Soil acidification poses a critical threat to sustainable agricultural production by compromising soil fertility. Conventional remediation strategies for acidic soils face persistent challenges including short-lived efficacy, structural deterioration, and secondary pollution risks. This study presents an innovative bioremediation approach utilizing Alcaligenes faecalis (A. faecalis), a potent alkaline-metabolizing microorganism, coated with calcium silicate hydrate (CSH) and humic acid (HA) as a biocarrier for acidic farmland soil restoration. Through microcosm experiments and high-throughput sequencing analysis, we demonstrat that the remediation approach achieved a substantial soil pH increase from 4.66 to 6.41 within 21 d. Soil available nitrogen (AN) and silicon (ASi) contents increased to 252.83–595.70 mg/kg and 89.24–133.57 mg/kg at 21 d, respectively; and available phosphorus (AP) content increased from 15.59–39.88 mg/kg to 20.44–55.98 mg/kg at 7 d. Positive correlations were observed between pH and all nutrient indicators for soil samples. Moreover, the restoration could also change the microbial diversity and structure. This led to an increase in the relative abundance of functional genera including Bacillus (from 0.44–0.65

Global precipitation regimes have been shifted in recent decades, imposing significant consequences in water-limited grassland ecosystems. However, the effects of increased precipitation on the succession of soil microbial communities remain unclear, mainly due to the scarcity of long-term experiments with time-series data. Here, we examined temporal succession of grassland soil microbial communities in a long-term increased precipitation experiment. Both soil microbial taxonomic and functional structures were significantly altered by increased precipitation. Increased precipitation significantly decelerated the succession rates of soil microbial functional structure (i.e. time-decay relationships). Consistent with the increased microbial decomposition and heterotrophic respiration, the abundances of soil microbial carbon decomposition genes were markedly enhanced by increased precipitation. Furthermore, increased precipitation stimulated genes involved in nutrient cycling processes, potentially promoting plant growth. Collectively, the contributions of stochastic processes in shaping microbial communities were increased under increased precipitation, suggesting that microbial successional trajectories may shift toward multiple alternative states characterized by greater stochasticity under future altered precipitation regimes.

A key uncertainty in understanding whether warming accelerates soil carbon (C) loss lies in how this response depends on other co-occurring environmental changes and the underlying mechanisms. Here we show that, in a 12-year grassland experiment, warming reduces soil C by 12.2% under drought but increases it by 6.7% under wet conditions. Such C losses during drought primarily result from the declines in mineral-associated organic C. These contrasting responses are closely linked to microbial processes: warming elevates microbial metabolic quotient under drought but suppresses it under wet conditions, accompanied by shifts in microbial community composition and C-degrading genes. Integrating these microbial metrics into an ecosystem model substantially improves predictions of soil C dynamics. These findings demonstrate the pivotal role of microbial processes in mediating soil C-climate feedbacks and underscore their critical importance for accurately projecting soil C dynamics in a warmer, potentially drier world.

Aspergillus fijiensis is an industrially important filamentous fungus, whose genetic analysis has been limited by the absence of species-specific tools. This study establishes an optimized CRISPR-Cas9 genome editing platform for A. fijiensis, from protoplast preparation to DNA repair pathway engineering. Antibiotic screening first identified hygromycin B and 5-FOA (5-fluoroorotic acid) as effective positive and counter-selection markers. A high-efficiency protoplast regeneration protocol was developed depending on specific osmotic stabilization and mycelial competence. Evaluation of a plasmid-based CRISPR system revealed that while autonomous replication was feasible, gene editing was constrained by low efficiency and a predominant bias toward NHEJ (non-homologous end joining). We implemented a Cas9-sgRNA RNP (ribonucleoprotein) delivery approach, with RNP delivery alone producing frequent indels. However, targeted integration remained inefficient when using conventional MMEJ (Microhomology-mediated end joining) donors. By employing donors containing short (5 bp) microhomology arms between cleavage sites, we effectively engaged the MMEJ pathway, enabling precise insertions and large-fragment deletions in 92% of the analyzed transformants. Donor templates containing minimal 5 bp microhomology sequences could effectively shift the predominant repair pathway from NHEJ to MMEJ. These findings demonstrate that MMEJ is the superior pathway with a unique mechanism for genome engineering in A. fijiensis, providing a versatile toolkit for unlocking the biotechnological potential of this recalcitrant species and a successful paradigm for establishing genetic systems in other species.

