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

Stochastic and deterministic mechanisms jointly drive the assembly of microbial communities in cold-rolling wastewater across China

Microorganisms play a pivotal role in industrial wastewater treatment, serving as a critical barrier to water purification and safeguarding human and environmental health. Despite their importance, the biogeographic distribution and assembly mechanisms of microbial communities in cold-rolling wastewater treatment systems remain poorly understood. This study analyzed 101 microbial samples from nine regions using high-throughput sequencing, revealing rich microbial diversity and distinct regional aggregation patterns. Random forest analysis identified key biomarkers, often low-abundance species, while a unique core microbial community was strongly correlated with pollutant removal efficiencies, including chemical oxygen demand (COD), total organic carbon (TOC), and total nitrogen (TN). Neutral community model analysis demonstrated that microbial community assembly is driven by both stochastic and deterministic processes. Co-occurrence network analysis further highlighted o__1-20 and g__Ellin6067 as pivotal taxa influencing community structure. Among environmental factors, nitrite nitrogen (NO₂-N) and COD were identified as critical drivers of community assembly. This study provides the first comprehensive characterization of microbial biogeographic patterns in cold-rolling wastewater treatment plants across China. The findings deepen our understanding of microbial diversity, distribution, and community dynamics in industrial wastewater systems, offering valuable insights for optimizing treatment processes.

A novel tiered ecological risk framework linking metal-driven pollution to soil microbial dynamics in a fragile ecosystem

Widespread soil heavy metal (HM) pollution has caused great concerns worldwide. A refined and cost-effective ecological risk assessment (ERA) is critical for managing these risks. Herein, we propose a novel tiered ERA framework to evaluate indigenous pollution-effect associations in contaminated soils. This framework progressively applies source apportionment, spatial regression, deterministic and probabilistic risk characterization, ecological surveys of soil phospholipid fatty acids (PLFAs), and successive multivariable statistics to provide comprehensive ERA evidence, as demonstrated in an ecologically fragile mining area. The risk screening phase identified Zn, Pb, Cd, Cu, and Hg as priority contaminants, and mining activities contributed 86.5 % (Zn), 87.2 % (Pb), 83.3 % (Cd), 64.6 % (Cu), and 52.3 % (Hg) of the total soil concentrations in the study area determined by the positive matrix factorization (PMF) model. The risk quotient of ecological criteria tailored to different land uses exhibited ecologically relevant risk grading. The risk quantification phase determined the overall risk probabilities to be 53.98 %, 11.12 %, 9.69 %, 5.03 % and 1.34 % for Zn, Pb, Cu, Cd and Hg, respectively, and provided adaptive HM priority lists with different risk grades. The risk causeeffect attribution phase confirmed that HMs significantly reduced soil fungal PLFA abundance and indirectly altered the PLFA structure by decreasing the soil pH. The proposed framework offers a cost-effective, refined and feasible technical support for ecological risk management in contaminated areas.

Distinct response of nitrogen metabolism to exogenous cadmium (Cd) in river sediments with and without Cd contamination history

The role of metal resistance on nitrogen metabolism function and community resilience against Cd is important for elucidating the evolutionary dynamics of key ecological functions in river ecosystems. In this study, the response of nitrogen transforming function to Cd exposure in river sediments from the Yangtze River Basin with varying levels of heavy metal contamination history (Cd-contaminated and Cd-free sediments) was compared to understand how Cd influenced nitrogen metabolism under varying metal resistance conditions. The results showed that chronic and persistent Cd pollution of sediments caused an elevation of transport efflux metal resistance genes (MRGs) and a reduction in the uptake MRGs, leading to a stronger tolerance to Cd for Cd-contaminated sediment than Cd-free ones. Specifically, denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) respectively responded to Cd through different mechanisms. Exogenous Cd (5-100 mg kg-1) influenced denitrification rates (-70 %-100 % deviation to control group) by regulating key genera (Thiobacillus, Magnetospirillum, Sideroxydans etc.) and gene clusters for denitrification. Both adaptive nature of anammox bacteria and co-regulation of key genera (Candidatus_Scalindua, Candidatus_Jettenia, Planctomyces etc.) and gene hzsA were drivers of differential responses in sediments from various contamination history. Environmental factors rather than contamination history, key genera or genes were probably critical ones determining Cd-resistance in DNRA, being more tolerant to Cd in sediments with higher TOC and NH4+. Stimulation of N2O reduction process (genera Gemmatimonas and Gemmatirosa and genes nosZ) in Cd-contaminated sediments by exogenous Cd lowered N2O emission risk, whereas the reverse was true for Cd-free sediments. These results enrich our understanding about the linkages among MRGs and nitrogen reduction functions in river.

