Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine

Fate and potential ecological risk of rare earth elements in 3000-year reclaimed soil chronosequences

The introduction of anthropogenic inputs into natural systems may lead to enduring alterations in the innate characteristics of Rare Earth Elements (REEs). Against this backdrop, the evolutionary processes and environmental drivers of REEs in soil remain uncertain. A 3000-year soil chronosequence with uniform parent material was established in reclaimed farmland along the Yangtze River, reconstructing, for the first time, the dynamic processes of REE accumulation and fractionation over a long-time scale. Analysis of 122 soil samples showed REE concentrations ranging from 146.00 to 216.56 μg/g. Based on reclamation duration, three significant stages of REE evolution were identified: natural leaching, rapid accumulation, and stable accumulation with differentiation. Reclaimed soil after 3000 years exhibited a 14.1 % increase in REE concentrations compared to fresh sediments, attributed to anthro -pedogenic processes. Moreover, Heavy Rare Earth Elements (HREEs) accumulated faster than Light Rare Earth Elements (LREEs), particularly in deeper soils (60-100 cm), where HREE concentrations rose by 34.3 %, mainly due to acidic environments promoting HREE fixation. Additionally, the potential ecological risk posed by REEs heightened with reclamation duration, with HREEs exhibiting a sensitivity of 83 % to 94 %. Our findings stress the urgency of carefully monitoring exogenous REEs introduced through anthropogenic activities, particularly HREEs.

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.

Miscanthus sp. root exudate alters rhizosphere microbial community to drive soil aggregation for heavy metal immobilization

The heavy metals (HMs) spatial distribution in soil is intricately shaped by aggregation processes involving chemical reactions and biological activities, which modulate HMs toxicity, migration, and accumulation. Pioneer plants play a central role in preventing HMs at source, yet the precise mechanisms underlying their involvement in soil aggregation remain unclear. This study investigates HMs distribution within rhizosphere and bulk soil aggregates of Miscanthus sp. grown in tailings to elucidate the impact of root exudates (REs) and rhizosphere microbes. The results indicate that Miscanthus sp. enhance soil stability, increasing the proportion of macroaggregates by 4.06 %-9.78 %. HMs tend to concentrate in coarse-aggregates, particularly within rhizosphere environments, while diminishing in fine-aggregates. Under HMs stress, lipids and lipid-like molecules are the most abundant REs produced by Miscanthus sp., accounting for under up to 26.74 %. These REs form complex with HMs, promoting microaggregates formation. Charged components such as sugars and amino acids further contribute to soil aggregation. REs also regulates rhizosphere bacteria and fungi, with Acidobacteriota, Chloroflexi were the dominant bacterial phyla, while Ascomycota and Basidiomycota dominate the fungal community. The synergistic effect of REs and microorganisms impact soil organic matter and nutrient content, facilitating HMs nanoparticle heteroaggregation and macroaggregates formation. Consequently, soil structure and REs shape the distribution of HMs in soil aggregation. Pioneer plants mediate REs interaction with rhizosphere microbes, promoting the distribution of HMs into macroaggregates, leading to immobilization. This study sheds light on the role of pioneer plants in regulating soil HMs, offering valuable insights for soil remediation strategies.

Pioneer plants enhance soil multifunctionality by reshaping underground multitrophic community during natural succession of an abandoned rare earth mine tailing

Spontaneous natural succession in metal mine tailings is fundamental to the rehabilitation of bare tailing. Here, an abandoned rare earth element (REE) mine tailing with spontaneous colonisation by pioneer plants with different functional traits was selected. Soil nutrient cycling, fertility, organic matter decomposition as well as underground organismal communities and their multitrophic networks were investigated. Compared with the bare tailing, the colonisation with Lycopodium japonicum, Miscanthus sinensis, and Dicranopteris dichotoma increased soil multifunction by 222%, 293%, and 525%, respectively. This was accompanied by significant changes in soil bacterial and protistan community composition and increased soil multitrophic network complexity. Rhizospheres of different plant species showed distinct microbial community composition compared to that of bare tailing. Some WPS-2, Chloroflexi, and Chlorophyta were mainly present in the bare tailing, while some Proteobacteria and Cercozoa were predominantly seen in the rhizosphere. Pearson correlation and Random Forest revealed the biotic factors driving soil multifunction. Structural equation modelling further revealed that pioneer plants improved soil multifunction primarily by decreasing the microbial biodiversity and increasing the multitrophic network complexity. Overall, this highlights the importance of subterrestrial organisms in accelerating soil rehabilitation during natural succession and provides options for the ecological restoration of degraded REE mining areas.

Hyperaccumulator extracts promoting the phytoremediation of rare earth elements (REEs) by Phytolacca americana: Role of active microbial community in rhizosphere hotspots

The increased usage of rare earth elements (REEs) leads to the extensive exploitation of rare earth mines, and the REEs pollution in soil caused by the legacy mine tailings has brought great harm to environment and human health. Although Phytolacca americana can remove REEs from contaminated soil to some extent, there is still an urgent problem to improve its efficiency. Hyperaccumulator extract is a new organic material with potential in metal phytoextraction, but its role in REEs phytoremediation and the related underlying processes remain unclear. In this study, hyperaccumulator extracts from P. americana root (PR), stem (PS), leaf (PL) and EDTA were used to improve the phytoremediation efficiency of REEs with P. americana. Soil zymography was applied to assess the enzyme hotspots' spatial distribution in the rhizosphere, and the hotspots' microbial communities were also identified. The results indicated that the application of hyperaccumulator extracts improved the biomass and REEs uptake of P. americana, and the highest REEs content in plant was observed in the treatment of PS, which increased 299% compared to that of the control. Hotspots area of β-glucosidase, leucine aminopeptidase and acid phosphatase were concentrated in the pant rhizosphere along the roots and increased 2.2, 5.3 and 2.2 times after PS application compared to unamended soils. The PS application increased the relative abundance of Proteobacteria, Cyanobacteria, Bacteroidota and Firmicutes phyla in rhizosphere. Soil fungi have a higher contribution on promoting REEs activation than that of bacteria. Available P and extractable REEs were leading predictors for the plant biomass and REEs concentrations. The co-occurrence network showed that the application of PS creates a more efficient and stable microbial network compared to other treatments. In conclusion, stem-derived hyperaccumulator extract is excellent in stimulating REEs phytoremediation with P. americana by improving hotspots microbial activities and form a healthy rhizosphere microenvironment.

Impacts of multiple environmental factors on soil bacterial community assembly in heavy metal polluted paddy fields

Soil microorganisms play pivotal roles in driving essential biogeochemical processes in terrestrial ecosystems, and they are sensitive to heavy metal pollution. However, our understanding of multiple environmental factors interaction in heavy metal polluted paddy fields to shape microbial community assembly remain limited. In the current study, we used 16S rRNA amplicon sequencing to characterize the microbial community composition in paddy soils collected from a typical industry town in Taihu region, eastern China. The results revealed that Cd and Pb were the major pollutant, and Proteobacteria, Acidobacteria and Chloroflexi were the dominate indigenous bacterial phyla. Linear regression and random forest analysis demonstrated that soil pH was the most important predictor of bacterial diversity. Mantel analysis showed that bacterial community structure was mainly driven by pH, CEC, silt, sand, AK, total Cd and DTPA-Cd. The constructed bacterial co-occurrence network, utilizing a random matrix theory-based approach, exhibited non-random with scale-free and modularity features. The major modules within the networks also showed significant correlations with soil pH. Overall, our study indicated that soil physiochemical properties made predominant contribution to bacterial community diversity, structure and their association in Cd/Pb polluted paddy fields. These findings expand our knowledge of the key environmental drivers and co-occurrence patterns of bacterial community in polluted paddy fields.

