Bioavailable metals, microbial community dysfunction, and plant growth constraints in a tropical mining waste dump: implications for ecological risk assessment and remediation

Mining waste dumps in tropical regions suffer severe ecological degradation with plant growth inhibition, yet the synergistic limiting factors remain unclear. This study systematically assessed a tropical mining waste dump (Democratic Republic of the Congo), analyzing soil physicochemical properties, total/bioavailable metals, and microbial community structure/function of four soil types (KE, PG, TS, YS), alongside on-site water quality. Results showed three core limiting factors for plant growth: (1) Severe metal phytotoxicity, with KE's bioavailable Cu (261.4667 mg/kg) exceeding the toxicity critical value and TS's total Cu/Co surpassing USEPA screening levels; (2) Deteriorated soil physiochemistry, including water content imbalance, severe salinization in PG, and extreme N/P/K deficiency in KE/TS/YS; (3) Microbial community dysfunction, featuring low α-diversity, dominance of metal-tolerant genera, scarce plant growth-promoting rhizobacteria, and weak nutrient cycling functions. These factors formed a "toxicity-deficiency-dysbiosis" vicious cycle. Notably, on-site water met WHO standards, suitable for restoration irrigation. Correlation analysis revealed bioavailable metals shaped microbial communities, and PG's salinization stemmed from abnormal K/S accumulation. Targeted restoration measures (metal immobilization, soil physicochemical improvement, microbial function enhancement) were proposed. This holistic study fills the gap in tropical mining waste dumps, providing scientific support for ecological risk assessment and restoration of similar regions globally.

Mining activities are critical for global resource supply but inevitably cause severe ecological degradation, particularly at dump sites where intensive anthropogenic disturbances (e.g., waste accumulation, metal release, soil structure destruction) create extreme environments incompatible with plant colonization. Plant growth is the cornerstone of ecological restoration in degraded ecosystems, as vegetation regulates soil erosion, improves soil aggregate structure, and drives nutrient cycling through litter decomposition (1, 2). However, in tropical mining waste dumps-characterized by high annual rainfall (1500–2000 mm) and temperatures (25-28 °C)-plant growth is often inhibited by multiple synergistic stressors. A field study in tropical agricultural soils showed that under rainstorm conditions, the average runoff coefficient and soil erosion rate representing 416% of moderate rain intensity and 261% of heavy rain intensity (4). High temperatures (25-28 °C) further enhance the bioavailability and phytotoxicity of metals (5). Tropical soil microbial communities also exhibiting higher baseline metabolic activity, while they show lower Q 10 values (2.1 in tropical vs. 2.9 in temperate soils) (6). The limiting factors affecting the restoration of tropical and temperate mining areas are different, however, the lack of relevant research and systematic identification of limiting factors has become the main bottleneck for tropical effective ecological restoration.

Democratic Republic of the Congo (DRC) is a global hub of critical minerals (e.g., Cu, Co, Au), accounting for a significant share of global supply, but intensive mining activities have led to widespread soil degradation and metal pollution (3). A tropical mining waste dump, located in the DRC’s tropical rainforest region, has long faced the challenge of plant non-growth. This issue not only disrupts local ecological balance but also increases the risk of metal leaching into surrounding water bodies, threatening the livelihoods and health of nearby communities that rely on natural ecosystems.

Plant growth is a holistic response to the soil ecosystem, integrating the combined effects of physicochemical conditions, metal stress, and microbial functions. Soil physicochemical properties (e.g., WC, salinity, nutrient status) provide the basic habitat framework for plants, as water scarcity/excess, osmotic stress from high salinity, and nutrient deficiency directly impair seed germination and root development (4). Metals-especially their bioavailable fractions-induce phytotoxicity by accumulating in plant tissues, disrupting enzyme activity, and triggering oxidative stress (5, 6). Soil microorganisms mediate key processes such as nutrient cycling (e.g., nitrogen fixation, phosphorus solubilization) and metal detoxification, and their community structure and functional stability are closely linked to plant growth and stress resistance (7, 8). However, most existing studies on mining waste dump have focused on single-factor analysis (e.g., metal contamination or nutrient deficiency), ignoring the synergistic interactions between multiple ecological factors. Additionally, few studies have integrated soil physiochemistry, metal bioavailability, and microbial functional potential to explore plant growth constraints in tropical mining ecosystems-leaving a critical research gap.

