Effects of long-term discharge of acid mine drainage from abandoned coal mines on soil microorganisms: microbial community structure, interaction patterns, and metabolic functions

Driving role of acid mine drainage on microbial community assembly and species coexistence in paddy soil profiles

The environmental impacts of acid mine drainage (AMD) from open-pit mining are profoundly detrimental, yet knowledge about its effects on paddy soil microbial communities, especially at greater depths, remains limited. In this investigation, we compared soils affected by AMD versus unaffected soil depth profiles in terms of bacterial diversity and community assembly. The profiles in AMD-polluted soils exhibited tight geochemical gradients, characterized by increased acidity, SO42-, NO3-, and heavy metal content compared to unpolluted soils. Notably, AMD significantly diminished soil bacterial biodiversity. A depth-wise analysis showed distinct microbial stratification, with certain bacteria like Candidatus_Solibacter and Candidatus_Koribacter predominated in polluted soils, while others like Haliangium and Nitrospira were more prevalent in control soils. Interestingly, despite variable soil conditions, predicted metabolic pathways, particularly those involving carbon, nitrogen, and sulfur, showed relative stability. AMD pollution induced the upregulation of methyl-coenzyme M reductase and sulfate reductase genes. Bacterial communities were more responsive to pH and nutrient content rather than heavy metals, with pH and SO42- being the primary drivers of microbial diversity and distribution. Additionally, pH was identified as the most significant influence on the predicted methane, sulfur, and nitrogen metabolism. Furthermore, deterministic processes played a more significant role in community assembly of polluted soils, while heterogeneous selection gained importance with increasing depth in control soils. Additionally, microbial co-occurrences, particularly positive interactions, were more prevalent in the polluted soils with reduced network modularity and keystone taxa. These findings offer insights into sustaining microbial diversity in extreme environments.

Iron at the helm: Steering arsenic speciation through redox processes in soils

The toxicity and bioavailability of arsenic (As) in soils are largely determined by its speciation. Iron (Fe) is widely present in soils with a strong affinity for As, and therefore the environmental behaviors of As and Fe oxides (including oxides, hydrates and hydrated oxides) are closely correlated with each other. The redox fluctuations of Fe driven by changes in the environment can significantly affect As speciation and its fate in soils. The interaction between Fe and As has garnered widespread attention, and the adsorption mechanisms of As by Fe oxides have also been well-documented. However, there is still a lack of systematic understanding of how Fe redox dynamics affects As speciation depending on the soil environmental conditions. In this review, we summarize the mechanisms for As speciation transformation and redistribution, as well as the role of environmental factors in the main Fe redox processes in soils. These processes include the biotic Fe oxidation mediated by Fe-oxidizing bacteria, abiotic Fe oxidation by oxygen or manganese oxides, dissimilatory Fe reduction mediated by Fe-reducing bacteria, and Fe(II)-catalyzed transformation of Fe oxides. This review contributes to a deeper understanding of the environmental behaviors of Fe and As in soils, and provides theoretical guidance for the development of remediation strategies for As-contaminated soils.

Anaerobic fermentation of straw with sulfate addition: A suitable approach for straw utilization in mercury-contaminated areas

Returning raw straw to the soil can significantly elevate soil methylmercury (MeHg) and crop mercury (Hg) levels, underscoring the need to investigate safer approaches to straw utilization in mercury-contaminated regions. In this study, rice straw underwent anaerobic fermentation with the addition of sulfate, and the resulting fermentation products were utilized in a pot experiment involving water spinach to assess the impact of anaerobically fermented straw return on soil Hg methylation and its bioaccumulation. Findings revealed that the addition of sulfate during straw fermentation markedly increased the fermentation degree of the products, and sulfate was converted into organic sulfur-containing ligands that can functionalize the fermentation residuals. These changes enhanced adsorption or complexation of the fermentation products with Hg. Consequently, compared with raw straw returning to the soil, adding co-fermentation products of straw and sulfate to the soil can significantly reduce the bioavailable Hg and MeHg in the soil, the total mercury (THg) and MeHg in plants, with the maximum reduction rates being 68%, 92%, 66% and 78%, respectively. Therefore, returning the straw that has been anaerobically co-fermented with sulfate to the soil can effectively mitigate Hg methylation and bioaccumulation, while simultaneously increasing biomass, offering a suitable straw utilization method in Hg-contaminated cultivation areas.