The impact of microbial community structure changes on the migration and release of typical heavy metal (loid)s during the revegetation process of mercury-thallium mining waste slag

The effect of changes in microbial community structure on the migration and release of toxic heavy metal (loid)s is often ignored in ecological restoration. Here, we investigated a multi-metal (mercury and thallium, Tl) mine waste slag. With particular focus on its strong acidity, poor nutrition, and high toxicity pollution characteristics, we added fish manure and carbonate to the slag as environmental-friendly amendments. On this basis, ryegrass, which is suitable for the remediation of metal waste dumps, was then planted for ecological restoration. We finally explored the influence of changes in microbial community structure on the release of Tl and As in the waste slag during vegetation reconstruction. The results show that the combination of fish manure and carbonate temporarily halted the release of Tl, but subsequently promoted the release of Tl and arsenic (As), which was closely related to changes in the microbial community structure in the waste slag after fish manure and carbonate addition. The main reason for these patterns was that in the early stage of the experiment, Bacillaceae inhibited the release of Tl by secreting extracellular polymeric substances; with increasing time, Actinobacteriota became the dominant bacterium, which promoted the migration and release of Tl by mycelial disintegration of minerals. In addition, the exogenously added organic matter acted as an electron transport medium for reducing microorganisms and thus helped to reduce nitrate or As (Ⅴ) in the substrate, which reduced the redox potential of the waste slag and promoted As release. At the same time, the phylum Firmicutes, including specific dissimilatory As-reducing bacteria that are capable of converting As into a more soluble form, further promoted the release of As. Our findings provide a theoretical basis for guiding the ecological restoration of relevant heavy-metal (loid) mine waste dumps.

Using Network Analysis and Predictive Functional Analysis to Explore the Fluorotelomer Biotransformation Potential of Soil Microbial Communities

Microbial transformation of per- and polyfluoroalkyl substances (PFAS), including fluorotelomer-derived PFAS, by native microbial communities in the environment has been widely documented. However, few studies have identified the key microorganisms and their roles during the PFAS biotransformation processes. This study was undertaken to gain more insight into the structure and function of soil microbial communities that are relevant to PFAS biotransformation. We collected 16S rRNA gene sequencing data from 8:2 fluorotelomer alcohol and 6:2 fluorotelomer sulfonate biotransformation studies conducted in soil microcosms under various redox conditions. Through co-occurrence network analysis, several genera, including Variovorax, Rhodococcus, and Cupriavidus, were found to likely play important roles in the biotransformation of fluorotelomers. Additionally, a metagenomic prediction approach (PICRUSt2) identified functional genes, including 6-oxocyclohex-1-ene-carbonyl-CoA hydrolase, cyclohexa-1,5-dienecarbonyl-CoA hydratase, and a fluoride-proton antiporter gene, that may be involved in defluorination. This study pioneers the application of these bioinformatics tools in the analysis of PFAS biotransformation-related sequencing data. Our findings serve as a foundational reference for investigating enzymatic mechanisms of microbial defluorination that may facilitate the development of efficient microbial consortia and/or pure microbial strains for PFAS biotransformation.

Soil organic matter degradation and methylmercury dynamics in Hg-contaminated soils: Relationships and driving factors

Biodegradation of soil organic matter (SOM), which involves greenhouse gas (GHG) emissions, plays an essential role in the global carbon cycle. Over the past few decades, this has become an important research focus, particularly in natural ecosystems. SOM biodegradation significantly affects contaminants in the environment, such as mercury (Hg) methylation, producing highly toxic methylmercury (MeHg). However, the potential link between GHG production from SOM turnover in contaminated soils and biogeochemical processes involving contaminants remains unclear. In this study, we investigated the dynamics of GHG, MeHg production, and the relationship between biogeochemical processes in soils from two typical Hg mining sites. The two contaminated soils have different pathways, explaining the significant variations in GHG and MeHg production. The divergence of the microbial communities in these two biogeochemical processes is essential. In addition to the microbial role, abiotic factors such as Hg species can significantly affect MeHg production. On the other hand, we found an inverse relationship between CH4 and MeHg, suggesting that carbon emission reduction policies and management could inadvertently increase the MeHg levels. This highlights the need for an eclectic approach to organic carbon sequestration and contaminant containment. These findings suggest that it is difficult to establish a general pattern to describe and explain the SOM degradation and MeHg production in contaminated soils within the specific scenarios. However, this study provides a case study and helpful insights for further understanding the links between environmental risks and carbon turnover in Hg mining areas.

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.

Unveiling nature's treasures: actinobacteria from Meghalaya's mining sites as sources of bioactive compounds

Coal and sillimanite mining sites present unique ecological niches favoring the growth of actinobacteria, a group of Gram-positive bacteria known for producing a wide array of bioactive compounds. Isolating these bacteria from such environments could unveil novel compounds with potential biotechnological applications. This study involved the isolation of actinobacteria from two mining sites in Meghalaya, India. The dominant genera from both sites were Streptomyces, Amycolatopsis, Nocardia, and Streptosporangium. Metabolic pathway prediction from 16S rRNA gene revealed several pathways beneficial for plant growth. Exploration of biosynthetic genes indicated a prevalence of the type-II polyketide synthase gene. Sequencing the ketosynthase-alpha domain of the gene led to predictions of various bioactive secondary metabolites. Around 44% of the isolates demonstrated antimicrobial properties, with some also displaying plant growth-promoting traits. Amycolatopsis SD-15 exhibited promising results in planta when tested on tomato plants. These findings highlight the potential of actinobacteria from Meghalaya's mining sites across medical, agricultural, and industrial domains.

Effects of microplastics on cold seep sediment prokaryotic communities

Cold seep sediments are an important reservoir of microplastics (MPs) whose impact on the structure and function of prokaryotic community is not well understood. In this study, the impact of 0.2% and 1% (w/w) polyethylene (PE), polystyrene (PS), and polypropylene (PP) MPs on the cold seep sediment prokaryotic community was investigated in a 120-day laboratory incubation experiment. The results revealed that exposure to MPs altered sedimentary chemical properties in a type- and concentration-dependent manner. Furthermore, MPs significantly altered the structure of bacterial community, with some MPs degradation-associated bacterial phyla significantly increasing (p < 0.05). However, in the case of archaea, the changes in the structure of microbial community were less pronounced (p > 0.05). Co-occurrence network analysis revealed that the addition of MPs reduced the network complexity, while PICRUSt2 and FAPROTAX analyses suggested that 0.2% PP and 1% PS MPs had the most significant effects on the nitrogen and carbon cycles (p < 0.05). Overall, this study provides new insights into the effects of MPs on the structure and function of microbial communities in cold seep sediments.