To fill this gap, this study conducted a systematic ecological survey of a tropical mining waste dump, with the core objectives: (1) Evaluate the suitability of soil physicochemical properties and on-site water quality for plant growth; (2) Quantify the phytotoxic risks of metals, with an emphasis on bioavailable fractions that directly affect plants; (3) Reveal the characteristics of microbial communities and their functional contributions to plant growth; (4) Identify the key limiting factors and their synergistic mechanisms. The innovations of this study lie in three prominent aspects closely oriented to tropical mining ecological characteristics: (1) We constructed a comprehensive coupled analysis framework covering soil physicochemical properties, total and bioavailable metal pollution, and microbial community diversity and functional potential, which effectively overcomes the limitation of single-factor independent analysis widely adopted in previous temperate mine restoration studies; (2) This research specifically targets tropical copper-cobalt waste dumps in the Congo Basin, systematically reveals the unique coupled stress mechanism of high-temperature accelerated metal activation and rainfall-induced nutrient leaching that do not exist in temperate mining areas, and fills the research blank of tropical critical metal mining sites; (3) On the basis of soil-microbe-metal multi-dimensional evaluation, we further incorporated in-situ surface water quality detection for tropical restoration irrigation, forming a complete technical reference system for ecological risk assessment and targeted remediation of tropical mine wastelands with strong regional applicability for mineral-rich tropical countries. This research aims to clarify the fundamental reasons for plant non-growth at the study site and provide a reference framework for ecological assessment and restoration of similar tropical mining waste dumps globally.

Study area and sampling design

The study area is a tropical mining waste dump in the DRC (global site coordinate: 11°21′12″ S, 25°58′43″ E), characterized by a tropical rainforest climate (9), with an annual average temperature of 25-28 °C and annual rainfall of 1500–2000 mm. Four geochemically distinct and with independent spatial distribution patches waste soil units (KE, PG, Top Soil (TS), Yellow Soil (YS)) were selected as sampling zones, with respective independent sampling plot areas of 20000 m² (KE), 1500 m² (PG), 100 m² (TS), and 50 m² (YS). Each patch is spatially isolated by waste rock accumulation ridges without cross-mixing of substrates, ensuring independent geochemical backgrounds for the four soil types. KE-derived from weathered waste rock, situated on the main tailings discharge point; PG-characterized by efflorescent salts and high electrical conductivity, located on another tailings discharge point; TS (Top Soil) -surface soil stripped during the mining process can serve as a reference and control sample for this study; and YS (Yellow Soil)-characterized by yellowish-brown oxidized materials, located on a moderately sloping toe slope of the waste dump.

The precise field sampling campaign was conducted on December 19, 2025, and all soil samples were collected 48 h after continuous moderate rainfall events (Figure 1). Three independent replicates randomly were arranged within each separate sampling plot, and sampling points within each unit were spaced 5–100 m apart, to eliminate intra-plot spatial heterogeneity and improve regional representativeness of measurements. Surface soil samples (0–20 cm) were collected using the five-point composite sampling method. Furthermore, a representative static surface water sample (W) for ecological restoration irrigation was synchronously collected from the central pond of the dump. All samples were transported back to the laboratory under low-temperature storage (4 °C): soil subsamples were sieved through a 2 mm mesh to remove gravel and plant debris and split into two fractions (one preserved at 4 °C for microbial community analysis, the other air-dried for soil physicochemical and total/bioavailable metal quantification). Water samples were filtered via 0.45 μm microporous membranes and acidified to pH < 2 with concentrated HNO 3 prior to ICP-MS metal testing.

Analytical methods

Soil physicochemical properties

Soil water content (WC) was determined by the oven-drying method (105 °C, 24 h). Electrical conductivity (EC) and pH were measured with a conductivity meter and pH meter (soil-to-water ratio = 1:5, w/v), respectively. Soil salt content (SC) was analysed by the gravimetric method (10). Total nitrogen (N) was determined via the Kjeldahl method (11), total phosphorus (P) by the molybdenum blue colorimetric method, and total potassium (K) by flame photometry (12). The nutrient index (NI) was calculated as (N/140 + P/20 + K/390) × 100, referring to the FAO soil nutrient grading standards (13).

