Variation in rhizosphere microbiota correlates with edaphic factor in an abandoned antimony tailing dump

Microbial-mediated metal(loid) immobilization in mulch-covered tailings

Mulch coverage of mining tailings can create anaerobic conditions and consequently establish an anoxic environment that promotes the metabolic processes of anaerobic microorganisms. This anoxic environment has the potential to decrease heavy metal mobility and bioavailability. While tailings exposed to sunlight have been extensively studied, research on the effects of microbial-mediated geochemical cycling of heavy metals in mulch-covered tailings is scarce. This study aimed to examine the effects of mulch coverage-induced alterations in the structures of tailing microbial communities on the biogeochemical processes associated with heavy metals. Mulch coverage significantly reduced the pH of the tailings and the tailings exhibited heavy metal bioavailability. Random forest analysis demonstrated that mulch coverage-induced changes in the As/Cd-contaminated fractions and nutrients (total organic carbon and total nitrogen) were the most crucial predictors of microbial diversity and ecological clusters in the tailings. Notably, different from direct metal(loid) immobilization, mulch coverage can facilitate heavy metal immobilization in tailings by promoting microbial-mediated Fe, S, and As reduction. Overall, this study demonstrated that mulch coverage of tailings contributed to a reduction in heavy metal mobilization, which can be attributed to shifts in microbial-mediated Fe, S, and As reduction processes.The study provides valuable insights into the potential of mulch coverage as a remediation strategy and underscores the importance of microbial-mediated processes in managing heavy metal pollution in tailing systems.

Differential Mechanisms of Microbial As(III) and Sb(III) Oxidation and Their Contribution to Tailings Reclamation

Mine tailings are extremely oligotrophic environments frequently contaminated with elevated As and Sb, making As(III) and Sb(III) oxidation potentially important energy sources for the tailing microbiome. Although they have been proposed to share similar metabolic pathways, a systemic comparison of the As(III) and Sb(III) oxidation mechanisms and energy utilization efficiencies requires further elucidation. In this study, we employed a combination of physicochemical, molecular, and bioinformatic analyses to compare the kinetic and genetic mechanisms of As(III) and Sb(III) oxidation as well as their respective energy efficiencies for fueling the key nutrient acquisition metabolisms. Thiobacillus and Rhizobium spp. were identified as functional populations for both As(III) and Sb(III) oxidation in mine tailings by DNA-stable isotope probing. However, these microorganisms mediated As(III) and Sb(III) oxidation via different metabolic pathways, resulting in preferential oxidation of Sb(III) over As(III). Notably, both As(III) and Sb(III) oxidation can facilitate nitrogen fixation and phosphate solubilization in mine tailings, with Sb(III) oxidation being more efficient in powering these processes. Thus, this study provided novel insights into the microbial As(III) and Sb(III) oxidation mechanisms and their respective nutrient acquisition efficiencies, which may be critical for the reclamation of mine tailings.

MICP mediated by indigenous bacteria isolated from tailings for biocementation for reduction of wind erosion

In this study, native ureolytic bacteria were isolated from copper tailings soils to perform microbial-induced carbonate precipitation (MICP) tests and evaluate their potential for biocement formation and their contribution to reduce the dispersion of particulate matter into the environment from tailings containing potentially toxic elements. It was possible to isolate a total of 46 bacteria; among them only three showed ureolytic activity: Priestia megaterium T130-1, Paenibacillus sp. T130-13 and Staphylococcus sp. T130-14. Biocement cores were made by mixing tailings with the isolated bacteria in presence of urea, resulting similar to those obtained with Sporosarcina pasteurii and Bacillus subtilis used as positive control. Indeed, XRD analysis conducted on biocement showed the presence of microcline (B. subtilis 17%; P. megaterium 11. 9%), clinochlore (S. pasteurii, 6.9%) and magnesiumhornblende (Paenibacillus sp. 17.8%; P. megaterium 14.6%); all these compounds were not initially present in the tailings soils. Moreover the presence of calcite (control 0.828%; Paenibacillus sp. 5.4%) and hematite (control 0.989%; B. subtilis 6.4%) was also significant unlike the untreated control. The development of biofilms containing abundant amount of Ca, C, and O on microscopic soil particles was evidenced by means of FE-SEM-EDX and XRD. Wind tunnel tests were carried out to investigate the resistance of biocement samples, accounted for a mass loss five holds lower than the control, i.e., the rate of wind erosion in the control corresponded to 82 g/m2h while for the biocement treated with Paenibacillus sp. it corresponded to only 16.371 g/m2h. Finally, in compression tests, the biocement samples prepared with P. megaterium (28.578 psi) and Paenibacillus sp. (28.404 psi) showed values similar to those obtained with S. pasteurii (27.102 psi), but significantly higher if compared to the control (15.427 psi), thus improving the compression resistance capacity of the samples by 85.2% and 84.1% with respect to the control. According to the results obtained, the biocement samples generated with the native strains showed improvements in the mechanical properties of the soil supporting them as potential candidates in applications for the stabilization of mining liabilities in open environments using bioaugmentation strategies with native strains isolated from the same mine tailing.

Rhizosphere microbiome of plants used in phytoremediation of mine tailing dams

Rhizospheric microbial communities improve the effectiveness of hyperaccumulators in the phytoremediation of heavy metals. However, limited access to tailing dams and inadequate assessment of plants' phytoremediation potential limit the characterization of native accumulators, hindering the effectiveness of local remediation efforts. This study evaluates the heavy metal sequestration potentials of Pennisetum purpureum, Leucaena leucocephala, and Pteris vittata and their associated rhizospheric microbial communities at the Marlu and Pompora tailing dams in Ghana. The results indicate shoot hyperaccumulation of Cd (334.5 ± 6.3 mg/kg) and Fe (10,647.0 ± 12.6 mg/kg) in P. purpureum and L. leucocephala, respectively. Analysis of rhizospheric bacterial communities revealed the impact of heavy metal contamination on bacterial community composition, associating Fe and Cd hyperaccumulation with Bacillus, Arthrobacter, and Sphingomonas species. This study reports the hyperaccumulation potentials of L. leucocephala and P. purpureum enhanced by associated rhizosphere bacterial communities, suggesting their potential application as an environmentally friendly remediation process of heavy metals contaminated lands.