The Effect of Cysteine on the Removal of Cadmium in Paddy Soil by Combination with Bioremediation and the Response of the Soil Microbial Community

Bioremediation is widely recognized as a promising and efficient approach for the elimination of Cd from contaminated paddy soils. However, the Cd removal efficacy achieved through this method remains unsatisfactory and is accompanied by a marginally higher cost. Cysteine has the potential to improve the bioleaching efficiency of Cd from soils and decrease the use cost since it is green, acidic and has a high Cd affinity. In this study, different combination modes of cysteine and microbial inoculant were designed to analyze their effects on Cd removal and the soil microbial community through the sequence extraction of Cd fraction and high-throughput sequencing. The results demonstrate that the mixture of cysteine and the microbial inoculant was the best mode for increasing the Cd removal efficiency. And a ratio of cysteine to microbial inoculant of 5 mg:2 mL in a 300 mL volume was the most economically efficient matching. The Cd removal rate increased by 7.7-15.1% in comparison with the microbial inoculant treatment. This could be ascribed to the enhanced removal rate of the exchangeable and carbonate-bound Cd, which achieved 94.6% and 96.1%, respectively. After the treatment, the contents of ammonium nitrogen (NH3-N), total phosphorus (TP), available potassium (AK), and available phosphorus (AP) in the paddy soils were increased. The treatment of combinations of cysteine and microbial inoculant had an impact on the soil microbial diversity. The relative abundances of Alicyclobacillus, Metallibacterium, and Bacillus were increased in the paddy soils. The microbial metabolic functions, such as replication and repair and amino acid metabolism, were also increased after treatment, which benefitted the microbial survival and adaptation to the environment. The removal of Cd was attributed to the solubilizing, complexing, and ion-exchanging effects of the cysteine, the intra- and extracellular adsorption, and the production of organic acids of functional microorganisms. Moreover, cysteine, as a carbon, nitrogen, and sulfur source, promoted the growth and metabolism of microorganisms to achieve the effect of the synergistic promotion of microbial Cd removal. Therefore, this study underscored the potential of cysteine to enhance the bioremediation performance in Cd-contaminated paddy soils, offering valuable theoretical and technical insights for this field.

Response of bacterial communities in desert grassland soil profiles to acid mine drainage pollution

Acid mine drainage (AMD) causes serious environmental pollution, which imposes stresses on soil ecosystems. Therefore, it is critical to study the responses of soil bacterial communities to AMD pollution in ecologically fragile desert grasslands. Here, the bacterial community composition, structure, and assembly processes in vertical soil profiles of an AMD contaminated desert grassland were explored using 16S rRNA high-throughput sequencing. The results showed that the surface layers of the profiles exhibited lower pH and higher heavy metals (HMs) content due to AMD influence. The AMD contamination led to reduced bacterial diversity in the surface soil layer of the profiles and significantly changed the bacterial community composition and structure. Gradients in pH, TK, TN, and HMs were the main factors driving bacterial community variability. In contrast to the uncontaminated profile, deterministic processes were important in shaping soil bacterial community in the AMD contaminated profiles. These findings will enhance understanding about the responses of soil bacteria in desert grassland soil to the environmental changes caused by AMD contamination and will improve the remediation of AMD contaminated soil.

Effects of acid mine drainage and sediment contamination on soil bacterial communities, interaction patterns, and functions in alkaline desert grassland