Metal detection

Total concentrations of phytotoxic metals (Cu, Co, Pb, Zn, Cr) were determined by inductively coupled plasma mass spectrometry (ICP-MS, Agilent 7900) after microwave digestion with HNO 3 -HCl-HF (1:3:1, v/v/v) (14). The DTPA-TEA-CaCl 2 buffered extractant at pH 7.3 followed by ICP-MS quantification (15), was used to quantify plant-available Cu and Co, which method has been broadly utilized to evaluate trace metal bioavailability in neutral tropical mineral soils and Cu-Co contaminated substrates across the African Copperbelt. Metal concentrations in water samples (Co, Cr, Cu, Mn, Pb, Ti, Zn) were detected by ICP-MS (16, 17). Quality control was performed using standard reference materials (GBW07405 for soil, GBW(E) 080548 for water).

Microbial community analysis

Total soil DNA was extracted using the Fast DNA ® Spin Kit for Soil (MP Biomedicals, USA). The V3-V4 region of the 16S rRNA gene was amplified with primers 338F (5′-ACTCCTACGGGAGGCAGCAG-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′). High-throughput sequencing was conducted on the Illumina MiSeq platform (Illumina, USA) (18). Raw sequences were filtered and clustered into operational taxonomic units (OTUs) at 97% similarity using UPARSE. α-diversity indices (Chao1, Shannon) were calculated with QIIME 2. Microbial community structure was visualized by community barplots. All 16S raw data can be accessed on Fig-Share (https://doi.org/10.6084/m9.figshare.31292986). Functional predictions were performed using FAPROTAX (Functional Annotation of Prokaryotic Taxa) (19), which is a widely used tool for predicting ecological functions from 16S rRNA amplicon data, recent studies have validated its applicability to terrestrial soils, >97% of functionally assigned OTUs in agricultural and forest soils have been previously verified through independent studies (20). However, as a prediction-based approach, the inferred functions represent metabolic potential rather than direct measurements of in situ activity.

Statistical analysis

All raw data statistical analyses were conducted using SPSS 26.0 and R 4.2.0 statistical software (21). Separate one-way analysis of variance (ANOVA) was implemented for three groups of indicators, including soil physicochemical properties, total and bioavailable metal contents, and microbial α-diversity across the four soil subgroups (KE, PG, TS, YS) (22). Statistical significance was classified into three uniform thresholds throughout all result sections: p < 0.05 denotes significant difference, p < 0.01 denotes highly significant difference, and p < 0.001 denotes extremely significant difference. Pearson pairwise correlation analysis (23, 24) was performed covering all core ecological indicators, including soil pH, electrical conductivity, salt content, nutrient index, total and bioavailable Cu/Co concentrations, microbial α-diversity indices, and relative abundances of dominant bacterial genera.

Soil physicochemical deterioration: destruction of the plant growth foundation

Soil physicochemical properties are the direct environmental basis for plant growth, regulating water availability, nutrient supply, and osmotic balance in plant cells. As shown in Figure 2, multiple key physicochemical indicators deviated significantly from the optimal range for plant growth, creating an inhospitable habitat.

Soil WC imbalance

The WC of KE (19.50%) and YS (19.515%) were slightly below the lower limit (20%) required for plant growth, suggesting potential insufficient water supply during seed germination and root expansion-critical stages for plant establishment. In contrast, the WC of PG (39.895%) measured during the rainy season was close to the upper limit (40%), which could cause soil hypoxia, inhibit root respiration, and ultimately lead to root rot under sustained wet conditions. The WC of TS (27.765%) was within the suitable range and showed low variability, indicating relative stability in this zone. The experimental samples were collected during the rainy season, after a rainfall 48h, the WC of KE and YS areas were notably lower than those of PG and TS areas and below the lower limit (20%), indicating that the water-holding capacity of KE and YS areas is lower. However, as soil moisture is a highly dynamic parameter strongly influenced by precipitation events and seasonal climatic conditions, these single measurements primarily reflect the moisture status at the time of sampling (rainy season), mainly used for comparison between different soil samples.