Simulating the effects of drip and flood irrigation on the leaching, migration, and redistribution of heavy metals in contaminated soil

BACKGROUND

The extensive adoption of drip irrigation globally has adverse effects on the ecological integrity of soil, leading to significant changes in the distribution of heavy metals and other pollutants across various soil layers. However, the mechanisms underlying such changes are still unclear.

PURPOSE

This study explores the effects of different irrigation methods (drip and flood irrigation) on the heavy metal behaviors in contaminated soils, including leaching, migration, and redistribution within agricultural practices.

MATERIALS AND METHODS

The soil column leaching experiments simulating drip and flood irrigation were performed. The correlation tests and one-way analysis of variance were used for data analysis.

RESULTS

Compared to flood irrigation, drip irrigation resulted in higher leaching; as high as twice of heavy metal redistribution across soil columns. The average changes in heavy metal concentration before and after drip irrigation and flood irrigation were 16.3 % and 3.3 %, respectively. The soil redox potential and contact time were the main factors affecting the migration of heavy metals during the initial stages of irrigation implementation; however, hydrodynamic factors were also influential.

CONCLUSION

Drip irrigation may pose a serious threat to food safety in the areas with considerable heavy metal pollution due to increased heavy metal leaching and the accumulation of heavy metals near the soil surface, in particular at lower water volume.

Differentiation and response mechanisms of the endophytic flora of plants ecologically restored in the ilmenite area

Heavy metal contamination in soil is a serious environmental challenge, and abandoned mining areas are of particular concern. In order to rehabilitate the ecology of these areas. In this study, we used ICP-MS and potentiometric method to analyze the soil physicochemical and then endophytic bacteria of remediation plants with the help of 16sRNA sequencing, in order to investigate the ecological remediation of abandoned ilmenite mine and the effect of soil microbiology by seven common plants. The results revealed that the abandonment of ilmenite significantly increased the contents of total phosphorus, total potassium, available potassium, iron, and lead in the surrounding soils. It also affected the richness and diversity of endophytic bacterial communities. Pvi had the highest richness, while Tsi had the lowest richness (P < 0.05). A total of 28 phyla, 69 classes, 171 orders, and 521 genera were identified. A total of nine core OTUs were found: Stenotrophomonas, Chryseobacterium, Lactobacillus, Clostridium_sensu_stricto_12, Prevotella, Lactobacillus, Bradyrhizobium, Nocardioides, and Delftia. Beta diversity analysis revealed that the community structure of the endophytic bacteria differed during the remediation process at the ilmenite site. Functional prediction revealed upregulation of Dco transporter protein function, DNA-binding transcriptional regulators, glyoxalase or related metal-dependent hydrolases, acyl coenzyme A synthetases, ATPase components, amino acid synthesis, and cellular respiration-related functions. Pearson correlation analysis revealed that the SOC, TK, AN, AK, and Zn contents were significantly correlated with α diversity. Redundancy analysis (RDA) revealed that Actinobacteriota was significantly positively correlated with soil SOD, AN, TN, and TK contents. For the first time, this study revealed the interactions among plants, endophytic bacteria and soil pollutants, laying a theoretical basis for screening specific plant endophytic bacteria for ecological restoration.

Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage

Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE

Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.

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.

Bioremediation Potential of Rhodococcus qingshengii PM1 in Sodium Selenite-Contaminated Soil and Its Impact on Microbial Community Assembly

Soil microbial communities are particularly sensitive to selenium contamination, which has seriously affected the stability of soil ecological environment and function. In this study, we applied high-throughput 16S rRNA gene sequencing to examine the effects of low and high doses of sodium selenite and the selenite-degrading bacterium, Rhodococcus qingshengii PM1, on soil bacterial community composition, diversity, and assembly processes under controlled laboratory conditions. Our results indicated that sodium selenite and strain PM1 were key predictors of bacterial community structure in selenium-contaminated soils. Exposure to sodium selenite initially led to reductions in microbial diversity and a shift in dominant bacterial groups, particularly an increase in Actinobacteria and a decrease in Acidobacteria. Sodium selenite significantly reduced microbial diversity and simplified co-occurrence networks, whereas inoculation with strain PM1 partially reversed these effects by enhancing community complexity. Ecological modeling, including the normalized stochasticity ratio (NST) and Sloan's neutral community model (NCM), suggested that stochastic processes predominated in the assembly of bacterial communities under selenium stress. Null model analysis further revealed that heterogeneous selection and drift were primary drivers of community turnover, with PM1 inoculation promoting species dispersal and buffering against the negative impacts of selenium. These findings shed light on microbial community assembly mechanisms under selenium contamination and highlight the potential of strain PM1 for the bioremediation of selenium-affected soils.