The rhizosphere microbiome reduces the uptake of arsenic and tungsten by Blechnum orientale by increasing nutrient cycling in historical tungsten mining area soils

The growth of pioneer plants in metal mining area soil is closely related to their minimal uptake of toxic elements. Pioneer plants can inhibit the uptake of toxic elements by increasing nutrient uptake. However, few studies have focused on the mechanisms by which the rhizosphere microbiome affect nutrient cycling and their impact on the uptake of toxic elements by pioneer plants. In this study, we selected Blechnum orientale to investigate the potential roles of the rhizosphere microbiome in nutrient cycling and plant growth in a historical tungsten (W) mining area. Our results showed that while the arsenic (As) and W contents in the soil were relatively high, the enrichment levels of As and W in the B. orientale were relatively low. Furthermore, we found that the As and W contents in plants were significantly negatively correlated with soil nutrients (S, P and Mo), suggesting that elevated levels of these soil nutrients could inhibit As and W uptake by B. orientale. Importantly, we found that these nutrients were also identified as the most important factors shaping rhizosphere microbial attributes, including microbial diversity, ecological clusters, and keystone OTUs. Moreover, the genera, keystone taxa and microbial functional genes enriched in the rhizosphere soils from mining areas played a key role in nutrient (S, P and Mo) bioavailability, which could further increase the nutrient uptake by B. orientale. Taken together, our results suggest that rhizosphere microorganisms can improve pioneer plant growth by inhibiting toxic element accumulation via the increase in nutrient cycling in former W mining areas.

Cadmium levels and soil pH drive structure and function differentiation of endophytic bacterial communities in Sedum plumbizincicola: A field study

Sedum plumbizincicola is a promising hyperaccumulator for heavy metal phytoremediation. It grows in heavy metal polluted soil and stores specific endophyte resources with heavy metal tolerance or growth promotion characteristics. In this study, the endophyte communities of S. plumbizincicola, growing naturally in the field (two former mining locations and one natural location) were investigated, and their structure and function were comparatively studied. The bioaccumulation and translocation characteristics of cadmium (Cd) and selenium (Se) in S. plumbizincicola were also evaluated. The results showed that the heavy metal pollution reduced the richness and diversity of endophyte communities. Soil pH and Cd concentration could be the key factors affecting the composition of the endophyte community. Co-occurrence network analysis identified that 22 keystone taxa belonging to Actinobacteriota, Firmicutes, Myxococcota and Proteobacteria were positively correlated with Cd bioaccumulation and translocation. The predicted endophyte metabolic pathways were enriched in physiological metabolism, immune system, and genetic Information processing. These findings may help to understand how endophytes assist host plants to enhance their adaptability to harsh environments, and provide a basis for further exploration of plant-endophyte interactions and improvement in phytoremediation efficiency.

Geochemical properties, heavy metals and soil microbial community during revegetation process in a production Pb-Zn tailings

Lead-zinc (Pb-Zn) tailings pose a significant environmental threat from heavy metals (HMs) contamination. Revegetation is considered as a green path for HM remediation. However, the interplay between HM transport processes and soil microbial community in Pb-Zn tailings (especially those in production) remain unclear. This study investigated the spatial distribution of HMs as well as the crucial roles of the soil microbial community (i.e., structure, richness, and diversity) during a three-year revegetation of production Pb-Zn tailings in northern Guangdong province, China. Prolonged tailings stockpiling exacerbated Pb contamination, elevating concentrations (from 10.11 to 11.53 g/kg) in long-term weathering. However, revegetation effectively alleviated Pb, reducing its concentrations of 9.81 g/kg. Through 16 S rRNA gene amplicon sequencing, the dominant genera shifted from Weissella (44%) to Thiobacillus (17%) and then to Pseudomonas (comprising 44% of the sequences) during the revegetation process. The structural equation model suggested that Pseudomonas, with its potential to transform bioavailable Pb into a more stable form, emerged as a potential Pb remediator. This study provides essential evidence of HMs contamination and microbial community dynamics during Pb-Zn tailings revegetation, contributing to the development of sustainable microbial technologies for tailings management.

Root-associated bacterial microbiome shaped by root selective effects benefits phytostabilization by Athyrium wardii (Hook.)

The root-associated microbiome assembly substantially promotes (hyper)accumulator plant growth and metal accumulation and is influenced by multiple factors, especially host species and environmental stress. Athyrium wardii (Hook.) is a phytostabilizer that grows in lead (Pb)-zinc (Zn) mine tailings and shows high root Pb accumulation. However, there remains little information on the assembly of the root-associated microbiome of A. wardii and its role in phytostabilization. A field study investigated the structural and functional variation in the root-associated bacterial microbiome of Athyrium wardii (Hook.) exposed to different levels of contamination in Pb-Zn mine tailings. The root compartment dominated the variation in the root-associated bacterial microbiome but the levels of contaminants showed less impact. Bacterial co-occurrence was enhanced in the rhizosphere soil and rhizoplane but tended to be much simpler in the endosphere in terms of network complexity and connectivity. This indicates that the microbial community assembly of A. wardii was non-random and shaped by root selective effects. Proteobacteria, Chloroflexi, Actinobacteria, Cyanobacteria, and Acidobacteriota were generally the dominant bacterial phyla. The genera Crossiella and Bradyrhizobium were enriched in the rhizosphere and cyanobacterial genera were enriched in the endosphere, demonstrating substantial advantages to plant survival and adaptation in the harsh mine environment. Functional categories involved in amino acid and carbohydrate metabolism were abundant in the rhizosphere soil, thus contributing to metal solubility and bioavailability in the rhizosphere. Membrane transporters, especially ATP-binding cassette transporters, were enriched in the endosphere, indicating a potential role in metal tolerance and transportation in A. wardii. The study shows substantial variation in the structure and function of microbiomes colonizing different compartments, with the rhizosphere and endophytic microbiota potentially involved in plant metal tolerance and accumulation during phytostabilization.

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.

Evaluation of the rhizospheric microbiome of the native colonizer Piptatherum miliaceum in semiarid mine tailings

The study of the rhizospheric microbiome in native plants should be a prerequisite before carrying out the phytomanagement of mine tailings. The goal of this work was to evaluate the rhizospheric microbiome of Piptatherum miliaceum in semiarid mine tailings. A comprehensive edaphic characterization was performed including the description of soil microbial composition in the rhizosphere of P. miliaceum growing at a mine tailings pile and at a control site. Plant nutritional and isotopic compositions were also determined. Neutral pH of the tailings (7.3) determined low metal extractability in 0.01 M CaCl2 (e.g. < 1 mg/kg for Zn). In spite of the contrasting edaphic fertility conditions of both sites, N (~ 15 g kg-1) and P (~ 400 mg kg-1) leaf concentrations were similar. The lower δ15N at the tailings plants (- 4.50‰) compared to the control (6.42‰) indicated greater efficiency of P. miliaceum for uptaking N under the low fertility conditions of the tailings (0.1% total soil nitrogen). The presence at the tailings of bacterial orders related to the cycling of N, such as Rhizobiales, could have contributed to enhance N acquisition. The lower leaf δ13C values at the tailings (- 30.22‰) compared to the control (- 28.47‰) indicated lower water use efficiency of the tailing plants. Some organotrophic bacterial and fungal groups in the tailings' rhizospheres were also found in the control site (e.g. Cytophagales, Sphingobacteriales for bacteria; Hypocreales, Pleosporales for fungi). This may indicate that P. miliaceum is able to shape its own specific microbiome at the tailings independently from the initial microbial composition of the tailings.