Severe salinization in PG

The EC value (222 μS/cm) and SC (142.5 mg/L) of PG were 2.2-fold and 2.0-fold higher than the upper limits (100 μS/cm and 70 mg/L), creating a high-osmotic-pressure environment. This forces plants to consume excessive energy to synthesize osmolytes (e.g., proline, betaine) to maintain cell turgor, thereby diverting resources from growth and photosynthesis. High salinity also damages root membrane integrity and reduces the activity of nutrient transporters, impairing the absorption of N and K, which further exacerbates nutrient limitation, restricts the growth of plants.

Extreme nutrient deficiency in KE/TS/YS

The nutrient indices of KE (7.75), TS (5.5), and YS (4.1) were far below the lower limit (10), while PG (34.2) exceeded the upper limit (30). Specifically, the N concentrations in KE/TS/YS (5–10 ppm) were only 1/14~1/7 of the optimal level for plant growth (70 ppm), and P (1 ppm) and K (6–8 ppm) were also at extremely low levels. N is a key component of chlorophyll, proteins, and nucleic acids (25); P is involved in energy metabolism (e.g., ATP synthesis) and cell signaling (26); K regulates stomatal movement and enzyme activation (27). Deficiencies in these three macronutrients directly lead to reduced photosynthetic efficiency, stunted growth, and increased sensitivity to environmental stressors (e.g., metals).

Notably, the pH values of all soil samples (6.70–6.905) were within the suitable range (6.5–7.5) for plant growth indicating that pH is not a limiting factor here. The pH range of 6.70–6.905, consistent with the optimum working pH range of the standard DTPA test (28), therefore, the DTPA test of bioavailable metal is appropriate.

XRD elemental composition analysis: geochemical evidence for habitat degradation

XRD elemental composition analysis reveals inherent soil geochemical characteristics, providing critical evidence for understanding elemental accumulation and habitat degradation. As shown in Table 1, significant variations in key elements among soil types further explain plant growth constraints.

Abnormal K/S accumulation in PG

The K concentration in PG (9482 ppm) was 6.1-fold, 2.5-fold, and 3.9-fold higher than that in KE (1541 ppm), TS (3737 ppm), and YS (2424 ppm), respectively (p < 0.001). The S concentration in PG (4343 ppm) was also the highest among all zones (p < 0.05). K is a major component of soil soluble salts, and its excessive accumulation directly contributes to PG’s high EC and SC, exacerbating salinization stress. S is closely linked to soil sulfur cycling; high S content promotes the activity of sulfur-oxidizing/reducing microorganisms, leading to soil acidification and increased metal mobility-consistent with the high sulfur compound respiration function observed in microbial analysis. This successfully connects XRD geochemical elemental characteristics with soil salinization, acidification and metal mobility changes.

Phytotoxic element enrichment in KE/TS

The Cu concentration in KE (975 ppm) and TS (937 ppm) was significantly higher than in PG (268 ppm) and YS (487 ppm) (p < 0.01). The Co concentration in PG (683 ppm), TS (671 ppm), and YS (574 ppm) was higher than in KE (440 ppm) (p < 0.05). This confirms that KE/TS are enriched in phytotoxic Cu/Co, laying a geochemical foundation for metal phytotoxicity. The excessively high total Cu and Co contents in KE and TS soils revealed by XRD establish the fundamental geochemical toxic foundation of the study area. Coupled with the perennial high rainfall climate in tropical regions, large amounts of solid-bound Cu and Co in waste rock may be continuously converted into plant-bioavailable forms. This transformation eventually may cause the bioavailable Cu concentration of KE soil to surpass the plant toxicity critical value.

Low nutrient-related element content in KE/TS/YS

The Ca concentration in TS (2976 ppm) was higher than in other zones (p < 0.05), while KE (741 ppm) and YS (752 ppm) had low Ca content. Ca is involved in plant cell wall synthesis and stress resistance (29); low Ca content may further weaken plants’ ability to cope with metal toxicity. However, XRD primarily quantifies total elemental content, so the extreme N/P/K deficiency (bioavailable nutrients) is not reflected here.