Sulfur-bearing minerals are key reservoirs in the global sulfur cycle, and microorganisms mediate sulfur release from these minerals. Labile carbon inputs may modify microbial sulfur metabolism, but their net effects on sulfide mineral oxidation remain unclear. Here, we conducted a 56-day soil incubation with glucose input and combined geochemical measurements, mineralogical characterization, qPCR, metagenomics, 16S rRNA amplicon sequencing, and DNA-stable isotope probing (DNA-SIP) to identify glucose-assimilating microorganisms and their roles in regulating sulfide mineral oxidation. Glucose significantly suppressed sulfide mineral oxidation, resulting in 60.00% lower sulfate (SO42-) and a 33.23% higher pH than the control by day 56. Glucose also reshaped microbial community and functions potentials. Sulfur-oxidizing bacteria (SOB) decreased, sulfatereducing bacteria (SRB) increased, and genes annotated in sulfur oxidation (soxB, soxX, soxY, soxZ) were depleted before day 42. This inhibition was reversed after glucose depletion, with sulfur oxidation genes becoming enriched. DNA-SIP using 13C-glucose linked Frateuria and Dyella to glucose assimilation and to the inhibitory phase of sulfur release. Glucose-amended microcosms maintained a lower redox potential and showed a delayed rise relative to the control, consistent with oxygen competition that may constrain sulfur oxidizers such as Bradyrhizobium. Notably, Dyella harbored a complete assimilatory sulfate reduction pathway, driven by ATP and NADPH produced through the central carbon metabolism (CCM). This metabolic coupling reduced oxygen availability for terminal sulfur oxidation, suggesting a dual mechanism of sulfur release suppression via both assimilatory reduction and respiratory competition. Our findings highlight a previously underappreciated link between labile carbon metabolism and sulfur cycling in soil. This mechanism offers insights into microbial controls over sulfur fluxes and presents implications for managing soil acidification and sulfur-driven water pollution in mineral-rich environments.

Rapid expansion of industrialization increased the area of impermeable cement layers, disrupting substance and energy exchanges between soil and atmosphere. However, the impacts of cement hardening on soil microbial community and microbiological process remain unclear. This study compared bacterial and fungal communities between cement-hardened and bare soils across five abandoned factories. The results indicated that soil cement hardening reduced exogenous nutrients input and heavy metal accumulation. Fungal alpha-diversity responded more strongly than bacterial diversity to cement hardening. Both bacterial and fungal community compositional dissimilarities shifted significantly (p < 0.05), driven mainly by species replacement processes (74.9 and 71.1%). Microbial network’s size and complexity increased under cement hardening, but the fungal network stability presented by robustness was decreased. Cement hardening narrowed the niche breadth of bacterial community (3.4) compared to bare soils (4.0), accompanied by an increased proportion of specialist species (increased by 52.7%). Deterministic process became more important in shaping the microbial community assembly in hardened soils, and heterogeneous selection dominated the phylogenetic variation, particularly for fungi (96%). Functionally, cement hardening enriched bacterial taxa involved in aerobic and anaerobic respiration, but reduced bacterial xenobiotics catabolism potential and inferred fungal saprophytic functions. Path modeling showed cement hardening directly altered bacterial composition and diversity, which indirectly influenced its function. In contrast, cement hardening directly influenced fungal community composition and functional diversity while indirectly modulating community diversity and functional composition. These findings offer new sights into the effect of cement hardening on soil microbial ecosystem and facilitates the ecological management of industrial areas.