A critical review on the migration and transformation processes of heavy metal contamination in lead-zinc tailings of China

The health risks of lead-zinc (Pb-Zn) tailings from heavy metal (HMs) contamination have been gaining increasing public concern. The dispersal of HMs from tailings poses a substantial threat to ecosystems. Therefore, studying the mechanisms of migration and transformation of HMs in Pb-Zn tailings has significant ecological and environmental significance. Initially, this study encapsulated the distribution and contamination status of Pb-Zn tailings in China. Subsequently, we comprehensively scrutinized the mechanisms governing the migration and transformation of HMs in the Pb-Zn tailings from a geochemical perspective. This examination reveals the intricate interplay between various biotic and abiotic constituents, including environmental factors (EFs), characteristic minerals, organic flotation reagents (OFRs), and microorganisms within Pb-Zn tailings interact through a series of physical, chemical, and biological processes, leading to the formation of complexes, chelates, and aggregates involving HMs and OFRs. These interactions ultimately influence the migration and transformation of HMs. Finally, we provide an overview of contaminant migration prediction and ecological remediation in Pb-Zn tailings. In this systematic review, we identify several forthcoming research imperatives and methodologies. Specifically, understanding the dynamic mechanisms underlying the migration and transformation of HMs is challenging. These challenges encompass an exploration of the weathering processes of characteristic minerals and their interactions with HMs, the complex interplay between HMs and OFRs in Pb-Zn tailings, the effects of microbial community succession during the storage and remediation of Pb-Zn tailings, and the importance of utilizing process-based models in predicting the fate of HMs, and the potential for microbial remediation of tailings.

Variations in microbial assemblage between rhizosphere and root endosphere microbiomes contribute to host plant growth under cadmium stress

IMPORTANCE

In this study, we revealed that the variation in rhizosphere and root endosphere microbial assemblage between host plant ecotypes contribute to their differential abilities to withstand cadmium (Cd) stressors. Furthermore, our study found that phenolic compounds, such as benzenoids and flavonoids, could function as both essential carbon sources and semiochemicals, thereby contributing to the assemblage of rhizosphere microbiome to resist Cd stress. Our findings provide new insights into the mechanisms that drive the differential assemblage of rhizosphere and root endosphere microbiomes to enhance plant growth under abiotic stress.

Comparative assessment of bacterial diversity and composition in arsenic hyperaccumulator, Pteris vittata L. and non-accumulator, Pteris ensiformis Burm

The use of arsenic (As) for various industrial and agricultural applications has led to worldwide environmental contamination. Phytoremediation using hyperaccumulators is a sustainable soil As mitigation strategy. Microbial processes play an important role in the tolerance and uptake of trace elements such as in plants. The rhizospheric and endophytic microbial communities are responsible for accelerating the mobility of trace elements around the roots and the production of plant growth-promoting compounds and enzymes. Several studies have reported that the As hyperaccumulator, Pteris vittata L. (PV) influences the microbial community in its rhizosphere and roots. Deciphering the differences in the microbiomes of hyperaccumulators and non-accumulators is crucial in understanding the mechanism of hyperaccumulation. We hypothesized that there are significant differences in the microbiome of roots, rhizospheric soil, and bulk soil between the hyperaccumulator PV and a non-accumulator of the same genus, Pteris ensiformis Burm. (PE), and that the differential recruitment of bacterial communities provides PV with an advantage in As contaminated soil. We compared root endophytic, rhizospheric, and bulk soil microbial communities between PV and PE species grown in As-contaminated soil in a greenhouse setting. There was a significant difference (p < 0.001) in the microbiome of the three compartments between the ferns. Differential abundance analysis showed 328 Amplicon Sequence Variants (ASVs) enriched in PV compared to 172 in PE. The bulk and rhizospheric soil of both ferns were abundant in As-resistant genera. However, As-tolerant root endophytic genera were present in PV but absent in PE. Our findings show that there is a difference between the bacterial composition of an As hyperaccumulator and a non-accumulator species grown in As-contaminated soil. These differences need to be further explored to develop strategies for improving the efficiency of metal uptake in plants growing in As polluted soil.

Reed restoration decreased nutrients in wetlands with dredged sediments: Microbial community assembly and function in rhizosphere

Using dredged sediments as substrate for aquatic plants is a low-cost and ecological friendly way for in situ aquatic ecological restoration. However, the limited information available about how aquatic plant restoration affects the microbial ecology and nutrients in dredged sediments. In this study, nutrient contents, enzyme activities, and bacterial and archaeal communities in vertical sediment layers were determined in bulk and reed zones of wetlands constructed with dredged sediments in west Lake Taihu for three years. Reed restoration significantly decreased total nitrogen, total phosphorus, and organic carbon contents and increased alkaline phosphatase, urease, and sucrase activities compared to bulk area. Bacterial communities in vertical sediment layers had higher similarity in reed zone in comparison to bulk zone, and many bacterial and archaeal genera were only detected in reed rhizosphere zones. Compared with the bulk zone, the reed restoration area has a higher abundance of phylum Actinobacteriota, Hydrothermarchaeota, and class α-proteobacteria. The assembly process of the bacterial and archaeal communities was primarily shaped by dispersal limitation (67.03% and 32.97%, respectively), and stochastic processes were enhanced in the reed recovery area. Network analysis show that there were more complicated interactions among bacteria and archaea and low-abundance taxa were crucial in maintaining the microbial community stability in rhizosphere of reed zone. PICRUST2 analysis demonstrate that reed restoration promotes metabolic pathways related to C and N cycle in dredged sediments. These data highlight that using dredged sediments as substrates for aquatic plants can transform waste material into a valuable resource, enhancing the benefits to the environment.

Piriformospora indica alter root-associated microbiome structure to enhance Artemisia annua L. tolerance to arsenic

Microorganisms in the rhizosphere are crucial allies for plant stress tolerance. Recent research suggests that by interacting with the rhizosphere microbiome, microorganisms can aid in the revegetation of soils contaminated with heavy metal(loid)s (HMs). However, it is unknown that how Piriformospora indica influences the rhizosphere microbiome to mitigate arsenic-toxicity in arsenic-enriched environments. Artemisia annua plants were grown in the presence or absence of P. indica and spiked with low (50) and high (150 µmol/L) concentrations of arsenic (As). After inoculation with P. indica, fresh weight increased by 37.7% and 10% in control and high concentration treated plants, respectively. Transmission electron microscopy showed that cellular organelles were severely damaged by As and even disappeared under high concentration. Furthermore, As was mostly accumulated by 5.9 and 18.1 mg/kg dry weight in the roots of inoculated plants treated with low and high concentrations of As, respectively. Additionally, 16 S and ITS rRNA gene sequencing were applied to analyze the rhizosphere microbial community structure of A. annua under different treatments. A significant difference was observed in microbial community structure under different treatments as revealed by non-metric multidimensional scaling ordination. The bacterial and fungal richness and diversity in the rhizosphere of inoculated plants were actively balanced and regulated by P. indica co-cultivation. Lysobacter and Steroidobacter were found to be the As-resistant bacterial genera. We conclude that P. indica inoculation could alter rhizosphere microecology, thereby mitigating As-toxicity without harming the environment.