Acid mine drainage and sediments (AMD-Sed) contamination pose serious ecological and environmental problems. This study investigated the geochemical parameters and bacterial communities in the sediment layer (A) and buried soil layer (B) of desert grassland contaminated with AMD-Sed and compared them to an uncontaminated control soil layer (CK). The results showed that soil pH was significantly lower and iron, sulfur, and electroconductivity levels were significantly higher in the B layer compared to CK. A and B were dominated by Proteobacteria and Actinobacteriota, while CK was dominated by Firmicutes and Bacteroidota. The pH, Fe, S, and potentially toxic elements (PTEs) gradients were key influences on bacterial community variability, with AMD contamination characterization factors (pH, Fe, and S) explaining 48.6 % of bacterial community variation. A bacterial co-occurrence network analysis showed that AMD-Sed contamination significantly affected topological properties, reduced network complexity and stability, and increased the vulnerability of desert grassland soil ecosystems. In addition, AMD-Sed contamination reduced C/N-cycle functioning in B, but increased S-cycle functioning. The results highlight the effects of AMD-Sed contamination on soil bacterial communities and ecological functions in desert grassland and provide a reference basis for the management and restoration of desert grassland ecosystems in their later stages.

Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas

The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.

The influence of cysteine in transformation of Cd fractionation and microbial community structure and functional profile in contaminated paddy soil

Remediating cadmium (Cd) contaminated paddy soil is vital for agroecology, food safety, and human health. Soil washing is more feasible to reduce remediation method due to its high efficiency. However, green, low-cost and more efficient washing agents are still required. In this study, we investigated the ability of cysteine as a washing agent for soil washing to remove Cd from contaminated paddy soil. Through a batch experiment, we evaluated the removal efficiency of cysteine as a washing agent by comparing their removal rate with that of a microbial inoculant and sulphuric acid as other washing agents. The transformation of Cd fractionation and microbial community structure and functional profile in paddy soils after cysteine leaching was studied by using sequential extraction and high-throughput sequencing. Results showed that cysteine had better efficiency in the removal of Cd from paddy soil in comparison to sulphuric acid and the microbial inoculant, and could achieve a maximum removal rate of 97 % Cd in paddy soil. Cysteine decreased the proportion of Cd in the exchangeable fraction, carbonate bound fraction, iron and manganese bound fraction, and organic matter bound fraction and was best for the removal of the residual fraction, which contributed to its higher Cd removal ability. Considering the economic benefits of the reagents used, cysteine was shown to be economically feasible for use as a leaching agent. In addition, cysteine could significantly increase the relative abundance of Thermochromatium, Sideroxydans, Streptacidiphilus, and Frankia which promoted the nitrogen and sulfur metabolism in the paddy soil. In summary, this study revealed that cysteine was readily available, cheap, non-toxic, highly efficient, and even has fertilizing properties, making it eco-friendly and ideal for remediation of Cd-contaminated paddy soils. Besides, the health of paddy soils would also benefit from cysteine's promotion of microbial nitrogen and sulfur metabolism.

Practical application for legacy acid mine drainage (AMD) prevention and treatment technologies in karst-dominated regions: A case study

Acid mine drainage (AMD) from abandoned mines in karst-dominated regions in southwestern China was causing contamination of groundwater and surface streams. To avert the unwise decisions of "pollution first before treatment" during pre-mining, mid-mining and post-mining activities, this paper proposes a contaminant migration prevention technical framework covering 4 comprehensive processes. The formation mechanism of spring pollution, engineering remediation processes and contamination treatment effects were described in Longdong Spring. In 2018, the Longdong Spring water had Fe 33.83 mg/L and Mn 3.60 mg/L, exceeding the Chinese surface water standard (0.3 mg/L and 0.1 mg/L in GB 3838-2002) by 112 and 36 times, respectively. In 2020, after grout blocking, in situ treatment and wetland remediation, the highest Fe was 4.5 mg/L in a short period, and the spring water pollution days in this year were 42 days compared with the previous 320 spring water pollution days in 2018. In 2021, two years of remediation with the implementation of terminal remediation wetlands, the Fe was less than 0.03 mg/L compared with the previous 33.83 mg/L, and the water quality reached water standard (less than 0.3 mg/L). At present, Longdong Spring has become one of the most beautiful natural local landscapes.