Heavy metals such as arsenic (As), cadmium (Cd), and lead (Pb) can accumulate through the soil–plant-food chain, posing severe threats to food safety and human health. Traditional remediation materials often fail to immobilize As, Cd, and Pb synchronously in mixed-contaminated soils and enhance soil fertility simultaneously. From a geochemical perspective, calcium (Ca), magnesium (Mg), and iron (Fe) could synchronously anchor and passivate heavy metal ions (As, Cd and Pb) through isomorphic substitution, surface precipitation, and complexation. Intercalated silicate (SiO32−) and phosphate (H2PO4−) simultaneously enhanced heavy metal immobilization and soil fertility. This modified layered double hydroxide (LDH) was synthesized via chemical co-precipitation and was referred to asCaMgFe/SiO3/H2PO4-LDH. Batch experiments showed that As (V), Cd (II), and Pb (II) adsorption followed Langmuir isotherms and pseudo-second-order kinetics, with higher adsorption performance in mixed systems. Soil incubation experiments demonstrated that 3

Endophytic fungi have emerged as significant alternative sources of plant-derived bioactive metabolites, such as flavonoids that exhibit antioxidant, antibacterial, and anticancer activities. This study presents a genome-guided discovery of the biosynthesis and bioactivity of liquiritigenin in the endophytic fungus Fusarium solani R1 isolated from the root tissue of Glycyrrhiza uralensis in China. Whole-genome sequencing produced a 54.3 Mb draft genome and identified phenylpropanoid and flavonoid pathway genes, including PAL, 4CL, HCT, DFR, FLS, and β-glucosidase, as well as a T3PKS cluster in antiSMASH Region 10.1, indicating a potential role in aromatic polyketide or flavonoid-like metabolism. Metabolic profiling using high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC–MS) confirmed that F. solani R1 produced a liquiritigenin titer of 25 mg/L in the fermentation extract. The crude extract demonstrated strong, concentration-dependent antioxidant activity in both DPPH and phosphomolybdenum assays, which correlated with elevated total flavonoid contents. Additionally, the extract displayed broad-spectrum antibacterial activity and induced significant cytotoxicity in HeLa cervical cancer cells, as evidenced by apoptotic morphological changes. Collectively, these results identify F. solani R1 as a promising microbial source of bioactive flavonoids with potential therapeutic applications.

As droughts become increasingly severe and prolonged worldwide, understanding how belowground biodiversity changes over time under water limitation is critical for assessing ecosystem resilience. However, long-term and continuous observations of soil microbial responses to drought remain rare. Here, using a 6-y experimental drought in a tallgrass prairie ecosystem, we showed that experimental drought reshaped the community compositions of soil bacteria, fungi, and protists, accompanied by progressive declines in microbial diversity and biomass. Analyses of time-decay relationships and paired community differences between drought and ambient conditions revealed increasingly divergent successional trajectories of soil microbiota under drought. Although stochastic processes dominated community assembly overall, their relative importance declined over time, particularly for bacteria in drought-treated soils, suggesting increasingly strong deterministic environmental filtering imposed by drought. In addition, drought reduced microbial network size but increased the complexity and stability of bacterial networks by favoring drought-tolerant taxa. Furthermore, drought-driven shifts in microbial community compositions significantly altered functional genes and associated ecosystem functioning. These findings suggest that microbial communities may become less variable but more vulnerable, and the detrimental effects of biodiversity loss on ecosystems could be more severe in an increasingly drought-prone world.

Chalcopyrite is the most abundant copper-bearing sulfide mineral, characterized by a stable crystal structure. Bioleaching of chalcopyrite is inherently slow and further constrained by surface passivation layers during prolonged bioleaching. In this study, bacteriophages released from Acidithiobacillus ferrooxidans were introduced to promote chalcopyrite bioleaching. Mineralogical characterization, microbial profiling, and functional gene analysis were employed to reveal the underlying mechanisms. One day after phage introduction, phage abundance was 9.42 × 105 VLPs mL−1 in the phage-treated group, 150-fold higher than in the control (6.26 × 103 VLPs mL−1). Over a 60-day leaching period, the copper leaching efficiency of the phage-treated group was 31.72