Shift in rhizospheric and endophytic microbial communities of dominant plants around Sunit Alkaline Lake

Alkaline lakes are a special type of extreme saline-alkali ecosystem, and the dominant plants store a large number of microbial resources with salinity-tolerant or growth-promoting properties in the littoral zones. In this study, high-throughput sequencing technology and molecular ecological networks were used to analyze the bacteria and fungi from different rhizocompartments of three dominant plants along the salinity gradient in the littoral zones of Sunit Alkali Lake. The study found that fungal communities were more tolerant of environmental abiotic stress, and salinity was not the main environmental factor affecting the composition of microbial communities. Mantel test analysis revealed that SOC (soil organic carbon) was the primary environmental factor affecting the rhizosphere bacterial community as well as the rhizosphere endophyte bacteria and fungi, while CO₃^2- (carbonate ions) had a greater impact on the rhizosphere fungal communities. In addition, keystones identified through the associated molecular network play an important role in helping plants resist saline-alkali environments. There were significant differences in the metabolic pathways of microorganisms from different rhizocompartments predicted by the PICRUSt2 database, which may help to understand how microorganisms resist environmental stress. This study is of great importance for understanding the salt environments around alkaline lakes and excavating potential microbial resources.

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

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

Indigenous cyanobacteria enhances remediation of arsenic-contaminated soils by regulating physicochemical properties, microbial community structure and function in soil microenvironment

Biocrust was widely used for the immobilization and removal of arsenic (As) in drainage systems of rice fields and mining areas. In this study, the role of an indigenous cyanobacteria (Leptolyngbya sp. XZMQ) was explored in the bioremediation of As-contaminated farmland and tailing soil. After 80 d of inoculation with cyanobacteria, total As (As(T)) accumulated in the cyanobacterial crust of farmland and tailing soil was 279.89 mg kg^-1 and 269.57 mg kg^-1, respectively, and non-EDTA exchangeable fraction was the major fraction of it. The As(T) in farmland and tailing soil of micro-environment decreased by 10.76% and 12.73%, respectively. Meanwhile, the available As (As(a)) decreased by 21.25% and 27.65%, respectively. The XRD results showed that hematite and SiO₂ existed in cyanobacterial crust of farmland and tailing soil. FTIR spectra indicated that the adsorption of As in cyanobacterial crust was mediated by OH and CO. After inoculation of Leptolyngbya sp. XZMQ, in subcrust soil, As biotransformation gene aioA was the most abundant, followed by arsM. The dominant phyla of soil biota were Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroiota, which could play critical roles in shaping aioA and arsM harboring microbe communities in soil. Redundancy analysis (RDA) showed that soil organic carbon (OC), pH, and chlorophyll a (Chl a) were the most important environmental factors in altering soil bacterial communities. Correlation analysis showed the Leptolyngbya had a positive correlation with Chl a, effective nitrogen (N(a)), electrical conductivity (EC), OC, pH in the soil, respectively, while it had a significant negative correlation with As(a), As(III) and As(T). These results emphasized on the significance of cyanobacteria in the behavior of As in mine soils and offered a promising strategy for bioremediation of As-contaminated soil in the mining area.

Evaluation of Pollution Level, Spatial Distribution, and Ecological Effects of Antimony in Soils of Mining Areas: A Review

The first global-scale assessment of Sb contamination in soil that was related to mining/smelting activities was conducted based on 91 articles that were published between 1989 and 2021. The geographical variation, the pollution level, the speciation, the influencing factors, and the environmental effects of Sb that were associated with mining/smelting-affected soils were analyzed. The high Sb values mainly occurred in developed (Poland, Italy, Spain, Portugal, New Zealand, Australia) and developing (China, Algeria, Slovakia) countries. Sb concentrations of polluted soil from mining areas that were reported in most countries significantly exceeded the maximum permissible limit that is recommended by WHO, except in Turkey and Macedonia. The soil Sb concentrations decreased in the order of Oceania (29,151 mg/kg) > North Africa (13,022 mg/kg) > Asia (1527 mg/kg) > Europe (858 mg/kg) > South America (37.4 mg/kg). The existing extraction methods for Sb speciation have been classified according to the extractant, however, further research is needed in the standardization of these extraction methods. Modern analytical and characterization technologies, e.g., X-ray absorption spectroscopy, are effective at characterizing chemical speciation. Conditional inference tree (CIT) analysis has shown that the clay content was the major factor that influenced the soil Sb concentration. Non-carcinogenic risks to the public from soil Sb pollution were within the acceptable levels in most regions. An Sb smelter site at the Endeavour Inlet in New Zealand, an abandoned open-pit Sb mine in Djebel Hamimat, Algeria, an old Sb-mining area in Tuscany, Italy, and Hillgrove mine in Australia were selected as the priority control areas. Cynodon dactylon, Boehmeria, Pteris vittata, and Amaranthus paniculatus were found to be potential Sb accumulators. All of the values of bioaccumulation factors for the crops were less than one. However, ingestion of Sb through crop consumption posed potential non-carcinogenic health risks, which should not be neglected. The soil variables (pH, Eh, total sulfur, carbon nitrogen ratio, total organic carbon, and sulfate), the total Sb and the bioavailable Sb, and heavy metal(loid)s (As, Pb, and Fe) were the major parameters affecting the microbial community compositions.

Indigenous rhizosphere microbial community characteristics of the phytostabilizer Athyrium wardii (Hook.) grown in a Pb/Zn mine tailing

Plant rhizosphere microbiome usually changes dramatically in adaptation to the mine environment to endure high heavy metal concentration, which in turn improves the process of revegetation and phytostabilization of mine tailing and deserves deep investigation. A field study was conducted to investigate the indigenous microbial community of a mining ecotype (ME) of the phytostabilizer Athyrium wardii (Hook.) grown in a Pb/Zn mine tailing and a corresponding non-mining ecotype (NME) grown in an uncontaminated adjacent site. Our study found a slight difference in microbial α-diversity between the ME and NME, and no significant difference between the rhizosphere and bulk soil. Both bacterial and fungal community compositions differed between the ME and NME, for which the differences were mainly driven by pH and metal contaminants. The ME harbored a unique microbial community in the rhizosphere soils different from the bulk soil and NME counterparts. The dominant phyla in the ME rhizosphere were Proteobacteria, Chloroflexi, Actinobacteria, Nitrospirae, and Ascomycota. Several genera from Proteobacteria, Acidobacteria, and Ascomycota were more abundant in the ME rhizosphere than in the NME rhizosphere. Network analysis revealed that keystone taxa were different in the two sites. Some keystone taxa from Gemmatimonadaceae, and Burkholderiaceae and Ascomycota played a critical role in microbial interactions within the mine tailing network. The unique microbial community with high tolerance in the rhizosphere soils of ME may show great benefit for plant growth and metal tolerance of the ME and thereby contributing to the process of revegetation and phytostabilization of mine tailings.