Phytoremediation with application of anaerobic fermentation residues regulate the assembly of ecological clusters within co-occurrence network in ionic rare earth tailings soil: A pot experiment

The cultivation of energy plants (Pennisetum hybrid) with anaerobic fermentation residues has become an important phytoremediation approach in ionic rare earth elements (REEs) tailings because of its advantages in low cost and sustainability recently. In this study, a comparative pot experiment was carried out to determine the interaction pattern and key ecological clusters in microbial community respond to phytoremediation. Results showed that the application of biogas residues or slurry could effectively mitigate soil acidification, increase soil nutrients, alter REEs bioavailability and promote plant growth. Without fertilization, plant growth was restricted and soil acidification and nutrient-deficiency would be further aggravated. This difference in phytoremediation effect was associated with the assembly of seven key ecological clusters in co-occurrence network of rhizosphere soil. And such assembly pattern of cluster, determined by the environmental preference (e.g. pH, REEs), nutrient demand and interaction among clusters, could alter the microbial communities in response to the changes in soil context rapidly and exert corresponding ecological function during phytoremediation, such as participating in soil nutrient cycling, affecting plant biomass and altering REEs bioavailability. These findings provided new insights for anaerobic fermentation residues application, and can be beneficial to support for studying microbe-plant combined remediation in the future.

Environmental risk of ion-absorbed rare earth ores: concentration of leaching agent and fractionation of Pb

Rare earth (RE) is an important strategic resource; however, there has been a growing concern about the environmental problems caused by RE mining, such as ammonia nitrogen pollution and heavy metal pollution. There is a limited research about the behavior of leaching agents and the fractionation of RE and heavy metal during the mining process for ion adsorption of rare earth ore (IRE-ore) in the previously available papers. In this study, (NH4)2SO4 solution, which commonly used in the production of mining IRE-ore, was used as a leaching agent. The adsorption behavior of ore soils on ammonium ions was explored by batch experiments. The adsorption process of IRE-ore on ammonium ions followed a pseudo-second-order equation and was controlled by the kinetics of surface adsorption and intra-particle diffusion; the ammonium ion adsorption isotherm conformed to the Freundlich isotherm equilibrium equation, and the higher concentration advantage made the ore soils possess a higher adsorption capacity of ammonium ion. In addition, the fractionation characteristics of lanthanum (La), cerium (Ce), and lead (Pb) in the ore soil during the leaching process were simulated based on the batch and column leaching experiments. The results demonstrated that the exchangeable states of La and Ce in IRE-ore were high, and the exchangeable, carbonate-bound La and Ce were almost all leached out by (NH4)2SO4 leaching agent, while the most of exchangeable Pb flowed out along with leaching agent, and a small amount of leached Pb in the ore soil was converted to iron and manganese oxide-bound Pb and enriched in the direction of migration of the leaching solution, and when the environment (e.g., pH and Eh) changed, this part of Pb may be re-activated. Our research might serve as crucial baseline knowledge for the adsorption of ammonium ions by ore soils, and provide a data reference for reducing the use of leaching agents and developing sustainable technologies for green mining of ion-adsorption RE ores.

Metabolic and Microbial Profiling of Soil Microbial Community under Per- and Polyfluoroalkyl Substance (PFAS) Stress

Per- and polyfluoroalkyl substances (PFAS) represent significant stress to organisms and are known to disrupt microbial community structure and function. Nevertheless, a detailed knowledge of the soil microbial community responding to PFAS stress at the metabolism level is required. Here we integrated UPLC-HRMS-based metabolomics data with 16S rRNA and ITS amplicon data across soil samples collected adjacent to a fluoropolymer production facility to directly identify the biochemical intermediates in microbial metabolic pathways and the interactions with microbial community structure under PFAS stress. A strong correlation between metabolite and microbial diversity was observed, which demonstrated significant variations in soil metabolite profiles and microbial community structures along with the sampling locations relative to the facility. Certain key metabolites were identified in the metabolite-PFAS co-occurrence network, functioning on microbial metabolisms including lipid metabolism, amino acid metabolism, and secondary metabolite biosynthesis. These results provide novel insights into the impacts of PFAS contamination on soil metabolomes and microbiomes. We suggest that soil metabolomics is an informative and useful tool that could be applied to reinforce the chemical evidence on the disruption of microbial ecological traits.

Halophyte Elymus dahuricus colonization regulates microbial community succession by mediating saline-alkaline and biogenic organic matter in bauxite residue

Alkalinity regulation and nutrient accumulation are critical factors in the construction of plant and microbial communities and soil formation in bauxite residue, and are extremely important for sustainable vegetation restoration in bauxite residue disposal areas. However, the establishment and succession of microbial communities driven by plant colonization-mediated improvements in the physicochemical properties of bauxite residues remain poorly understood. Thus, in this study, we determined the saline-alkali properties and dissolved organic matter (DOM) components under plant growth conditions and explored the microbial community diversity and structure using Illumina high-throughput sequencing. The planting of Elymus dahuricus (E. dahuricus) in the bauxite residue resulted in a significant decrease in total alkalinity (TA), exchangeable Na, and electrical conductivity (EC) as well as the release of more tryptophan-like protein compounds and low-molecular-weight humic substances associated with biological activities into the bauxite residue substrate. Taxonomical analysis revealed an initial-stage bacterial and fungal community dominated by alkaline-tolerant Actinobacteriota, Firmicutes, and Ascomycota, and an increase in the relative abundances of the phyla Bacteroidota, Cyanobacteria, Chloroflexi, and Gemmatimonadota. The biological activities of phylum Actinobacteriota, Bacteroidota, and Gemmatimonadota were significantly associated with protein-like and UVA-like humic substances. As eutrophic bacteria, Proteobacteria participate in the transformation of humic substances and can not only utilize small molecules of organic matter and convert them into humic substances but also promote the gradual conversion of humic acids into simple molecular compounds. Our results suggest that plant roots secrete organic matter and microbial metabolites as the main biogenic organic matter that participates in the establishment and succession of the microbial community in bauxite residues. Root length affects bacterial and fungal diversity by mediating the production of protein-like substances.

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.

The translocation and fractionation of rare earth elements (REEs) via the phloem in Phytolacca americana L

Rare earth elements (REEs) are considered to be emerging contaminants due to their widespread use and lack of recycling. Phytolacca americana L. has great potential for REEs phytoextraction. Our understanding of REEs in P. americana focuses mostly on root absorption and xylem translocation, but the role of phloem translocation has received little attention. In this research, the translocation and fractionation of REEs from phloem to organs in P. americana were investigated. In addition, the effect of organic acids in the REEs translocation via phloem exudates was also examined. The results showed that REEs could transport bidirectionally via the phloem, and 86% of REEs exported from old leaves could move downwards to the root, whereas only 14% of them transported upwards to the young leaves. Heavy rare earth elements (HREEs) enrichment was found in the REEs fractionation processes both from phloem to leaf and from stem to root, indicating that HREEs were preferentially transferred not only down to roots, but also up to the young leaves. The concentration of oxalic acid in phloem exudates was much higher than other organic acids. 94.7% oxalic acid in phloem exudates was preferred to combine with REEs, especially HREEs. Additionally, the concentrations of HREEs had a high positive correlation with oxalic acid in phloem exudates, which demonstrated oxalic acid may play a significant role in the long-distance transport of HREEs in phloem. In conclusion, HREEs have higher translocation ability than light rare earth elements (LREEs) in both xylem and phloem of P. americana. As far as we know, this is the first report focused on the phloem translocation and redistribution of REEs in P. americana, which provides a valuable understanding of the mechanism for phytoremediation of REEs contaminated soils.

Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes

Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.

Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China

Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.

Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome

BACKGROUND

Keystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to recalcitrant pollution and are a key to bioremediation. However, the characterization and manipulation of such taxa is a major challenge due to the complexity of microbial communities and rapid turnover in both time and space. Here, microcosms were set up with benzo[a]-pyrene (BaP) and/or nitrate based on C-rich, S-rich, and N-limited mangrove sediments as reductive experimental models to trigger and track the turnover of keystone taxa to address this challenge.

RESULTS

Based on microbial co-occurrence network analysis, two keystone taxa, Sulfurovum and Sulfurimonas, were found to exhibit significant role transitions in different microcosms, where these two taxa played nonkeystone roles with neutral relationships in in situ mangrove sediments. However, Sulfurimonas transitioned to be keystone taxa in nitrate-replenished microcosms and formed a keystone guild with Thioalkalispira. Sulfurovum stood out in BaP-added microcosms and mutualized in a densely polycyclic aromatic hydrocarbon (PAH)-degrader-centric keystone guild with Novosphingobium and Robiginitalea, where 63.25% of added BaP was removed. Under the occurrence of nitrate and BaP, they simultaneously played roles as keystone taxa in their respective guilds but exhibited significant competition. Comparative genomics and metagenome-assembled genome (MAG) analysis was then performed to reveal the metabolic potential of those keystone taxa and to empirically deduce their functional role in keystone guilds. Sulfurimonas possesses a better sense system and motility, indicative of its aggressive role in nitrate acquisition and conversion; Sulfurovum exhibited a better ability for oxidation resistance and transporting nutrients and electrons. High-efficiency thermal asymmetric interlaced polymerase reaction (hiTAIL-PCR) and enhanced green fluorescent protein (eGFP)-labeling approaches were employed to capture and label the BaP key degrader to further experimentally verify the roles of keystone taxa Sulfurovum in the keystone guilds. Observations of the enhancement in reactive oxygen species (ROS) removal, cell growth, and degradation efficiency by co-culture of isolated keystone taxa strains experimentally demonstrated that Sulfurovum contributes to the BaP degradative microbiome against BaP toxicity.

CONCLUSIONS

Our findings suggest that the combined use of co-occurrence network analysis, comparative genomics, and co-culture of captured keystone taxa (3C-strategy) in microbial communities whose structure is strongly shaped by changing environmental factors can characterize keystone taxa roles in keystone guilds and may provide targets for manipulation to improve the function of the microbiome. Video Abstract.

Rare earth elements detoxification mechanism in the hyperaccumulator Dicranopteris linearis: [silicon-pectin] matrix fixation

Dicranopteris linearis is the best-known hyperaccumulator species of rare earth elements (REEs) and silicon (Si), capable of dealing with toxic level of REEs. Hence, this study aimed to clarify how D. linearis leaves cope with excessive REE stress, and whether Si plays a role in REE detoxification. The results show that lanthanum (La - as a representative of the REEs) stress led to decreased biomass and an increase of metabolism related to leaf cell wall synthesis and modification. However, the La stress-induced responses, especially the increase of pectin-related gene expression level, pectin polysaccharides concentration, and methylesterase activity, could be mitigated by Si supply. Approximately 70% of the Si in D. linearis leaves interacted with the cell walls to form organosilicon Si-O-C linkages. The Si-modified cell walls contained more hydroxyl groups, leading to a more efficient REE retention compared to the Si-free ones. Moreover, this [Si-cell wall] matrix increased the pectin-La accumulation capacity by 64%, with no effect on hemicellulose-La and cellulose-La accumulation capacity. These results suggest that [Si-pectin] matrix fixation is key in REE detoxification in D. linearis, laying the foundation for the development of phytotechnological applications (e.g., REE phytomining) using this species in REE-contaminated sites.

Rare Earth Elements (REEs) Adsorption and Detoxification Mechanisms in Cell Wall Polysaccharides of Phytolacca americana L

The cell wall (CW) is critical for the accumulation of heavy metals in metal-tolerant plants. Polysaccharides, the main component of the CW, contribute significantly to the immobilization of heavy metals. However, the mechanisms of rare earth elements (REEs) adsorption and detoxification by polysaccharides in the cell walls of Phytolacca americana L. (P. americana) remain unclear. In this work, we explored the binding sites of REEs and the modifications to polysaccharides in the cell walls of roots and leaves in P. americana, in order to elucidate the adsorption and fixation mechanism of REEs by the cell wall. Our findings indicated that up to 40.7% and 48.1% of cell-wall-bound REEs were present in the root and leaf pectin, respectively. The removal of pectin led to a 39.8% and 23.6% decrease in the maximum adsorption of REEs in the CW, suggesting that pectin was the main binding site for REEs in the cell walls of P. americana. Hydroxyl (-OH) and carboxyl (-COOH) groups in the cell wall interacted mainly with REEs ions under stress conditions, which played a key role in REEs binding. An obvious REEs fractionation was found during the various fractions of the CW, and all fractions of the root cell wall were enriched with HREEs, whereas all fractions of the leaf cell wall were enriched with LREEs. Moreover, P. americana modulated cell wall composition in reaction to REEs stress. In conclusion, cell wall pectin is the main binding site of REEs, and the functional groups on the cell wall play a significant role in the binding of REEs. At the same time, plants can control the selective adsorption and fixation of REEs by adjusting the composition of cell walls. This study offers valuable insights into the mechanisms of REEs adsorption and fixation in cell walls of P. americana, contributing to a theoretical basis for the bioremediation of REEs pollution.

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.

Revealing the response of microbial communities to polyethylene micro(nano)plastics exposure in cold seep sediment

To date, multiple studies have shown that the accumulation of microplastics (MPs)/nanoplastics (NPs) in the environment may lead to various problems. However, the effects of MPs/NPs on microbial communities and biogeochemical processes, particularly methane metabolism in cold seep sediments, have not been well elucidated. In this study, an indoor microcosm experiment for a period of 120 days exposure of MPs/NPs was conducted. The results showed that MPs/NPs addition did not significantly influence bacterial and archaeal richness in comparison with the control (p > 0.05), whereas higher levels of NPs (1 %, w/w) had a significant adverse effect on bacterial diversity (p < 0.05). Moreover, the bacterial community was more sensitive to the addition of MPs/NPs than the archaea, and Epsilonbacteraeota replaced Proteobacteria as the dominant phylum in the MPs/NPs treatments (except 0.2 % NPs). With respect to the co-occurrence relationships, network analysis showed that the presence of NPs, in comparison with MPs, reduced microbial network complexity. Finally, the presence of MPs/NPs decreased the abundance of mcrA, while promoting the abundance of pmoA. This study will help elucidate the responses of microbial communities to MPs/NPs and evaluate their effects on methane metabolism in cold seep ecosystems.

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.