Soil colloids play a critical role in the migration of toxic metal(loid)s in contaminated environments. However, it remains unclear how soil colloidal attributes such as mineral composition and surface charge control the partitioning and transport of arsenic (As), cadmium (Cd) and lead (Pb) among aqueous, colloid-associated and solid-bound phases. This study examined the capacity of soil colloids to adsorb toxic metal(loid)s and mediate their migration using soil erodibility assessment, colloid extraction, adsorption isotherm experiments, co-migration column tests and DLVO-based calculations. Results showed that soils with higher K values were more prone to soil colloid release under rainfall or surface runoff, which significantly enhanced metal migration. Colloids isolated from three soil types (S1, S2, S3) exhibited distinct physicochemical properties, among which S1 derived colloids had the highest stability and adsorption capacity for toxic metal(loid)s. Compared with bulk soils, soil colloids exhibited much higher adsorption affinities for As, Cd and Pb, particularly associated with their kaolinite and hematite content. The co-migration of soil colloid-metal complexes was strongly governed by colloidal properties such as zeta potential, specific surface area and mineral composition. Column experiments showed that colloids from different soils enhanced metal breakthrough to different extents, with SC3 > SC1 > SC2. DLVO calculations indicated that the repulsive energy barrier of colloids was positively correlated with their metal-carrying capacity. Overall, this study provides mechanistic insights into colloid-facilitated migration of As, Cd and Pb in acidic soils, highlighting the importance of colloidal properties for evaluating pollutant mobility and informing remediation strategies.

With the rapid growth of livestock farming, the use of antibiotics and heavy metals as feed additives has raised environmental and health concerns. This study systematically analyzed the contamination levels of antibiotics and heavy metals in manure samples collected from five farms of varying scales in Liuyang City, Hunan Province. Utilizing 16S rDNA high-throughput sequencing technology, the study also examined the structural and functional characteristics of manure microbial communities. Ecological risk and human health risk assessments were also conducted. Results revealed that antibiotic residues in pig manure were generally higher than those in chicken manure, with significant differences in antibiotic usage across farms of varying scales. Cu and Zn levels exceeded standards in some samples, particularly from small-scale farms. Microbial community structures showed marked differences, with pig manure exhibiting higher microbial diversity. Functional prediction indicated active metabolism, strong environmental adaptability, and robust pollutant degradation capacity. Risk assessments revealed moderate to high ecological and human health risks from certain antibiotics and heavy metals, with significant non-carcinogenic and carcinogenic risks particularly for children. The study emphasizes that rational control of antibiotic and heavy metal use, coupled with enhanced manure management and resource utilization, is crucial for safeguarding ecological security and public health.

Paris polyphylla (P. polyphylla) is a valuable traditional Chinese medicinal plant, yet the spatial distribution of its compartment-specific bacterial microbiomes and their correlative relationships with bioactive polyphyllins remain poorly characterized. Here, we combined 16S rRNA amplicon sequencing, metabolite analysis, and bioinformatics to investigate the distribution patterns of bacterial communities and polyphyllins across bulk soil (BS), rhizosphere soil (RS), root endospheres (REs), stem endospheres (SEs), and leaf endospheres (LEs) of P. polyphylla. A spot inoculation assay was further used to verify the interactions between the dominant genus Pseudomonas (strain Pseudomonas palleroniana P6) and key polyphyllin I and VII. The results showed that polyphyllin I and II were highly accumulated in aerial SEs and leaves, whereas polyphyllin VI, VII, and diosgenin were predominantly concentrated in REs. Bacterial diversity and richness showed a gradual decline from BS to LE, with ecological niche differentiation identified as the primary driver of bacterial community divergence across compartments, which was further modulated by polyphyllin content. Pseudomonas, the dominant genus in all compartments, displayed a decreasing relative abundance with ascending compartmental niches, and its abundance was significantly negatively correlated with polyphyllin I levels but positively correlated with polyphyllin VII levels—a trend experimentally validated by gradient polyphyllin concentration-based microbial growth assays. Redundancy analysis (RDA) indicated that polyphyllin content (especially VI, VII, and diosgenin) significantly influenced bacterial community composition. Additionally, P. polyphylla exhibited selective enrichment of beneficial microbes, with selection pressure intensifying progressively across compartments. This study clarifies the compartment-specific distribution patterns of bacterial microbiomes and polyphyllins in P. polyphylla and their correlative relationships, deepens the understanding of plant-microbiome interactions in medicinal plants, and provides a theoretical basis for optimizing P. polyphylla cultivation strategies and developing microbial inoculants for sustainable agricultural production.