Herbivore camping reshapes the taxonomy, function and network of pasture soil microbial communities

Although the effects of herbivore camping on soil physicochemical properties have been studied, whether the effects alter the soil microbial communities (e.g., composition, functions, taxonomic and functional diversities, network) remain unknown, especially below the surface. Here, using paired subsoil samples from half month-camping and non-camping, we showed for the first time that camping significantly changed the relative abundance of 21 bacterial phylotypes and five fungal phylotypes. Specifically, we observed significant increases in the relative abundance of putative chitinase and terpenes vanillin-decomposition genes, nitrite reduction function (nirB, nasA), decreases in the relative abundance of putative carbon fixation genes (ackA, PGK, and Pak), starch-decomposition gene (dexB), gene coding nitrogenase (anfG), and tetracycline resistance gene (tetB) for bacterial communities, and significant decreases in the relative abundance of animal endosymbiont and increases in the relative abundance of litter saprotroph and endophyte for fungal communities. However, camping did not significantly impact the taxonomic and functional diversity. The niche restriction was the main driving force of bacterial and fungal community assembly. Compared to no camping, camping increased the stability of bacterial networks but decreased the stability of fungal networks. Camping exerted a positive effect on the network by compressing the niche width and reduced the change in the network by reducing the niche overlap. Our results suggest that camping restructures the soil microbial composition, function, and network, and provides a novel insight into the effect of animal camping on soil microbial communities in grassland.

The Difference of Lead Accumulation and Transport in Different Ecotypes of Miscanthus floridulus

Miscanthus floridulus is a plant with a high biomass and heavy metal tolerance, which is a good candidate for phytoremediation. Pot experiments were conducted to compare the growth response, Pb enrichment ability, and the effect on Pb speciation of two ecotypes of M. floridulus from the Dabaoshan Mining Area and the non-mining area of Boluo County, Huizhou, in soils with different Pb contents. The results showed that two ecotypes of M. floridulus had different growth responses to Pb concentrations in soil. Under a low concentration of Pb (100 mg·kg−1) treatment, the aboveground biomass of the non-mining area plant ecotype was significantly affected, while the plants with the mining area ecotype were not significantly affected. When the concentration of Pb increased, the aboveground biomass of the non-mining ecotype was 30.2–41.1% of the control, while that of the mining ecotype was 57.8–65.0% of the control. The root biomass of the non-mining ecotype decreased with the increase of treatment concentration, accounting for 57.8–64.2% of the control, while that of the mining ecotype increased significantly, accounting for 119.5–138.6% of the control. The Pb content in the shoots and roots of the mining ecotype M. floridulus increased rapidly with the increase of the Pb treatment concentration in the soil, and the increase in speed was obviously faster than that of the non-mining ecotype. The total amount of Pb accumulated in the roots of the ecotype from the mining area was much greater than that of the ecotype from the non-mining area, and increased significantly with the increase of Pb concentration in the soil (p < 0.05). With the aggravation of Pb stress, the transfer coefficient and tolerance index of the two ecotypes decreased by different degrees. The transfer coefficient and tolerance index of the mining ecotype were significantly higher than those of the non-mining ecotype. Pearson correlation analysis showed that root biomass was positively correlated with shoot biomass, and shoot biomass was negatively correlated with Pb content in both root and shoot, indicating that Pb accumulation in root and shoot was toxic to plants and inhibited the growth of M. floridulus. The mining ecotypes showed stronger tolerance to and enrichment of Pb.

Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient

Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future.

Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China

Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.

Bio-Matrix Pot Addition Enhanced the Vegetation Process of Iron Tailings by Pennisetum giganteum

The barrenness of large mine tailing sand reservoirs increases the risks for landslides and erosion that may be accompanied with transfer of contaminants into the surrounding environment. The tailing sand is poor in nutrients, which effectively complicates the vegetation process. We investigated direct planting of Pennisetum giganteum into tailing sand using two pit planting methods: the plants were transplanted either directly into pits filled with soil or into soil-filled bio-matrix pots made of organic material. After growing P. giganteum in iron tailing sand for 360 days, the dry weight of the plants grown in the bio-matrix pot (T2) was approximately twofold higher than that of the plants grown in soil placed directly into the sand (T1). At 360 days, the organic matter (OM) content in the soil below the pit was the lowest in the not-planted treatment (T0) and the highest in T2, the available N (AN) contents were higher in T1 and T2 than in T0, and the available P and K contents were the highest in T2. At 360 days, the Shannon diversity of the soil microbial communities was higher in T1 and T2 than in T0, and the community compositions were clearly separated from each other. The profiles of predicted C cycle catabolism functions and N fixation-related functions in T1 and T2 at 360 days were different from those in the other communities. The results showed that P. giganteum grew well in the iron tailing sand, especially in the bio-matrix pot treatment, and the increased nutrient contents and changes in microbial communities indicated that using the bio-matrix pot in planting had potential to improve the vegetation process in iron tailing sands effectively.

Immobilization of Sb in a smelting residue by micro-sized zero-valent iron: Long-term performance under accelerated exposure to strong acid rain

This study investigated the long-term leachability of antimony (Sb) in a smelting residue immobilized by three commercial micro-sized zero-valent iron (ZVI) products. Effect of oxic incubation time (14 days and 120 days) on the immobilization efficiency of Sb were compared, and the long-term leaching risk was evaluated by an accelerated exposure test, in which the slag was consecutively extracted by simulated strong acid rain (SSAR, HNO₃: H₂SO₄ = 1:2, pH = 3.20). Notably, all ZVI treatments efficiently immobilized the Sb in this slag in a short term (14 days); the one-step SSAR-leached Sb was reduced by 89%-91% compared to the original slag (5.9 mg/L) and was far below the environmental standard (0.6 mg/L) established by the US EPA. The sequential SSAR leaching results reflected that the 14-d incubated slags after ZVI treatments had strong H⁺ resistance, and the immobilized Sb was not easily activated by continuous SSAR corrosion. The binding of Sb with amorphous phase Fe oxyhydroxides (e.g. ferrihydrite) derived from ZVI corrosion played a dominant role in the Sb immobilization efficiency. However, the longer aging process (120 days) easily resulted in the reduction of Sb immobilization by ZVI treatments. The changes in crystallinity of Fe oxyhydroxides (transformation from poorly-crystalline to crystalline ones) and the pH elevation to alkaline range might explain the weakening of the immobilization of Sb in ZVI-amended slags with 120 days of incubation. In total, the effectiveness of Sb immobilization in smelting residue greatly depended on the type of ZVI and the aging process. Our work has demonstrated that the ZVI treatment was potentially feasible to mitigate the Sb leaching risk from smelting slags; however, the ZVI type needs to be carefully selected and its long-term performance should be adequately verified before practical application.