The characteristics of soil microbial co-occurrence networks across a high-latitude forested wetland ecotone in China

To understand the effect of seasonal variations on soil microbial communities in a forested wetland ecotone, here, we investigated the dynamics of the diversities and functions of both soil bacterial and fungal communities inhabiting three wetland types (forested wetland, shrub wetland and herbaceous vegetation wetland) from forest-wetland ecotone of northern Xiaoxing'an Mountains spanning different seasons. β-diversity of soil microbial communities varied significantly among different vegetation types (Betula platyphylla-Larix gmelinii, Alnus sibirica, Betula ovalifolia, and Carex schmidtii wetlands). We totally detected 34 fungal and 14 bacterial indicator taxa among distinctive groups by using Linear discriminant analysis effect size (LEfSe) analysis, and identified nine network hubs as the most important nodes detected in whole fungi, bacteria, and fungi-bacteria networks. At the vegetation type-level, bacterial and fungal microbiome living in C. schmidtii wetland soil possessed fewer positive interactions and lower modularity than those in other types of wetland soil. Furthermore, we also discovered that ectomycorrhizal fungi were dominant in the fungal microbiota existing in forested and shrub wetland soils, whereas arbuscular mycorrhizal fungi were predominated in those residing in herbaceous vegetation wetland soil. The distribution of the predicted bacterial functional enzymes also obviously varied among different vegetation-types. In addition, the correlation analysis further revealed that the key fungal network modules were significantly affected by the contents of total N and soil water-soluble K, whereas most of the bacterial network modules were remarkably positively driven by the contents of total N, soil water-soluble K, Mg and Na. Our study suggested that vegetation type are substantive factors controlling the diversity, composition and functional group of soil microbiomes from forest-wetland ecotone of northern Xiaoxing'an Mountains.

Metagenomic study of carbon metabolism in black soil microbial communities under lead-lanthanum stress

Pollution of soil environments with heavy metals (HMs) and rare earth elements (REEs) cannot be ignored. We aimed to determine the effects of lead combined with lanthanum (Pb-La) on microbial community structure, carbon metabolism, and differences in carbon source utilization in black soils using EcoPlates™ and a macrogenomic approach. We found that Pb and La contents and the microbial community structure together influence and shape the response of soil carbon metabolism to Pb-La. Compared with controls, microorganisms under pollution stress preferentially use phenolic and carboxylic acids as growth carbon sources. Under Pb-La stress, the relative abundance of Proteobacteria significantly increased, thereby selectively displacing heavy metal-sensitive phyla, such as Chloroflexi, Acidobacteria, and Thaumarchaeota. Altered functional potential of the microbial carbon cycle manifested as differences in carbon metabolism, methane metabolism, and carbon fixation pathways. Furthermore, an appropriate concentration of La can reduce the environmental toxicity of Pb, whereas a high concentration of La has synergistic toxicity with Pb. These findings have important implications for understanding the impact of HM-REE contamination in microbial communities and the functions associated with carbon metabolism in black soils.

Metagenomics reveals the increased antibiotics resistome through prokaryote rather than virome after overuse of rare earth element compounds

Rare earth elements (REE) are extensively exploited in the agricultural ecosystems due to their various beneficial roles on plant growth. However, the ecotoxicological effects and environmental risk of REE are poorly assessed. Here, we investigated the effects of lanthanum and cerium nitrate on soil prokaryote and viral metal resistance genes (MRGs) and antibiotics resistance genes (ARGs) using a metagenomic-based approach. We found that relative abundances of prokaryote phyla Bacteroidetes and Chloroflexi decreased with increasing of both REE compounds. In addition, low level REE nitrate (0.05 and 0.1 mmol kg^-1 soil) inhibited the viral family Phycodanaviridae, Rudiviridae, Schitoviridae, whereas high level (0.16 and 0.32 mmol kg^-1 soil) REE nitrate suppressed the viral family Herelleviridae, Iridoviridae, Podoviridae. ARGs were not significantly affected by low level of REE nitrate. However, high level of both REEs nitrate increased the abundances of dominant prokaryote genes resisting to most of the drug classes, such as aminoglycoside, elfamycin, fluoroquinolone, macrolide, rifamycin. Abundance of MRGs in prokaryote did not change consistently with REE nitrate compound type and input rate. MRGs were only partially detected in the virome in some of the treatments, while ARGs was not detected in virome. Together, we demonstrated that overuse of REE nitrate in agriculture would increase the risk of dissemination of ARGs through prokaryotes but not virus, although viral community was substantially shifted.

Heavy metal contamination affects the core microbiome and assembly processes in metal mine soils across Eastern China

Mining activities in metal mine areas cause serious environmental pollution, thereby imposing stresses to soil ecosystems. Investigating the ecological pattern underlying contaminated soil microbial diversity is essential to understand ecosystem responses to environment changes. Here we collected 624 soil samples from 49 representative metal mines across eastern China and analyzed their soil microbial diversity and biogeographic patterns by using 16 S rRNA gene amplicons. The results showed that deterministic factors dominated in regulating the microbial community in non-contaminated and contaminated soils. Soil pH played a key role in climatic influences on the heavy metal-contaminated soil microbial community. A core microbiome consisting of 25 taxa, which could be employed for the restoration of contaminated soils, was identified. Unlike the non-contaminated soil, stochastic processes were important in shaping the heavy metal-contaminated soil microbial community. The largest source of variations in the soil microbial community was land use type. This result suggests that varied specific ecological remediation strategy ought to be developed for differed land use types. These findings will enhance our understanding of the microbial responses to anthropogenically induced environmental changes and will further help to improve the practices of soil heavy metal contamination remediation.

Co-occurrence network of microbial communities affected by application of anaerobic fermentation residues during phytoremediation of ionic rare earth tailings area

The long-term exploitation of ionic rare earth elements (REEs) in southern China has produced a large-scale of abandoned tailings area. While the application of anaerobic fermentation residues to cultivate economically valuable remediation plants (e.g. energy plant) has become a hotspot due to their merits in low-cost and sustainability in recent years, the succession and co-occurrence patterns of these microbial communities remain unclear. In this study, soil samples were collected from the sustainable restoration area, natural restoration area and tailings area. The composition and diversity of bacterial and fungal communities on five soil samples were evaluated using high-throughput sequencing technology. The results shown that the phytoremediation with anaerobic fermentation residues could significantly improve the physicochemical properties (especially for soil nutrients) and microbial diversity of soil within 3 years, while these parameters in natural restoration area were lower. The nonmetric multidimensional scaling (NMDS) ordinations revealed the shifts of microbial communities depending on soil physicochemical properties and plant species, and soil nutrients were the main factors affecting the microbial variation explained by the variation partition analysis (VPA). The soil nutrient accumulation obviously changed the proportion of oligotrophic and copiotrophic groups, among which the copiotrophic groups were significantly increased, such as Proteobacteria, Bacteroidetes, Gemmatimonadetes and Glomeromycota. The microbial co-occurrence network analysis indicated that application of anaerobic fermentation residues could significantly improve the topological properties and the stability of microbial network. The copiotrophic groups (e.g. Proteobacteria, Ascomycota) became the key to assemble stable network structure. Moreover, herbaceous plants could increase the proportion of fungi (e.g. Ascomycota) in microbial network, which improved the topological properties with bacteria synergistically. Therefore, the soil environment of REEs tailings area was effectively optimized by anaerobic fermentation residues and herbaceous plants, which furthered understanding of co-occurrence pattern and mutualistic relationships of microbial communities during sustainable restoration.