Tailings pedogenesis plays a fundamental role in the ecological restoration of mining wastelands by converting barren tailings into soil-like substrates through physical, chemical, and biological processes. To systematically investigate the contributions and interactions of natural weathering and plant regeneration in the tailings pedogenesis, this study analyzed the microstructure, chemical composition, and rhizosphere microbial communities of original tailings samples (OR), 15-year naturally weathered samples (PW), and naturally regenerated samples spontaneously colonized by Miscanthus (PM), Lolium perenne (LP), and Cynodon dactylon (CD). X-ray micro-computed tomography revealed that natural weathering increased the total soil porosity of the tailings by 13.45 %, with negligible effects on chemical properties. After natural regeneration, soil porosity further increased from 18.74 % to 41.45 %. Scanning Electron Microscope revealed microaggregates attaching to the root surfaces. In addition, plant species exhibited distinct influences on soil chemical properties. Specifically, PM significantly increased soil organic matter and nitrate nitrogen content, whereas CD primarily promoted the accumulation of rapidly available potassium. Compared to the OR, natural weathering initiated the reconstruction of microbial communities, which were further enriched by plant root systems during natural regeneration. Notably, PM enriched functional genera such as Haliangium and Bryobacter, which were positively associated with heavy metal stabilization, suggesting its role as a critical pioneer species for ecological restoration of tailings. This study highlights the distinct and synergistic roles of natural weathering and plant regeneration in tailings pedogenesis, offering insights for plant selection and ecological restoration strategies.

Acid mine drainage (AMD) environments feature extreme acidity (pH ≤ 2) and high heavy metal concentrations. Acidophiles survive these conditions through unique genetic adaptations and secondary metabolite (SM) pathways. Leptospirillum ferriphilum, known for its acid and heavy metal resistance, serves as a model for AMD bioremediation, though systematic multi-omics studies on its key SMs and biosynthesis pathways remain underexplored. In this study, L. ferriphilum YR01 was isolated and identified from the AMD of the Zijinshan copper mine, China. Pangenomic analysis revealed that YR01 possesses the largest number of genes (2623) among the eight sequenced L. ferriphilum strains. Comparative genomics, antiSMASH, BiG-SCAPE, and metabolomic analyses (LC-MS and HPLC-MS) were integrated to comprehensively explore its biosynthetic capacity. A total of 39 biosynthetic gene clusters (BGCs) were identified, of which 60% shared <50% similarity with known clusters, indicating substantial novel biosynthetic potential. The sequence alignment of SM biosynthetic gene clusters (BGCs) demonstrated the potential of L. ferriphilum to synthesize conserved clusters for ectoine, choline, carotenoids, terpenoids, and terpene precursors. YR01 harbors complete BGCs for all five SM types. Notably, key nonribosomal peptide synthetase (NRPS) modules implicated in N-acyl homoserine lactone (AHL) synthesis were identified. Untargeted metabolomics (LC-MS) revealed the production of diverse SMs (18 types) putatively involved in environmental adaptation, including phosphocholine, carotenoids (e.g., anteraxanthin), cholera autoinducer-1 (CAI-1), and multiple AHLs. Targeted detection (HPLC-MS) further confirmed that YR01 could produce ectoine (0.10 ng/mL) and specific AHLs (C14-HSL, C12-HSL, C12-OH-HSL), which were beneficial for the survival of the strain in extremely acidic environments and interspecies communication through SMs. This study represents the first comprehensive multi-omics characterization of BGCs in L. ferriphilum and experimentally validates the production of key SMs. Collectively, this study provides a comprehensive elucidation of the SM biosynthetic repertoire and environmental adaptation strategies in L. ferriphilum, advancing our understanding of microbial adaptation and interspecies communication in AMD systems, and offering potential implications for biomining applications.