Improved phytoremediation of heavy metal contaminated soils by Miscanthus floridulus under a varied rhizosphere ecological characteristic

Miscanthus floridulus is a plant with high biomass and heavy metal tolerance, which is a good candidate for phytoremediation. It is essential to explore how to improve its remediation ability, especially the rhizosphere ecological characteristics which are significant for phytoremediation efficiency. Therefore, the heavy metals accumulation of M. floridulus, rhizosphere soil physicochemical properties, enzyme activities, and bacterial community of different distances from the tailing were measured, focusing on the relationship between phytoremediation ability and rhizosphere ecological characteristics. The results show that the stronger the phytoremediation ability is, the better is the soil environment, and the higher the coverage with plants. Soil rhizosphere environment and the phytoremediation ability are shaped by heavy metals. Rhizosphere microecology may regulate phytoremediation by improving soil nutrients and enzyme activities, alleviating heavy metal toxicity, changing rhizosphere microbial community structure, increasing beneficial microbial abundance, promoting heavy metals accumulation by plants. This study not only clarified the relationship between rhizosphere ecological factors, but also elucidated the phytoremediation regulatory mechanism. Some of microbial taxa might developed as biological bioinoculants, providing the possibility to promote the growth of plants with ecological restoration ability and improve the phytoremediation efficiency.

A field study reveals links between hyperaccumulating Sedum plants-associated bacterial communities and Cd/Zn uptake and translocation

Hyperaccumulating ecotypes of Sedum plants are promising Cd/Zn phytoextractors, with potential for leveraging its rhizospheric or endophytic microbiomes to improve phytoremediation efficiency. However, research of bacteria associated with Sedum at field scale is still lacking. Here, we presented a detailed investigation of the bacterial microbiome of hyperaccumulating Sedum ecotypes (S. alfredii and S. plumbizincicola) and a non-hyperaccumulating S. alfredii ecotype, which grow at different soil environments. Moreover, we evaluated the heavy metal uptake and translocation potential of Sedum plants at different locations. The results showed that both HE ecotypes, contrary to the NHE, were efficient for phytoremediation in mine areas and farmlands. For NHE plants, rhizosphere co-occurrence networks were more complex than the networks of other compartments, while networks of HE plants were more complex in bulk soil and roots. The proportion of positive correlations within co-occurrence networks was higher for the HE plants, suggesting a greater potential for mutualistic interactions. Plant compartment and location predominantly shaped the microbiome assembly, and Proteobacteria, Actinobacteria and Acidobacteria dominated the bacterial communities of Sedum plants. Keystone taxa related to Zn hyperaccumulation are similar to those related to Cd hyperaccumulation, and nine bacterial genera had significantly positive correlation with Cd/Zn hyperaccumulation. Taxa, linked to phytoremediation in both mine and farmland (i.e. Actinospica and Streptomyces from Actinobacteria), could be targets for further investigation of their ability to promote metal phytoremediation of Sedum species.

Accumulation, regional distribution, and environmental effects of Sb in the largest Hg-Sb mine area in Qinling Orogen, China

In this study, knowledge gaps on Sb concentration in rocks, ores, tailings, soil, river water, sediments, and crops of mine areas were identified and discussed in terms of contamination levels, spatial distribution, and environmental effects. Accordingly, Xunyang Hg-Sb mine, the largest Hg-Sb deposit in China as research region in this study, field sampling and laboratory analysis were conducted. The results showed elevated concentrations of Sb in the soil, sediment, and river water. The X-ray diffraction analysis indicated that the main minerals of the rocks were quartz, dolomite, calcite, and margarite. Based on the TESCAN integrated mineral analyzer analysis, the main ore minerals in the Gongguan mine were dolomite (93.97%), cinnabar (2.50%), stibnite (2.48%), calcite (0.38%), and quartz (0.38%). The μ-XRF analysis indicated that Sb distribution was similar to those of S and O, instead of those of Hg and As. The clear spatial variation of Sb concentration in environmental media, mines, tailings, and settling ponds affected Sb accumulation. Actinobacteriota, Proteobacteria, Acidobacteriota, and Chloroflexi were the dominant phyla in the soil. Patescibacteria, Proteobacteria, and Bdellovibrionota were negatively correlated with Sb in the soil (p < 0.05). Exposure to Sb through maize grain and cabbage consumption poses serious non-carcinogenic health risk for residents. This work provides a scientific basis for the environmental quality assessment of Sb mine areas and development of applicable guidelines.

Effects of environmental factors on soil bacterial community structure and diversity in different contaminated districts of Southwest China mine tailings

A mass of tailings left by mineral exploitation have caused serious environmental pollution. Although many studies have shown that soil microorganisms have the potential to remediate environmental pollution, the interaction mechanism between microorganisms and the surrounding environment of tailings is still unclear. In this study, 15 samples around pyrite mine tailing were collected to explore the ecological effects of environmental factors on bacterial community. The results showed that most of the samples were acidic and contaminated by multiple metals. Cadmium (Cd), copper (Cu), nickel (Ni) migrated and accumulated to into downstream farmlands while chromium (Cr) was the opposite. Proteobacteria, Chloroflex and Actinobacteria were the dominant phyla. Soil pH, total phosphorus (TP), total nitrogen (TN), available potassium (AK), available phosphorus (AP), the bacteria abundance and diversity all gradually increased with the increase of the distance from the tailing. Invertase, acid phosphatase, total organic carbon (TOC), pH, TP and Cr were the main influencing factors to cause the variation of bacterial community. This work could help us to further understand the changes in soil microbial communities around pollution sources.

Phytoremediation of cadmium-contaminated sediment using Hydrilla verticillata and Elodea canadensis harbor two same keystone rhizobacteria Pedosphaeraceae and Parasegetibacter

Aquatic macrophytes have been widely employed for in-situ phytoremediation of cadmium (Cd) polluted sediments. But, little is known about the responses of rhizosphere bacteria and their interspecific interactions to phytoremediation. In this study, the α-diversity, community composition, co-occurrence network and keystone species of sediment bacteria in rhizosphere zones of two typical macrophytes, Hydrilla verticillata and Elodea canadensis, were investigated using 16S rRNA gene high-throughput sequencing. The results showed that after fifty days of phytoremediation, a group of specialized sediment bacteria were assembled in the rhizosphere zones closely associated with different host macrophytes. Rhizosphere micro-environments, i.e., the increases of redox potential and organic matter and the decreases of pH, nitrogen and phosphorus, reduced bacterial α-diversity through niche-based species-sorting process, which in turn reduced interspecific mutualistic relationships. But meanwhile, benefiting from the nutrients supplied from macrophyte roots, more bacterial species survived in the highly Cd-contaminated sediments (50 mg kg^-1). In addition, the co-occurrence network revealed that both macrophytes harbored two same keystone bacteria with the high betweenness centrality values, including the family Pedosphaeraceae (genus_unclassified) and genus Parasegetibacter. Their relative abundances were up to 28-fold and 25-fold higher than other keystone species, respectively. Furthermore, these two keystone bacteria were metabolic generalists with vital ecological functions, which posed significant potentials for promoting plant growth and tolerating Cd bio-toxicity. Therefore, the identified keystone rhizobacteria, Pedosphaeraceae and Parasegetibacter, would be potential microbial modulations applied for the future optimization of phytoremediation in Cd-contaminated sediment.