XRD reflects the inherent geochemical background and total elemental accumulation of mining waste rock, which determines the long-term potential toxic stock of the dump. Overall, XRD analysis confirms geochemical abnormalities (K/S accumulation, Cu/Co enrichment) that reinforce soil physicochemical deterioration and metal toxicity, providing complementary evidence for plant growth inhibition.

Metal toxicity: direct damage to plant cells

Metals, especially their bioavailable fractions, are direct phytotoxic factors that can accumulate in plant tissues, disrupt physiological and metabolic processes, and inhibit growth (30–32). The total and bioavailable concentrations of phytotoxic metals in the study area showed distinct spatial patterns, with Cu and Co being the primary toxicants (Figure 3).

Total metal concentrations

USEPA Ecological Soil Screening Level (Eco-SSL) are risk-based screening values developed for ecological risk assessment at contaminated sites, targeting specific ecological receptors (plants, soil invertebrates, birds, and mammals) rather than being classified by agricultural or industrial land use (33). As shown in Figure 3, the total Cu concentrations in TS (1020 ppm) and KE (889.94 ppm) were 5.7-fold and 4.9-fold higher than the Eco-SSL for copper (180 mg/kg) (33, 34). The total Co concentrations in all samples (90.5–238.5 ppm) exceeded the Eco-SSL for cobalt (85 mg/kg, protective of plants) (p < 0.05). In contrast, the total concentrations of Pb (8.85-12.2 ppm), Zn (3.0-76.0 ppm), and Cr (9.8-17.2 ppm) were within the safe range (Pb < 400 ppm, Zn < 300 ppm, Cr < 100 ppm) (p > 0.05), posing negligible phytotoxicity. The high total Cu and Co concentrations in TS and KE are likely derived from industrial waste discharge during mining activities (e.g., ore processing residues), which accumulate in the surface soil and form long-term phytotoxic risks.

Bioavailable metal concentrations

DTPA extraction quantifies the soluble metal fractions that can be directly absorbed and utilized by plant roots (5). The bioavailable and total metal together form a dual evaluation system including metal actual plant phytotoxic risk and potential toxicity. The reported DTPA Cu toxicity values of different plants in tropical oxidized soil are as follows: Common bean: 18 mg/kg, Maize: 32 mg/kg, Upland rice: 28 mg/kg, Soybean: 6 mg/kg (soybean highly sensitive) (37). As shown in Figure 3, the bioavailable Cu concentration in KE (261.4667 mg/kg) was significantly higher than in other soil types (1.4-20.3 mg/kg) (p < 0.001), which is also much higher than the above threshold. Cu is an essential micronutrient for plants, but excessive bioavailable Cu can bind to sulfhydryl groups of key enzymes (e.g., superoxide dismutase, peroxidase), leading to enzyme inactivation and reactive oxygen species (ROS) accumulation (6). ROS can damage cell membranes, chloroplasts, and DNA, resulting in reduced cell viability and impaired photosynthetic capacity. For example, high bioavailable Cu has been shown to reduce chlorophyll content by 30-50% and inhibit photosystem II activity in plants, which is consistent with the plant non-growth phenomenon in KE.

The bioavailable Co concentrations (0.234-1.069 mg/kg) were relatively low but significantly higher in PG (1.069 mg/kg). Although Co is not an essential nutrient for most plants, long-term accumulation can interfere with plant respiration and nitrogen metabolism (34, 35). Co competes with Fe for binding sites in cytochrome c oxidase, a key enzyme in the mitochondrial electron transport chain, thereby reducing respiratory efficiency (36). It also inhibits nitrate reductase activity, blocking nitrate assimilation and exacerbating N deficiency (37). The bioavailable concentrations of Pb, Zn, and Cr were extremely low (0.01-0.364 mg/kg) for all samples, so their phytotoxicity can be ignored.

In summary, the excessive available Cu and high total Cu concentration in KE and the high total Cu/Co concentration in TS are key direct factors limiting plant growth, while the metal risks of PG and YS are relatively low, but the long-term cumulative effect of Co still needs attention.

On-site water quality assessment: feasibility for ecological restoration

Water quality is a critical factor for ecological restoration, as irrigation water directly affects plant growth and soil microbial activity. As shown in Table 2, the on-site water sample exhibited excellent suitability for ecological restoration.