Soil contamination with toxic metal(loids) such as arsenic (As), cadmium (Cd) and lead (Pb) poses significant threats to ecosystem by disrupting microbial community. However, the changes in soil microbial community structure and function induced by migration of toxic metal(loid)s at a lead–zinc smelting site remain poorly understood. This study investigated microbial community structure and function in soils after As, Cd, and Pb migration and retention using 16S rDNA sequencing and PICRUSt2 prediction. And Partial Least Squares Path Modeling (PLS-PM) was used to determine key factors influencing microbial community after toxic metal(loid)s retention. Results showed that after As, Cd, and Pb retention, Pb had stronger impact on soil microbial community structure than As and Cd. The difference in toxic metal(loid)s-sensitive genera (Escherichia, Lactobacillus) and toxic metal(loid)s-resistant genera (Bacteroides, Rhodanobacter, Acidibacter) were identified. pH regulated the resistance of dominant genera to toxic metal(loid)s. The retention of As, Cd, and Pb induced stress that reduced the metabolic capacity of microbial communities, while increasing the relative abundance of their environmental processing functions. Soil microbial communities appeared to respond to As stress by enhancing amino acid synthesis, DNA repair capacity, and membrane fluidity, while they resisted Cd and Pb stress through metabolic accumulation and repair mechanisms. Soil pH had significantly stronger influence on microbial communities than the stress effect of bio-Cd. The total content of As and Pb was primary factor directly affecting microbial community structure in the soil. Rhodanobacter, Ralstonia, and Acidibacter were potentially influencing the migration ability of As, Cd and Pb. This finding provides theoretical guidance for predicting the ecology risks in toxic metal(loid)-contaminated soils, assessing shifts in microbial indicators and promoting potential microbial-mediated remediation strategies.

Ecological restoration is a promising approach to alleviate eutrophication. However, its impacts on greenhouse gas (GHG) emissions and the underlying microbial mechanisms in different habitats of lakes remain unclear. To address this knowledge gap, we measured carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes at both water-air and sediment-water interfaces of eutrophic (Caohai) and restored area (Dapokou) of Dianchi Lake, a typical eutrophic lake in China. Meanwhile, we investigated the responses of planktonic and sedimentary bacterial and fungal communities by high-throughput sequencing. Our results indicated that 6 years of ecological restoration significantly reduced CO2 and N2O fluxes by 1.0-3.6 and 2.2-2.8 folds respectively, with more pronounced variations at the water-air interface than the sediment-water interface. Ecological restoration also shifted the structures of planktonic bacterial and fungal communities remarkably, leading to a significant reduction in the relative abundances of Actinobacteriota (by 70.94%), Bacteroidota (by 61.65%), Planctomycetota (by 74.18%) and Chytridiomycota (by 95.44%). Correlation analyses further suggested that GHG fluxes at the water-air interface were significantly correlated with planktonic microbial community composition (P < 0.05), and the significant reduction of CO2 and N2O fluxes under ecological restoration could be attributed to the decreased abundances of organic matter decomposers (such as hgcI_clade, Sporichthyaceae and Acidibacter) and increased abundances of autotrophs (such as Hydrogenophaga and Cyanobium_PCC-6307) in water. Collectively, our findings verify the importance of ecological restoration in reducing GHG emissions in inland lake ecosystems, providing new insights for addressing global climate change and advancing carbon neutrality.