Microbiome divergence across four major Indian riverine water ecosystems impacted by anthropogenic contamination: A comparative metagenomic analysis

Rivers are critical ecosystems that support biodiversity and local livelihoods. This study aimed to evaluate the effects of metal contamination and anthropogenic activities on microbial and phage community dynamics within major Indian river ecosystems, focusing on the Ganga, Narmada, Cauvery, and Gomti rivers -using metagenomic techniques, Biolog, and ICP-MS analysis. Significant variations in microbial communities were observed both within each river and across the four systems, influenced by ecological factors like geography and hydrology, as well as anthropogenic pressures. Downstream sites consistently exhibited higher microbial diversity, with prevalence of Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes, and Nitrospirae dominating, while Proteobacteria and Bacteroides declined. The Ganga River showed a higher abundance of bacteriophages compared to other rivers, which gradually reduced with the increment of anthropogenic impact. Functional gene analysis revealed correlations between carbon utilization and metal resistance in contaminated sites. ICP-MS analysis indicates elevated chromium and lead levels in downstream sites of all rivers compared to upstream sites. Interestingly, pristine upstream sites in the Ganga had higher trace element levels than those in Narmada and Cauvery, likely due to its Himalayan origin. Both the Ganga and Cauvery rivers contained numerous metal resistance genes. The Alaknanda was identified as the primary source of microbial communities, bacteriophages, trace elements, and heavy metals in the Ganga. These findings offer new insights into anthropogenic influences on river microbial dynamics and highlight the need for targeted monitoring and management strategies to preserve river health.

Assembly Mechanism of Rhizosphere Fungi in Plant Restoration in Lead Zinc Mining Areas

BACKGROUND

So far, the assembly and response mechanism of soil fungi in the ecological restoration process of lead zinc mines is still unclear.

METHODS

In this study, we selected three plants for the ecological restoration of abandoned lead zinc mining areas and explored the community assembly mechanism by which soil fungi assist plants in adapting to the environment during the ecological restoration process.

RESULTS

The results revealed that the mining of lead zinc mines led to a significant decrease in soil fungal diversity, whereas the planting of three plants significantly increased the diversity of rhizosphere fungi. Mining activities significantly reduced the abundance of soil Fusarium, Macroventuria, Cladosporium, and Solicocozyma and increased the abundance of soil Helvella. After three ecologically restored plants were planted, the abundances of Fusarium and Cladosporium increased significantly, whereas the abundance of Helvella decreased significantly. In addition, Capronia was significantly enriched in the rhizosphere soils of three plant species in the mining area. β diversity and fungal guild analysis revealed that mining activities had a great impact on fungal communities and guilds. The ecological restoration of plants changed the guilds of rhizosphere fungi, making them closer to those of the control sample. In addition, the endophyte guild was significantly enriched in the rhizosphere soil of three ecologically restored plants, increasing their adaptability.

CONCLUSIONS

The results provide a reference for screening lead zinc mine bioremediation strains and developing fungal plant joint remediation strategies.

Do the residual metals in multiple environmental media surrounding mines pose ecological and health risks? A case of an abandoned mining area in central south China

Despite effective mining environmental regulations, residual metal pollution persists, leading to significant ecological harm and posing substantial risks to human well-being. This study employed multiple-criteria methods to investigate the ecological and health risks caused by metals in multiple environmental media (e.g., arable soil, indoor dust, PM10, homegrown vegetables, and rice) around abandoned mine areas (MA) in central south China. The study also aimed to identify predominant risk factors and the main exposure pathway. The findings revealed that metal levels and risks in the environmental media surrounding the MA were significantly higher than those in the control areas (away from abandoned mines, CA). This indicates that the accumulation of metals in the environmental media surrounding the MA was attributed to the previous mining activities. Variations in metal content were observed among different environmental media in MA, with Cd from mining source being the primary pollutant in arable soil, indoor dust, PM10, and vegetables, while As from agricultural source was the main pollutant in rice. Additionally, the consumption of Cd-contaminated vegetables and As-contaminated rice emerged as the primary routes of health hazards for the local population, leading to significant non-carcinogenic and carcinogenic risks. Consequently, it is imperative for the government and mining companies to promptly establish risk control and remedial strategies for mitigating residual metal levels in multiple environmental media surrounding the MA.