Mechanistic study of antimonate reduction by Escherichia coli W3110

Microbial-assisted antimonate [Sb(V)] reduction immobilizes this redox-sensitive metalloid in the subsurface. Most indigenous aerobes in antimony (Sb)-contaminated areas do not contain Sb(V)-reducing genes but can resist high levels of Sb(V) threat. Herein, to unravel the mechanisms of Sb(V) resistance by aerobes, we used Escherichia coli W3110 as a model aerobe and incubated it with 10 μM Sb(V). We found that strain W3110, without known Sb(V)-reducing genes, was able to reduce Sb(V) to Sb(III). Our transcriptome analysis and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) results show that the Sb(V) threat at the 10 μM level had a negligible effect on the gene expression of strain W3110. In vitro incubation experiments further indicate that Sb(V) reduction was attributable to extracellular polymeric substances (EPS). Moreover, the three-dimensional excitation-emission matrix fluorescence spectroscopy reveals that the tryptophan-like components in EPS were involved in Sb(V) binding as evidenced by its weakened fluorescence intensity upon Sb(V) addition. The FTIR and XPS analyses indicate that hemiacetal and amide groups in EPS contributed to the reduction of Sb(V). Preculture with 10 μM Sb(V) did not exhibit a significant difference in Sb(V)-reducing capacity, suggesting that Sb(V) stress probably did not stimulate EPS secretion of W3110. Our results highlight the importance of EPS as the first line of defense against toxins, especially for those bacteria without such functional genes.

Biodiversity of Root Endophytic Fungi from Oxyria sinensis Grown in Metal-Polluted and Unpolluted Soils in Yunnan Province, Southwestern China

Oxyria sinensis adopts a tolerant strategy as a metal excluder to survive toxic metal concentrations. Biodiversity and the endophytic fungal community colonizing the O. sinensis roots were assessed from a mining area (MA) and a neighboring non-mining area (nMA) in southwestern China. All O. sinensis roots formed fully developed dark septate endophytes (DSEs) and arbuscular mycorrhizal fungi (AMF). Total DSE colonization was higher for the MA versus nMA, in contrast to the total AMF colonization in the two sites. The DSE colonization was higher than AMF colonization regardless of the site. Pure-culture data showed that the fungi closely related to Exophiala, Cadophora and Phialophora dominantly colonized the O. sinensis roots. A total of 450 operational taxonomic units (OTUs) were identified showing the presence of a distinct fungal community in MA and nMA, which was shaped by soil physiochemical properties, including soil Zn concentrations and organic matter. We found that O. sinensis accumulates and adapts efficiently to local endophytic fungi to achieve the expansion of its community, including the spontaneously reclaimed DSE. This property may be targeted to achieve its colonization with a pioneer plant for phytoremediation in the restoration of a vegetation cover in a metal-contaminated area.

Mass balance of nine trace elements in two karst catchments in southwest China

High geological background levels of trace elements (TEs) and high population density in the karst areas of southwest China have imposed environmental pressure on the fragile ecosystems in this region. Understanding the mass budget of TEs, especially the toxic ones, is of great importance to sustain future developments. This study investigates the mass balance and fate of nine TEs (cadmium, arsenic, lead, chromium, copper, nickel, zinc, thallium, and antimony) in two karst catchments (Huilong and Chenqi) in southwest China through estimation of their mass budgets in throughfall, open field precipitation, total suspended particulate matter (TSP), litterfall, fertilization, harvested crops, surface runoff, and underground runoff. The estimated net fluxes are positive, indicating a source region, for four elements (Cu, Cr, Ni, and Tl) and negative, indicating a sink region, for five elements (As, Cd, Pb, Sb, and Zn) in both catchments. The net fluxes for the nine elements in Chenqi catchment are within a relatively small range (2.6, 2.0, 1.6, 0.6, -0.05, -0.5, -0.5, -2.9, and -3.3 mg m^-2 yr^-1 for Cu, Ni, Cr, Tl, Cd, Zn, Sb, Pb, and As, respectively), but in Huilong catchment in quite a large range (15.5, 6.0, 1.0, 0.8, -0.3, -0.9, -4.5, -7.5, and -8.7 mg m^-2 yr^-1 for Tl, Cr, Ni, Cu, Cd, Sb, As, Pb, and Zn, respectively). Rainfall (12.3%-66.2%) and litterfall (18.4%-81.3%) are the major input flux pathways, while crops harvest (16%-99%) is the major output flux pathway for the TEs in both catchments, indicating that the fate of TEs is shaped by both natural factors such as precipitation and litterfall and human activities such as fertilization and crop harvesting in these forestland-farmland compound karst catchments. Results from this study suggest that restoring forests from low-yield sloping farmlands will be useful for controlling TEs pollution in these fragile karst regions with high geological background TEs.

A Comparative Analysis on the Structure and Function of the Panax notoginseng Rhizosphere Microbiome

Panax notoginseng, an important Chinese medicinal herb, can be mainly cultivated in two planting patterns, cropland planting (DT) and understory planting (LX). We speculate that the rhizosphere microbiome may vary in DT and LX and may play an important role in promoting the growth and health of P. notoginseng. In the present study, culture-independent Illumina HiSeq was employed to investigate the rhizosphere bacteria and fungi under DT and LX planting patterns. Predominant phyla include Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Ascomycota in the two planting patterns. DT has higher alpha diversity index than LX. The predominant LX-core genera include Bradyrhizobium, Streptomyces, and Actinomadura, and the predominant DT-core genera include Sphingomonas, Variovorax, and Novosphingobium. Total relative abundance of the disease-suppression phylum (Proteobacteria, Firmicutes, and Actinobacteria) and the potential plant growth-promoting rhizobacteria (PGPR) were both significantly higher in LX than in DT. We also identified over-presented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition, and plant growth promotion in P. notoginseng rhizosphere. Our findings provide a valuable reference for studying beneficial microbes and pathogens of P. notoginseng planted in DT and LX.