Optimal pH

The pH value was 7.22, within the range (6.5-8.5) suitable for plant growth and microbial metabolism. Neutral pH avoids soil acidification or alkalization during irrigation, which is crucial for maintaining soil nutrient availability and reducing metal mobility.

Ultra-low metal concentrations

All detected metals were far below the WHO drinking water standards: Co (0.430 μg/L < 50 μg/L), Cr (3.37 μg/L < 50 μg/L), Cu (15.2 μg/L < 2000 μg/L), Mn (0.189 μg/L < 400 μg/L), Pb (<0.09 μg/L < 10 μg/L), Ti (20.2 μg/L, non-toxic to plants), Zn (39.9 μg/L < 3000 μg/L). No harmful substances or excessive ions were detected, eliminating the risk of secondary pollution to soil or plants (38, 39).

Practical implications

The water sample’s high quality confirms its high feasibility for ecological restoration. It can be used for irrigation to mitigate water scarcity in KE/YS, supplement soil moisture for seed germination and seedling growth, and support microbial activity without introducing additional contaminants. This provides a reliable water resource for subsequent restoration measures (e.g., plant seeding, microbial inoculation).

Microbial community dysfunction: amplification of soil degradation

Soil microorganisms are key drivers of soil fertility and plant-microbe symbiosis, participating in nutrient cycling, organic matter decomposition, and metal detoxification (40, 41). However, the microbial community in the dump site showed obvious dysfunction, which further exacerbated the adverse effects of metal toxicity and nutrient deficiency on plant growth (42).

Low α-diversity and imbalanced community structure

The Chao1 and Shannon indices (Figure 4) indicated that microbial richness and diversity were relatively low in all soil samples. TS had the highest diversity (Chao1 = 1023 ± 223, Shannon= 6.00 ± 0.43), while YS had the lowest diversity in solid sample (Chao1 = 230, Shannon=3.70) (p < 0.05). KE showed intermediate diversity (Chao1: 358 ± 209, Shannon: 4.46 ± 0.86). Low microbial diversity is mainly attributed to metal stress and nutrient deficiency-toxic metals can damage microbial cell membranes and DNA, inhibiting growth and reproduction (43), while low nutrient levels limit the survival of heterotrophic microorganisms.

The community barplot (Figure 5) revealed that at the genus level, Burkholderia - Caballeronia - Paraburkholderia (10-15%), Sphingomonas (8-12%), and Pseudarthrobacter (5-8%) were dominant to all associated with metal tolerance or pollutant degradation (44–46). For example, Burkholderia - Caballeronia - Paraburkholderia can produce siderophores and organic acids to chelate metals, reducing their toxicity (47), while Sphingomonas is capable of degrading complex organic pollutants (48). However, plant growth-promoting rhizobacteria (PGPR) such as Bradyrhizobium had extremely low abundances, and Azospirillum is not within the top 20 genera (7). Bradyrhizobium forms nodules with legumes to fix atmospheric N 2, and Azospirillum produces indole-3-acetic acid (IAA) to promote root growth (8, 49). The low abundance of these PGPR significantly reduces the potential for plant-microbe symbiosis, further limiting plant growth.

Weak functional potential for plant growth

FAPROTAX functional prediction results (Figure 6) showed that the predicted dominant functional groups were aerobic chemo heterotrophy (30-40%), sulfur compound respiration (15-20%), and hydrocarbon degradation (10-15%), which are closely related to pollutant degradation and energy metabolism in polluted environments. In contrast, predicted functions critical for plant growth had extremely low relative abundances: nitrogen fixation (0.5-1.0%), cellulolysis (0.3-0.8%), and ureolysis (0.2-0.5%). It should be noted that these values represent predicted functional potentials inferred from 16S rRNA taxonomic assignments, not directly measured enzymatic activities.