Effects of different straw returning amounts and fertilizer conditions on bacteria of rice's different part in rare earth mining area

Pot experiments were conducted to explore the effects of different rice straw returning soil on the community structure and function of bacteria in rice root, rhizosphere, leaf and phyllosphere under 7 conditions of rice straw combined with different fertilizers respectively. The results showed that: rice straw returning in different ways increased the content of soil pH and K, and reduced the accumulation of N, P and organic matter in soil, and different rice straw returning ways had different effects; rice straw returning reduced dry weight of rice grain, 2% of rice straw returning reduced rice grain greater than that of 1% rice straw returning; The reduction of NP combined fertilization is greater than that of NK combined fertilization and NPK combined fertilization. Except for the decrease of chao_1 index in rice root at maturity, rice straw returning significantly improved the abundance, diversity and evenness of bacteria in rice root, rhizosphere, leaf and phyllosphere. Rice straw returning increased the content of REEs in rice, and 2% of rice straw returning soil increased rare earth element (REE) content in rice grain greater than that of 1% rice straw returning soil. Different ways of rice straw returning soil reduced the abundance of Bacillus, while the abundance of Exiguobacterium in rice leaves was hundreds of times higher than that of the control group, and the genus in leaves was dozens of times higher than that of the control group, 2% of rice straw returning soil increased the abundance of harmful bacteria and pathogens of Acidovorax, Clostridium sensu stricto, Citrobacter, Curtobacterium, and 1% of rice straw returning soil promoted the abundance of nitrogen fixing bacteria, plant growth-promoting bacteria, stress resistant bacteria such as Lactobacillus, Azospira, Acinetobacter, Bradyrhizobium and Acidocella; Environmental factors such as available P, organic matter, total nitrogen, nitrate nitrogen, rare earth element content in rice roots, available K and soil moisture are important factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at tillering stage of the rice. pH, REE content in rice roots, shoots, organic matter, total nitrogen, nitrate nitrogen and soil moisture content are the main environmental factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at maturity stage of rice. 2% rice straw returning soil promoted the formation of harmful bacteria, which may be an important reason for its significant reduction in the dry weight of rice grains.

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome

The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China

Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic-fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.

Solar park promoted microbial nitrogen and phosphorus cycle potentials but reduced soil prokaryotic diversity and network stability in alpine desert ecosystem

Solar park (SP) is rapidly growing throughout the planet due to the increasing demand for low-carbon energy, which represents a remarkable global land-use change with implications for the hosting ecosystems. Despite dozens of studies estimating the environmental impacts of SP based on local microclimate and vegetation, responses of soil microbial interactions and nutrient cycle potentials remain poorly understood. To bridge this gap, we investigated the diversity, community structure, complexity, and stability of co-occurrence network and soil enzyme activities of soil prokaryotes and fungi in habitats of ambient, the first, and sixth year since solar park establishment. Results revealed different response patterns of prokaryotes and fungi. SP led to significant differences in both prokaryotic and fungal community structures but only reduced prokaryotic alpha diversity significantly. Co-occurrence network analysis revealed a unimodal pattern of prokaryotic network features and more resistance of fungal networks to environmental variations. Microbial nitrogen and phosphorus cycle potentials were higher in SP and their variances were more explained by network features than by diversity and environmental characteristics. Our findings revealed for the first time the significant impacts of SP on soil prokaryotic and fungal stability and functional potentials, which provides a microbial insight for impact evaluation and evidence for the optimization of solar park management to maximize the delivery of ecosystem services from this growing land use.

Claroideoglomus etunicatum affects the structural and functional genes of the rhizosphere microbial community to help maize resist Cd and La stresses

Arbuscular mycorrhizal fungi (AMF) and plant rhizosphere microbes reportedly enhance plant tolerance to abiotic stresses and promote plant growth in contaminated soils. The co-contamination of soil by heavy metals (e.g., Cd) and rare earth elements (e.g., La) represents a severe environmental problem. Although the influence of AMF in the phytoremediation of contaminated soils is well documented, the underlying interactive mechanisms between AMF and rhizosphere microbes are still unclear. We conducted a greenhouse pot experiment to evaluate the effects of AMF (Claroideoglomus etunicatum) on maize growth, nutrient and metal uptake, rhizosphere microbial community, and functional genes in soils with separate and combined applications of Cd and La. The purpose of this experiment was to explore the mechanism of AMF affecting plant growth and metal uptake via interactions with rhizosphere microbes. We found that C. etunicatum (i) significantly enhanced plant nutritional level and biomass and decreased metal concentration in the co-contaminated soil; (ii) significantly altered the structure of maize rhizosphere bacterial and fungal communities; (iii) strongly enriched the abundance of carbohydrate metabolism genes, ammonia and nitrate production genes, IAA (indole-3-acetic acid) and ACC deaminase (1-aminocyclopropane-1-carboxylate) genes, and slightly altered the abundance of P-related functional genes; (iv) regulated the abundance of microbial quorum sensing system and metal membrane transporter genes, thereby improving the stability and adaptability of the rhizosphere microbial community. This study provides evidence of AMF improving plant growth and resistance to Cd and La stresses by regulating plant rhizosphere microbial communities and aids our understanding of the underlying mechanisms.

Nitrogen and sulfur fertilizers promote the absorption of lead and cadmium with Salix integra Thunb. by increasing the bioavailability of heavy metals and regulating rhizosphere microbes

Fertilization is an effective agronomic strategy to improve the efficiency of phytoextraction by Salix integra Thunb. However, the specific effects of the simultaneous application of nitrogen (N) and sulfur (S) fertilizers in the rhizosphere remain unclear. We investigated the bioavailability of lead (Pb) and Cadmium (Cd) along with the microbial metabolic functions and community structure in the rhizosphere soil of S. integra after the application of N (0, 100, and 200 kg·ha⁻¹·year⁻¹) and S (0, 100, and 200 kg·ha⁻¹·year⁻¹) fertilizers for 180 days. The simultaneous application of N and S fertilizers significantly enhanced the absorption of Pb and Cd by S. integra, whereas this effect was not observed for the single application of N or S fertilizer. The contents of acid-soluble Pb and Cd in the rhizosphere soil significantly increased after either single or combined fertilize applications. The microbial metabolic activity was enhanced by the N and S fertilizers, whereas the microbial diversity markedly decreased. The metabolic patterns were mainly affected by the concentration of N fertilizer. The dominant fungi and bacteria were similar under each treatment, although the relative abundances of the dominant and special species differed. Compared to the N200S100 and N200S200 treatments, the N100S100 and N100S200 treatments resulted in fewer pathogenic fungi and more rhizosphere growth-promoting bacteria, which promoted phytoremediation by S. integra. Redundancy analysis indicated that the pH and nitrate content were the key factors affecting the structure of the microbial community. Collectively, the results suggest interactive effects between N and S fertilizers on the rhizosphere soil, providing a potential strategy for plant-microbial remediation by S. integra.

Diversity and composition of soil bacteria between abandoned and selective-farming farmlands in an antimony mining area

Background and aims

Land abandonment and selective farming are two common management methods to restore the soil conditions of low-pollution farmland in mining areas. The soil bacterial community plays an important role in farmland soil restoration; however, few studies have compared the composition and diversity of soil bacteria between the abandoned farmlands (AFS) and selective-farming farmlands (FFS). Here, the effects of AFS and FFS on soil properties and bacterial diversity were evaluated in an antimony (Sb) mining area in southern China. This study aimed to identify effective land management methods in terms of positive or negative changes in soil environment and bacterial diversity.

