may be correlated with REEs. This study was the first to investigate the responses of bacterial communities to REE and HM co-contamination. The current results have major implications for the ecological risk assessment of environments co-contaminated with REEs and HMs.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (P_N) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and P_N values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH₃ and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

Recovering rare earth elements from contaminated soils: Critical overview of current remediation technologies

Rare earth elements (REE) are essential for sustainable energies such as solar and wind power, with rising demand due to the ambitious goal for a circular society. REE are currently mined from virgin ores while REE-rich contaminated soil is left untreated in the environment. Soil remediation strategies are needed that concomitantly cleanup soil and harvest metals that contribute to process circular economy. In this review we aim to (i) define REE concentrations in contaminated soils as well as (ii) identify soil remediation techniques used in remediating REE from soils, emphasizing the ones that extract REE. Current literature lists REE polluted soils in the vicinities of REE mines, coal mines, high traffic roads and agricultural soils (due to REE association with phosphate fertilizers). We first list the conventional separation methods used in the mining industry and their main strategies in extracting/precipitating REE. Solvent extraction is the most commonly conventional method used followed by electrodeposition of REE at high temperatures. We then highlight soil remediation techniques that are used to treat REE. These techniques can be separated into two types: the ones that (a) stabilize REE in soils, and the ones that (b) extract REE from soils. Bioremediation, soil amendments and others offer stabilization of REE, eventually creating a legacy problem since REE keep accumulating in the soil. Soil remediation techniques that achieve REE extraction are a step closer to resource recovery, contributing to the circularity of REE. Techniques such as phytoremediation, soil washing and electrokinetic treatment show promising extraction results.