Acid mine drainage (AMD) poses significant challenges, with arsenopyrite being a key sulfide mineral contributing to this issue. Microorganisms significantly influence arsenic behavior during arsenopyrite oxidation, yet there is limited analysis on the biooxidation process during the community coalescence of iron- and sulfur-oxidizing microorganisms. This study investigated the effects of changing the inoculation order of these microorganisms on arsenopyrite biooxidation. Geochemical analyses were used to assess solution physicochemical properties, while X-ray diffraction and X-ray photoelectron spectroscopy were used to examine the mineral phase composition. Additionally, microbial community structure and key species identification were performed using 16 S rDNA and metagenomic analyses. Results indicated that the order of achieving biooxidation steady-state was: preferential inoculation of sulfur oxidizers > preferential inoculation of iron oxidizers, reaching steady-state at 9, and 11 d, respectively. When sulfur oxidizers were preferentially inoculated, the relative content of S0 on arsenopyrite decreased from 17.87 to 7.89

The dynamic migration mechanisms of arsenic (As), cadmium (Cd), and lead (Pb) in soils contaminated by lead-zinc (Pb-Zn) smelting during runoff infiltration remain poorly understood. This study employed batch adsorption and dynamic column experiments to investigate the migration behavior of As, Cd and Pb in acidic red soils around typical Pb-Zn mining regions. Results demonstrated that surface soils exhibited significantly higher adsorption capacities than deeper layers. As(V) preferentially bound to surface aggregates in a monolayer configuration, while Cd(II) and Pb(II) adhered through a more complex, multilayered arrangement. The surface layer (S1) had lower Ks and D value, indicating a stronger pollutant retention capacity than the intermediate (S2) and deep (S3) layers. Column experiments established a descending mobility order of Cd(II) > Pb(II) > As(V) in acidic soils. At pH levels above 6.5, the deprotonation of soil adsorption sites enhanced Cd2+ and Pb2+ adsorption and complexation with Cd(OH)2 and Pb(OH)2, but simultaneously increased electrostatic repulsion against HAsO42-, HAsO3-, and AsO43-. A combined isothermal adsorption and non-equilibrium model effectively captured the migration trends of As, Cd, and Pb ions, though mid-migration hysteresis of Pb reduced predictive accuracy. Acidic soil chemical and mineral characteristics were instrumental in predicting As(Ⅴ) retention, whereas the retardation factors (Rf) for Cd(II) and Pb(II) were more closely associated with soil mineralogy, particularly Fe oxide content and speciation. These findings provide valuable insights into the controlling mechanisms of toxic metal migration in contaminated soils, which is crucial for developing effective remediation strategies for polluted soils in areas impacted by smelter.

Acid mine drainage (AMD), characterized by high concentrations of heavy metals and strong acidity, presents a significant challenge in environmental remediation. The acidophilic archaeon Ferroplasma facilitates soluble electron shuttles secreting and iron precipitate formation to immobilize heavy metals and demonstrating significant remediation capabilities in microbial consortia. However, its environmental adaptation mechanisms in highly polluted environments during remediation remain unclear. Biosynthetic gene clusters (BGCs), which encode specialized metabolites with ecological roles, and mobile genetic elements (MGEs), known to mediate genomic function through gene disruption, rearrangement, and regulatory interference, represent crucial evolutionary means for environmental adaptation. In this study, Ferroplasma acidiphilum ZJ was screened from the traditional AMD of the Zijinshan copper mine, China. Then, it was sequenced, annotated and compared to three other sequenced Ferroplasma strains focusing on the distribution and function of genes concerning MGEs and BGCs. Genome-wide analysis indicated that MGEs, especially IS4 family insertion sequences (ISs) as well as genomic islands (GIs), were located close to functional regions, such as those related to heavy metal translocation, structural stability of cells, and the formation of archaeal ether-linked membranes. Further analysis showed Ferroplasma strains contained over 10 BGCs, with predicted functions spanning antibiotics, exopolysaccharide (EPS), and quorum sensing (QS). The Ferroplasma employed specialized MGEs and BGCs as key environmental adaptation mechanisms. This study provides a genetic framework for understanding the survival strategies of extremophiles in contaminated environments and explores the potential role of archaeal secondary metabolism (SM) in enhancing microbial processes for sustainable AMD bioremediation, by contributing to the detoxification and stabilization of heavy metals typically found in such environments.