Methods

16S rRNA high-throughput sequencing was used to compare the diversity and composition of soil bacteria between AFS and FFS in the Xikuangshan (the largest Sb mine in the world).

Results

Compared to AFS, FFS had higher Sb concentration and nutritional properties (e.g., available N, P, and K) and lower Zn concentration (p < 0.05). The bacterial alpha diversity including Chao1 index, Simpson index, Shannon index and Pielou₋e index in FFS was higher than AFS (p < 0.05). At the phylum level, FFS had higher relative abundances of Chloroflexi, Acidobacteria, Gemmatimonadetes, and Rokubacteria, and lower relative abundances of Firmicutes, Actinobacteria, and Bacteroidetes. At the genus level, FFS had higher relative abundances of Acidothermus, Haliangium, and Rokubacteriales, and lower relative abundances of Bacillus, Rhodococcus, Sphingomonas, and 67-14. Redundancy analysis indicated that soil heavy metal content and soil fertility were closely correlated with the soil bacterial community. Altogether, selective farming of low-pollution farmland in the mining area can improve soil properties and soil bacterial diversity.

Biogeochemical dynamics of nutrients and rare earth elements (REEs) during natural succession from biocrusts to pioneer plants in REE mine tailings in southern China

The exploitation of ion-adsorption rare earth element (REE) deposits has resulted in large quantities of abandoned mine tailings, which pose significant risks to the surrounding environment. However, the natural evolutional patterns at early successional stages and related biogeochemical dynamics (e.g. nutrient and REE cycling) on such mine tailings remains poorly understood. To this end, a chronosequence of REE mine tailings abandoned for up to 15 years was investigated in a post-mining site in south China. Our results showed that biocrusts were the earliest colonizers on these tailings, reaching a peak of 10% of surface coverage after 10 years of abandonment. Later on, after 15 years, the biocrusts began to be replaced by pioneer plants (e.g. Miscanthus sinensis), suggesting a rather rapid succession. This ecological succession was accompanied by obvious changes in soil nutrients and microbial community structure. Compared to bulk soils, both the biocrusts and rhizospheric soils favored an accumulation of nutrients (e.g. P, S, N, C). Notably, the autotrophic bacteria (e.g. Chloroflexi and Cyanobacteria) with C and N fixation abilities were preferentially enriched in biocrusts, while heterotrophic plant growth promoting bacteria (e.g. Pseudoocardiaceae and Acidobacteriales) were mainly present in the rhizosphere. Moreover, the biocrusts showed a remarkably high concentration of REEs (up to 1820 mg kg^-1), while the rhizospheric soils tended to decrease REE concentrations (~400 mg kg^-1) in comparison with bulk soils, indicating that the REEs could be redistributed by biological processes. Principal component analysis and mantel tests showed that the concentrations of nutrients and REEs were the most important factors affecting the microbial communities in biocrusts, rhizospheric and bulk soils. In sum, based on the observation of nutrient accumulation and pollutant (i.e. REE) dynamics in the initial successional stages, this work provides a feasible theoretical basis for future restoration practices on REE mine tailings.

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.

Soil microbial communities of dryland legume plantations are more complex than non-legumes

Soil microorganisms play a crucial role in the vegetation restoration of dryland plantations and participating in biogeochemical cycles. However, how the co-occurrence networks of soil microbial communities respond to dryland legume and non-legume plantations is unclear. Here, we conducted a comparative analysis of legume (13-, 35-, and 55-years Caragana korshinskii) and non-legume (13- and 55-years Platycladus orientalis) plantations, including plant communities, soil physicochemical properties, and soil microbial communities, in the west of the Loess Plateau, China. The results showed higher richness and diversity, more keystone taxa and positive relationships, and larger connectivity and potential functions existed in soil bacterial and fungal communities of legume plantations. Meanwhile, richer plant communities and higher soil nutrients in legume plantations were found than those in non-legume plantations. We revealed that legume plantations shaped a more complex co-occurrence network, forming a virtuous cycling of "plant-soil-microbe" continuum in legume plantation ecosystems. Our results provided a new perspective on evaluating the ecological value and plantation stability of legume tree species in the vegetation restoration engineering of drylands.

Indigenous microbial populations of abandoned mining sites and their role in natural attenuation

Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.

Do the Reclaimed Fungal Communities Succeed Toward the Original Structure in Eco-Fragile Regions of Coal Mining Disturbances? A Case Study in North China Loess—Aeolian Sand Area

Mining activity has caused serious environmental damage, particularly for soil ecosystems. How the soil fungal community evolves in mine reclamation and what are the succession patterns of molecular ecological networks still needs to be studied in depth. We used high-throughput sequencing to explore the changes in soil fungal communities, molecular ecological networks, and interactions with soil environmental factors in five different ages (the including control group) during 14 years of reclamation in eco-fragile mines. The results showed that the abundance and diversity of soil fungi after 14 years of reclamation were close to, but still lower than, those in the undisturbed control area, but the dominant phylum was Ascomycota. Soil nitrate-N, C/N ratio, pH, and water content significantly affected the fungal community with increasing reclamation ages. Moreover, we found that Mortierellomycota, despite its high relative abundance, had little significant connectivity with other species in the molecular ecological network. Fungal molecular ecological networks evolve with increasing ages of reclamation, with larger modules, more positive connections, and tighter networks, forming large modules of more than 60 nodes by age 9. The large modules were composed mainly of Ascomycota and Basidiomycota, which can form mycorrhiza with plant roots, and are not only capable of degrading pollution but are also “encouraged” by most (more than 64%) physicochemical factors in the soil environment. The results can provide a basis for scientific mine ecological restoration, especially for eco-fragile regions.

Migration and Transformation of Multiple Heavy Metals in the Soil–Plant System of E-Waste Dismantling Site

E-waste generation has become a major environmental issue worldwide. Heavy metals (HMs) in e-waste can be released during inappropriate recycling processes. While their pollution characteristics have been studied, the migration and transformation of different multi-metal fractions in soil–plant system of e-waste dismantling sites is still unclear. In this study, pot experiments were conducted to investigate the migration and transformation of different multi-metal fractions (Cu, Pb, Zn and Al) in the soil–plant system using two Chinese cabbage cultivars (heavy metals low-accumulated variety of Z1 and non-low-accumulated Z2) treated with or without biochar. The result showed that the acid-soluble fraction of Cu, Pb, Zn and Al in soil decreased by 5.5%, 55.7%, 7.8% and 21.3%, but the residual fraction (ResF) of them increased by 48.5%, 1.8%, 30.9% and 43.1%, respectively, when treated with biochar and plants, compared to that of the blank soil (CK). In addition, Pb mainly existed as a reducible fraction, whereas Cu existed as an oxidisable fraction. Biochar combined with plants significantly increased the ResF of multi-metals, which reduced the migration ability of Pb among all other metals. The relative amount of labelled ¹³C in the soil of Z1 was higher than that of Z2 (25.4 fold); among them, the Gram-negative bacteria (18-1ω9c, 18-1ω7c) and fungi (18-2ω6c) were significantly labelled in the Z1-treated soil, and have high correlation with HM migration and transformation. In addition, Gemmatimonadete were significantly positive in the acid-soluble fraction of HMs, whereas Ascomycota mostly contributed to the immobilisation of HMs. Therefore, the distribution of fractions rather than the heavy metal type plays an important role in the HM migration in the soil–plant system of e-waste dismantling sites.