Key N-fixing genera, including Bradyrhizobium, Mesorhizobium, and Methylobacterium, were detected at only marginal levels across all samples-a pattern consistent with well-documented N-fixing lineages in soil systems (20). Nitrogen fixation is essential for converting atmospheric N 2 into plant-available ammonium, and the predicted low potential for this function in KE/TS/YS further exacerbates N deficiency. Cellulolytic microorganisms decompose plant residues and organic matter into soluble nutrients (e.g., glucose), and the predicted low abundance of this functional potential suggests reduced soil organic matter turnover and nutrient supply (50). Urease-producing microorganisms hydrolyze urea into ammonium, and weak ureolysis function limits the utilization of organic nitrogen (51). Additionally, the predicted high abundance of sulfur compound respiration (especially in PG and TS) may lead to soil acidification (52), which increases the mobility of metals (e.g., Cu, Co) and further enhances their phytotoxicity. This microbial functional dysbiosis amplifies the adverse effects of metal toxicity and nutrient deficiency, forming a “toxicity-deficiency-dysbiosis” vicious cycle that completely inhibits plant growth.

Correlation characteristics and ecological mechanisms of key ecological indicators in this tropical mining waste dump

To further explore the intrinsic coupling relationships among soil physicochemical properties, total and bioavailable metal concentrations, and microbial communities, Pearson correlation analysis was performed on all core ecological indicators, with the results visualized via a correlation heatmap (Figure 7). It is important to note that correlation analysis identifies statistical associations between variables but does not establish causal relationships. Distinct correlation characteristics were observed among soil physicochemical indicators: EC was extremely significantly positively correlated with SC, and both were extremely significantly positively correlated with total soil K and total N. This result quantitatively suggests that the extreme salinization in the PG zone was associated with the elevated K and N contents, highlighting a potential link between elemental accumulation and soil physicochemical degradation in this zone.

Members of the Pseudomonadota (green-colored taxa in the heatmap), such as Sphingomonas and norank_f_Xanthobacteraceae exhibited highly significant positive correlations with total Pb,total Cr (p < 0.001), and available Pb (p < 0.001) respectively. while Burkholderia-Caballeronia-Paraburkholderia and Bradyrhizobium was significantly negatively correlated with bioavailable Cu (p < 0.001). Methylobacterium, Ramlibacter and Novosphingobium were negatively correlated with total Cu and bioavailable Cu (p < 0.05), total Pb and total Cr (p < 0.05) and bioavailable Pb (p < 0.05) respectively. The significantly negative correlation between Bradyrhizobium and bioavailable Cu might arise from direct copper toxicity to rhizobial cells, excess bioavailable Cu disrupts membrane integrity and triggers DNA oxidative damage, while suppressing nitrogen-fixing enzyme activity and rhizosphere colonization capacity (53).Within the Actinomycetota (dark blue-colored taxa), Pseudonocardia showed a positive correlation with bioavailable Cr (p < 0.05), while Sinomonas was significantly negatively correlated with soil pH and bioavailable Co (p < 0.05). The single representative of Chloroflexota (orange-colored taxon, norank_c:AD3) showed significant positive correlations with total Co (p < 0.05), while showed more negative correlations with other factors. These positive correlations may suggest these microorganism potential tolerance to metal contamination (54, 55), the negative correlations with bioavailable metals may reflect either reduced taxon abundance under metal stress or active metal immobilization by these bacteria, thereby decreasing metal bioavailability. However, as Pearson correlations do not establish causation, these interpretations remain speculative and require experimental validation. These divergent responses highlight the functional diversity, some taxa acting as metal-tolerant colonizers and others as sensitive indicators of soil chemical conditions.

Collectively, the correlation heatmap indicates that soil bacterial community structure is associated with a complex interplay of basic physicochemical properties and metal contamination. While pH and macronutrients showed correlations with bacterial abundance, metals-particularly bioavailable fractions- exhibited more specific and pronounced correlation patterns among different bacterial phyla and genera. The identified key taxa (e.g., Sphingomonas, norank_o:Microtrichales) with highly significant correlations to bioavailable metals may represent potential targets for future studies investigating microbial responses to metal pollution and their potential application in bioremediation strategies, and further offer a preliminary scientific basis for formulating targeted ecological restoration strategies for tropical mining waste dumps.