One-step simultaneous biomass synthesis of iron nanoparticles using tea extracts for the removal of metal(loid)s in acid mine drainage

Acid Mine Drainage (AMD) contains various metal/metalloid ions such as Fe, Cu, and As, which all impact seriously on mine ecosystems. Currently, the commonly used chemical methods for treating AMD may cause secondary pollution to appear in the environment. In this study, one-step simultaneous biomass synthesis of iron nanoparticles (Fe NPs) using tea extracts for the removal of heavy metals/metalloids in AMD is proposed. Characterizations revealed that the Fe NPs presented severely agglomerated particles with an average particle size of 119.80 ± 4.94 nm, on which various AMD-derived metal(loid)s, including As, Cu, and Ni, were uniformly dispersed. The biomolecules participating in the reaction in the tea extract were identified as polyphenols, organic acids, and sugars, which acted as complexing agents, reducing agents, covering/stabilizing agents, and promoted electron transfer. Meanwhile, the best reaction conditions (reaction time = 3.0 h, volume ratio of AMD and tea extract = 1.0:1.5, concentration of extract = 60 g/L, and T = 303 K) were obtained. Finally, the simultaneous formation of Fe NPs and their removal of heavy metals/metalloids from AMD was proposed, mainly involving the formation of Fe NPs and adsorption, co-precipitation, and reduction processes of heavy metals/metalloids.

Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China

Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO₄-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO₄·HCO₃-Ca·Mg to SO₄-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.

Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China

In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.

Eukaryotic Community Structure and Interspecific Interactions in a Stratified Acidic Pit Lake Water in Anhui Province

The stratified acidic pit lake formed by the confluence of acid mine drainage has a unique ecological niche and is a model system for extreme microbial studies. Eukaryotes are a component of the AMD community, with the main members including microalgae, fungi, and a small number of protozoa. In this study, we analyzed the structural traits and interactions of eukaryotes (primarily fungi and microalgae) in acidic pit lakes subjected to environmental gradients. Based on the findings, microalgae and fungi were found to dominate different water layers. Specifically, Chlorophyta showed dominance in the well-lit aerobic surface layer, whereas Basidiomycota was more abundant in the dark anoxic lower layer. Co-occurrence network analysis showed that reciprocal relationships between fungi and microalgae were prevalent in extremely acidic environments. Highly connected taxa within this network were Chlamydomonadaceae, Sporidiobolaceae, Filobasidiaceae, and unclassified Eukaryotes. Redundancy analysis (RDA) and random forest models revealed that Chlorophyta and Basidiomycota responded strongly to environmental gradients. Further analysis indicated that eukaryotic community structure was mainly determined by nutrient and metal concentrations. This study investigates the potential symbiosis between fungi and microalgae in the acidic pit lake, providing valuable insights for future eukaryotic biodiversity studies on AMD remediation.

Purification and water resource circulation utilization of Cd-containing wastewater during microbial remediation of Cd-polluted soil

The purification and water resource circulation utilization of cadmium-containing leachate is a key link in the field application of microbial remediation in Cd-polluted soil. In this study, through a simulation experiment of microbial remediation of Cd-polluted paddy soil, the feasibility of the purification and recycling process of wastewater derived from microbial remediation of Cd-polluted soil was explored. The results of the microbial mobilization and removal experiment showed that the concentrations of Cd, N, P, and K in the leachate were 88.51 μg/L, 38.06, 0.53, and 98.87 mg/L, respectively. The leachate also contained a large number of microbial resources, indicating that it had high recovery values. To recycle this wastewater, activated carbon (C), humic acid (H), and self-assembled monolayers on mesoporous supports (SAMMS; S) were used as adsorbents. The results showed that the co-existing cations in the leachate had a major influence on the adsorption of Cd. In the ternary system of Fe, Al, and Cd, the removal efficiency of Cd increased to 91.2% when the S dosage was increased to 5‰, and the sorption of Cd occurred after Fe and Al. However, C and H exhibited poor adsorption performances. The isotherm models further showed that the maximum adsorption capacities of S, H, and C were 13.96, 6.41 and 2.94 mg/g, respectively. The adsorption kinetics of S showed that adsorption was a rapid process, and the C-H and O-Si-O of S were the key functional groups. The pH of the leachate significantly affected the adsorption efficiency of Cd. Finally, the purified leachate was successfully applied to microbial cultivation and soil remediation. Overall, the reclamation of Cd-containing wastewater can not only dampen the impacts of water shortages, but also achieve the purposes of Cd removal and resource recovery to lower costs by approximately 1166-3499 yuan per mu.