Fluorescent Mechanism in Zero-Dimensional Carbon Nanomaterials: A Review

Fluorescent carbon dots (CDs) have acquired growing interest from different areas over decades. Their fascinating property of tunable fluorescence by changing the excitation wavelength has attracted researchers worldwide. Understanding the mechanisms behind fluorescence is of great importance, as they help with the synthesis and applications, significantly when narrowed down to applications with color-tunable mechanisms. But, due to a lack of practical and theoretical information, the fluorescence mechanisms of CDs remain unknown, preventing the production of CDs with desired optical qualities. This review focuses on the PL mechanisms of carbon dots. The quantum confinement effect determined the carbon core, the surface and edge states determined by various surface defects and the connected functional/chemical groups on the surface/edges, the molecular state solely determined the fluorophores in the interior or surface of the CDs, and the Crosslink Enhanced Emission Effect are the currently confirmed PL mechanisms.

Interaction of the Fungal Metabolite Harzianic Acid with Rare-Earth Cations (La3+, Nd3+, Sm3+, Gd3+)

Rare-earth elements are emerging contaminants of soil and water bodies which destiny in the environment and effects on organisms is modulated by their interactions with natural ligands produced by bacteria, fungi and plants. Within this framework, coordination by harzianic acid (H₂L), a Trichoderma secondary metabolite, of a selection of tripositive rare-earth cations Ln³⁺ (Ln³⁺ = La³⁺, Nd³⁺, Sm^3+, and Gd³⁺) was investigated at 25 °C, and in a CH₃OH/0.1 M NaClO₄ (50/50 w/w) solvent, using mass spectrometry, circular dichroism, UV-Vis spectrophotometry, and pH measurements. Experimental data can be satisfactorily explained by assuming, for all investigated cations, the formation of a mono-complex (LnL⁺) and a bis-complex (LnL₂^-). Differences were found between the formation constants of complexes of different Ln³⁺ cations, which can be correlated with ionic radius. Since gadolinium is the element that raises the most concern among lanthanide elements, its effects on organisms at different levels of biological organization were explored, in the presence and absence of harzianic acid. Results of ecotoxicological tests suggest that harzianic acid can decrease gadolinium biotoxicity, presumably because of complex formation with Gd³⁺.

Biogeochemical cycles of nutrients, rare earth elements (REEs) and Al in soil-plant system in ion-adsorption REE mine tailings remediated with amendment and ramie (Boehmeria nivea L.)

The exploitation of ion-adsorption rare earth element (REE) deposits in South China has left large areas of mine tailings. However, limited remediation practices on these tailings have been reported, and how the remediation strategies and economic plants cultivation affect the biogeochemical cycles of nutrients, REEs and Al remains unclear. The aim of the present study was to investigate the effects of the combination of the addition of soil amendment and the root development and activity of a fiber plant ramie (Boehmeria nivea L.) on the availability and distribution of nutrients, as well as of REEs and other potentially toxic elements (e.g. Al) in the soil-plant system. The results showed that the application of organic amendment and ramie planting induced a significant increase in soil pH, total carbon (C), nitrogen (N), and other nutrient (e.g. P and Ca) concentrations, while led to a decrease of 80-90% and 60-90% in soil extractable REE and Al concentrations respectively. Matrices of correlation showed that soil pH, total C, N, and P concentrations were among the most important factors controlling the availability of soil REEs and Al, and root characteristics (e.g. fine root length). The total C, N, P and extractable nutrient concentrations, and electrical conductivity were higher in the rhizosphere soils of ramie than those in the bulk soils. Moreover, more than 60% of the quantity of REE and Al in the whole ramie plant was stored within the thick roots. These results showed that, in addition to amendment, the effects induced by the roots of ramie could further improve soil properties through C input, nutrient mobilization and toxic element stabilization. Our study concludes that ramie planting with organic amendment is a promising phytostabilization strategy for the remediation of REE mine tailings in South China.

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.

Phytoremediation mechanisms and plant eco-physiological response to microorganic contaminants in integrated vertical-flow constructed wetlands

Vegetations play a vital role in the ecological function of constructed wetlands (CW), but the systemic phytoremediation mechanism of CW is still unclear. An integrated vertical-flow constructed wetland (IVCW) was established to elucidate the phytoremediation mechanisms and plants eco-physiological response to an emerging contaminant, sulfamethoxazole (SMX). Attenuation of SMX in IVCW with and without vegetation (Acorus calamus) are comparatively analyzed. The results showed significant enhancement of removal efficiencies of total nitrogen (via intensified denitrification) and SMX by up to 10% respectively with vegetation. A unique micro-rhizo environment was created by stimulating the denitrifiers, Clostridium_sensu_stricto, Ignavibacterium, Rhodanobacter, and Geobacter. Free-living plant growth-promoting bacteria, unclassified_Burkholderiales and unclassified_Betaproteobacteria, proliferated in the rhizosphere, protecting the growth mechanism of A. calamus and, consequently, promoting performance of the IVCW. Overall, A. calamus exhibited tolerance to SMX, maintaining its photosynthesis rate and stabilizing the plant cell structure by an effective antioxidant system. The growth and defense mechanisms of A. calamus appeared to positively correlate with the IVCW performance, whereby the photosynthetic rate and antioxidant enzymes activities peaked together with the maximum removal efficiency of TN (77.81%) and SMX (99.88%). The contribution of vegetation to ecotoxicity reduction in CW might be underrated as absorbed SMX could be phytodegraded into less toxic metabolites via specific enzymes.

Microbial investigations of new hydrogel-biochar composites as soil amendments for simultaneous nitrogen-use improvement and heavy metal immobilization

Agricultural sustainability is challenging because of increasingly serious and co-existing issues, e.g., poor nitrogen-fertilizer use and heavy metal pollution. Herein, we introduced a new poly(acrylic acid)-grafted chitosan and biochar composite (PAA/CTS/BC) for soil amendment, and provided a first microbial insight into how PAA/CTS/BC amendment simultaneously improved nitrogen cycling and immobilized heavy metals. Our results suggest that the PAA/CTS/BC amendment significantly promoted soil ammonium retention, and reduced nitrate accumulation, nitrous oxide emission and ammonia volatilization during the rice cultivation. The availability of various heavy metals (Fe, Mn, Cu, Zn, Ni, Pb, Cr, and As) markedly decreased in the PAA/CTS/BC amended soil, thereby reducing their accumulation in rice root. The PAA/CTS/BC amendment significantly altered the structure and function of soil microbial communities. Importantly, the co-occurrence networks of microbial communities became more complex and function-specific after PAA/CTS/BC addition. For example, the keystone species related to organic matter degradation, denitrification, and plant resistance to pathogen or stresses were enriched within the network. In addition to direct adsorption, the effects of PAA/CTS/BC on shaping microbial communities played dominant roles in the soil amendment. Our findings provide a promising strategy of simultaneous nitrogen-use improvement and heavy metal immobilization for achieving crop production improvement, pollution control, and climate change mitigation.