Synergistic mechanism of limiting factors for plant growth

Comprehensive analysis revealed that plant non-growth at the dump site is the result of synergistic effects of three categories of factors: (1) Direct toxicity of metals. Excessive bioavailable Cu in KE and total Cu/Co in TS directly damage plant cells (e.g., enzyme inactivation, ROS accumulation), inhibiting photosynthesis, respiration, and nutrient absorption. This reduces plant vitality and makes them more susceptible to other stressors. (2) Deteriorated soil physiochemistry. Water scarcity in KE/YS limits seed germination and root expansion; severe salinization in PG causes osmotic stress and impairs nutrient uptake; extreme N/P/K deficiency in KE/TS/YS deprives plants of essential nutrients, weakening their growth and stress resistance. These factors form an inhospitable physical and chemical environment for plants. (3) Microbial functional dysfunction. Metal stress and nutrient deficiency reduce microbial diversity and the abundance of PGPR, leading to weakened nutrient cycling (e.g., nitrogen fixation, cellulolysis) and reduced soil fertility. This further exacerbates nutrient deficiency and reduces plant-microbe symbiosis potential, making it difficult for plants to cope with metal toxicity and physicochemical stress.

These factors interact synergistically to form a vicious cycle: metal pollution and physicochemical deterioration inhibit microbial growth and function, leading to impaired soil fertility; poor soil fertility and metal toxicity jointly suppress plant growth; and the absence of plants (which provide organic matter via litter) further reduces microbial activity and soil quality. This cycle maintains the degraded state of the dump site and prevents plant colonization.

Tropical-specific challenges and restoration implications

Tropical regions’ high rainfall and temperatures pose unique challenges for ecological restoration of dump sites. High rainfall accelerates nutrient leaching, leading to extreme N/P/K deficiency in KE/TS/YS, while high temperatures enhance the bioavailability and phytotoxicity of metals (e.g., Cu). Thus, restoration strategies must address these tropical-specific characteristics. Based on the results of this study, targeted restoration measures are recommended: Metal solidification agent can adsorb and immobilize Cu/Co, reducing their bioavailability; For KE/YS, improving water retention capacity to maintain soil WC within the suitable range (20-40%); For PG, apply organic amendments to reduce SC and improve soil structure; For KE/TS/YS, supplement slow-release N/P/K fertilizers to meet plant nutritional requirements, avoiding excessive fertilization that may cause secondary pollution; Inoculate PGPR to enhance nitrogen fixation, phosphorus solubilization, and plant stress resistance; Additionally, apply organic fertilizers to increase soil organic matter content, providing energy and nutrients for microorganisms and promoting the recovery of microbial diversity and function.

Long-term monitoring of soil properties (physiochemistry, metal bioavailability), microbial community (diversity, structure, function), and plant growth (germination rate, biomass, survival rate) is needed to optimize restoration strategies and ensure the sustainability of ecological restoration.

This study completed a systematic ecological assessment of a tropical mining waste dump in the Democratic Republic of the Congo, a typical tropical mining area, and clarified the core limiting factors and their synergistic mechanism that inhibit plant growth in this area. The results show that the failure of natural plant colonization is the combined effect of three key factors: excessive bioavailable Cu in KE soil and high total Cu/Co in TS soil cause direct phytotoxicity to plants, destroying cellular structure and metabolic processes; severe soil physicochemical deterioration including water content imbalance, extreme salinization in PG and serious N/P/K deficiency in KE, TS and YS damages the basic growth habitat of plants; microbial community dysfunction featured by low α-diversity, scarce plant growth-promoting rhizobacteria and predicted weakened nutrient cycling functions further amplifies the adverse effects of metal stress and nutrient limitation, forming a stable “toxicity-deficiency-dysbiosis” vicious cycle. Notably, the on-site water quality fully meets WHO standards, providing a safe and reliable irrigation resource for subsequent ecological restoration without secondary pollution risks. This study constructs a holistic analytical framework integrating soil physiochemistry, metal bioavailability and microbial functional potential, breaking the single-factor analysis limitation in previous research and filling the gap of targeted studies on tropical mining waste dumps. The proposed targeted restoration measures including metal immobilization, soil physicochemical improvement and microbial function enhancement have strong practicality, which not only provides a scientific basis for the ecological restoration of the study site, but also establishes a reference framework for ecological risk assessment and remediation of similar tropical mining waste dumps in the DRC and other global mineral resource-rich tropical regions.