Synergistic effects of antimony and arsenic contaminations on bacterial, archaeal and fungal communities in the rhizosphere of Miscanthus sinensis: Insights for nitrification and carbon mineralization

The impacts of metal(loids) on soil microbial communities are research focuses to understand nutrient cycling in heavy metal-contaminated environments. However, how antimony (Sb) and arsenic (As) contaminations synergistically affect microbially-driven ecological processes in the rhizosphere of plants is poorly understood. Here we examined the synergistic effects of Sb and As contaminations on bacterial, archaeal and fungal communities in the rhizosphere of a pioneer plant (Miscanthus sinensis) by focusing on soil carbon and nitrogen cycle. High contamination (HC) soils showed significantly lower levels of soil enzymatic activities, carbon mineralization and nitrification potential than low contamination (LC) environments. Multivariate analysis indicated that Sb and As fractions, pH and available phosphorus (AP) were the main factors affecting the structure and assembly of microbial communities, while Sb and As contaminations reduced the microbial alpha-diversity and interspecific interactions. Random forest analysis showed that microbial keystone taxa provided better predictions for soil carbon mineralization and nitrification under Sb and As contaminations. Partial least squares path modeling indicated that Sb and As contaminations could reduce the carbon mineralization and nitrification by influencing the microbial biomass, alpha-diversity and soil enzyme activities. This study enhances our understanding of microbial carbon and nitrogen cycling affected by Sb and As contaminations.

Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.

Analysis of microbial community structure and diversity in surrounding rock soil of different waste dump sites in fushun western opencast mine

It is importance to understand the correlation between the physicochemical properties of different surrounding rock soil and microbial communities in Fushun western opencast mining for the ecological restoration of land after mine closure. In this study, two layers of soil samples were collected from four different areas in Fushun western opencast mining: coal gangue area (CGA), green mudstone area (GMA), oil shale area (OSA) and mixed area (MA). Then, the effects of different surrounding rock soil physicochemical properties on the microbial communities were explored using the High-throughput sequencing technique. A wide diversity of taxonomical groups were present in four soil cores, and many were correlated with soil physicochemical properties. The obvious differences in microbial communities between different areas showed the influence of different surrounding rock soil on the microbial communities were significant. Redundancy analysis and the network diagram confirmed that soil physicochemical properties pH (Pondus Hydrogenii)-AN (Available Nitrogen)-EC (Electronic Conductivity)-WC (Water Content)-TK (Total Nitrogen), Cd (Cadmium)-Ni (Nickel) had great influence on the microbial communities. Therefore, this study can provide scientific judgments for the different surrounding rock soil physicochemical properties in coal mining, microbial-mediated rock mineralization and biogeochemical cycles.

Paenibacillus polymyxa, a Jack of all trades

The bacterium Paenibacillus polymyxa is found naturally in diverse niches. Microbiome analyses have revealed enrichment in the genus Paenibacillus in soils under different adverse conditions, which is often accompanied by improved growth conditions for residing plants. Furthermore, Paenibacillus is a member of the core microbiome of several agriculturally important crops, making its close association with plants an interesting research topic. This review covers the versatile interaction possibilities of P. polymyxa with plants and its applicability in industry and agriculture. Thanks to its array of produced compounds and traits, P. polymyxa is likely an efficient plant growth-promoting bacterium, with the potential of biofertilization, biocontrol and protection against abiotic stresses. By contrast, cases of phytotoxicity of P. polymyxa have been described as well, in which growth conditions seem to play a key role. Because of its adjustable character, we propose this bacterial species as an outstanding model for future studies on host-microbe communications and on the manner how the environment can influence these interactions.

Factors influencing the uptake and speciation transformation of antimony in the soil-plant system, and the redistribution and toxicity of antimony in plants

Antimony (Sb) is not an essential element for humans and plants although it can be used to treat some human diseases, such as schistosomiasis. Sb contamination has been documented in many regions around the world, particularly in China. The Sb contamination in the environment often stems from anthropogenic activities such as mining, smelting, and shooting. Within the latest decade, great progress has been made in research examining the physiochemical behavior of Sb in the environment, including 1) the extent of Sb pollution around the world particularly in China; 2) the mechanisms and factors influencing Sb migration in soils, especially the adsorption/desorption of Sb by minerals or organic materials; 3) the transformations influencing speciation catalyzed by soil microbes; 4) to a lesser extent, the toxicity of Sb to plants and soil animals. In this review, we highlighted the current knowledge with respect to 1) how soil physicochemical properties (including water regimes, pH, organic materials and Eh), and soil organisms will affect the soil bioavailability of Sb, and subsequently the uptake of Sb by plants; 2) the uptake pathway of antimonite and antimonate, the translocation of Sb from roots to shoots, and the redistribution and toxicity of Sb in plants.

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

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

Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation

Metal contamination released from tailings is a global environmental concern. Although phytoremediation is a promising remediation method, its practice is often impeded by the adverse tailing geochemical conditions, which suppress biological activities. The ecosystem services provided by indigenous microorganisms could alter environmental conditions and facilitate revegetation in tailings. During the process, the keystone taxa of the microbial community are assumed an essential role in regulating the community composition and functions. The identity and the environmental functions of the keystone taxa during tailing revegetation, however, remain unelucidated. The current study compared the microbial community composition and interactions of two contrasting stibnite (Sb₂S₃) tailings, one revegetated and one unvegetated. The microbial interaction networks and keystone taxa were significantly different in the two tailings. Similar keystone taxa were also identified in other revegetated tailings, but not in their corresponding unvegetated tailings. Metagenome-assembled genomes (MAGs) indicated that the keystone taxa in the revegetated tailing may use both organic and inorganic energy sources (e.g., sulfur, arsenic, and antimony). They could also facilitate plant growth since a number of plant-growth-promoting genes, including phosphorus solubilization and siderophore production genes, were encoded. The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth.

Low levels of salivary metals, oral microbiome composition and dental decay

Salivary microbiome composition can change following exposure to environmental toxicants, e.g., heavy metals. We hypothesized that levels of salivary nutrients and metals would correlate with salivary microbiome composition and be associated with dental decay. Here we assess the salivary concentrations of 5 essential minerals (cobalt, copper, manganese, molybdenum, and zinc), 4 metals with some evidence of normal physiological function (chromium, nickel, tungsten, and vanadium), and 12 with known toxicity (antimony, arsenic, barium, beryllium, cadmium, cesium, lead, mercury, platinum, thallium, tin, and uranium), and their associations with salivary microbiome composition and dental decay in 61 children and adults. 16 metals were detected in 54% of participants; 8 were found in all. Marked differences in salivary bacterial taxa were associated with levels of antimony, arsenic, and mercury, after adjusting for multiple testing. Further, antimony levels were associated with the presence of decayed teeth. Thus, salivary metal levels, even at low concentrations, may impact oral health.

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone-aquifer sediments

AIMS

This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone-aquifer sediments and their respective responses to environmental factors.

METHODS AND RESULTS

We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment-bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables.

CONCLUSIONS

Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone-aquifer continuum.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.

Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings

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