Dispersal limitation determines the ecological processes that regulate the seasonal assembly of bacterial communities in a subtropical river

Bacteria play a crucial role in pollutant degradation, biogeochemical cycling, and energy flow within river ecosystems. However, the underlying mechanisms governing bacterial community assembly and their response to environmental factors at seasonal scales in subtropical rivers remain poorly understood. In this study, we conducted 16S rRNA gene amplicon sequencing on water samples from the Liuxi River to investigate the composition, assembly processes, and co-occurrence relationships of bacterial communities during the wet season and dry season. The results demonstrated that seasonal differences in hydrochemistry significantly influenced the composition of bacterial communities. A more heterogeneous community structure and increased alpha diversity were observed during the dry season. Water temperature emerged as the primary driver for seasonal changes in bacterial communities. Dispersal limitation predominantly governed community assembly, however, during the dry season, its contribution increased due to decreased immigration rates. Co-occurrence network analysis reveals that mutualism played a prevailing role in shaping bacterial community structure. Compared to the wet season, the network of bacterial communities exhibited higher modularity, competition, and keystone species during the dry season, resulting in a more stable community structure. Although keystone species displayed distinct seasonal variations, Proteobacteria and Actinobacteria were consistently abundant keystone species maintaining network structure in both seasons. Our findings provide insights into how bacterial communities respond to seasonal environmental changes, uncovering underlying mechanisms governing community assembly in subtropical rivers, which are crucial for the effective management and conservation of riverine ecosystems.

Investigating the adsorption processes of polymer resins for the removal of micropollutants: A comprehensive review in the field of environmental remediation

The growing worry for human health stems from the fact that micropollutants (MPs), particularly dyes, are more common in aquatic settings. These particles pose a serious risk to both humans and animals since they have been found in a variety of bodily fluids and waste products from both humans and animals. MPs pose significant dangers to human health and other living things due to their extended half-lives, high fragmentation propensity, and capacity to absorb organic pollutants as well (MB, MR, MO and CV dyes) and heavy metals as well (Pb(II), Cd(II) Co(II) Cr(III) and Ag(I) ….). They also contribute to the degradation of terrestrial and aquatic habitats. Sustainable and effective methods for removing MPs from wastewater and treating organic micropollutants in an environmentally friendly manner are being developed in order to address this problem. This work offers a thorough review of adsorption technology as a productive and environmentally friendly means of eliminating MPs from aqueous environments, with an emphasis on developments in the application of polymeric resin in MP removal. The review examines the adsorption process and the variables that affect adsorption efficiency, including the characteristics of the micropollutant, the resin, and the solution. To improve understanding, a number of adsorption mechanisms and models are explored. The study also addresses the difficulties and future possibilities of adsorption technology, emphasising the need to optimize resin characteristics, create sustainable and affordable regeneration techniques, and take into account the environmental effects of adsorbent materials.

Soil heavy metal pollution promotes extracellular enzyme production by mediating microbial community structure during vegetation restoration of metallic tailing reservoir

Vegetation restoration in metallic tailing reservoirs is imperative to restore the post-mining degraded ecosystems. Extracellular enzymes determine microbial resource acquisition in soils, yet the mechanisms controlling the enzyme activity and stoichiometry during vegetation restoration in metallic tailing reservoirs remain elusive. Here, we investigated the variations and drivers of C-, N- and P-acquiring enzymes together with microbial community along a 50-year vegetation restoration chronosequence in the China's largest vanadium titano-magnetite tailing reservoir. We found a parabolic pattern in the enzyme activity and efficiency along the chronosequence, peaking at the middle restoration stage (∼30 years) with approximately six-fold increase relative to the initial 1-year site. The enzyme ratios of C:P and N:P decreased by 33 % and 68 % along the chronosequence, respectively, indicating a higher microbial demand of C and N at the early stage and a higher demand of P at the later stage. Soil nutrients directly determined the enzyme activities and stoichiometry, whereas microbial biomass and community structure regulated the temporal pattern of the enzyme efficiency. Surprisingly, increased heavy metal pollution imposed a positive effect on the enzyme efficiency indirectly by altering microbial community structure. This was evidenced by the increased microbial diversity and the conversion of copiotrophic to oligotrophic and stress-tolerant taxa along the chronosequence. Our findings provide new insights into microbial functioning in soil nutrient dynamics during vegetation restoration under increasing heavy metal pollution.

Modulation of rhizosphere microbial community and metabolites by bio-functionalized nanoscale silicon oxide alleviates cadmium-induced phytotoxicity in bayberry plants

Cadmium (Cd) is an extremely toxic heavy metal that can originate from industrial activities and accumulate in agricultural soils. This study investigates the potential of biologically synthesized silicon oxide nanoparticles (Bio-SiNPs) in alleviating Cd toxicity in bayberry plants. Bio-SiNPs were synthesized using the bacterial strain Chryseobacterium sp. RTN3 and thoroughly characterized using advanced techniques. A pot experiment results demonstrated that Cd stress substantially reduced leaves biomass, photosynthesis efficiency, antioxidant enzyme activity, and induced oxidative damage in bayberry (Myrica rubra) plants. However, Bio-SiNPs application at 200 mg kg-1 significantly enhanced plant biomass, chlorophyll content (26.4 %), net photosynthetic rate (8.6 %), antioxidant enzyme levels, and mitigated reactive oxygen species production under Cd stress. Bio-SiNPs modulated key stress-related phytohormones by increasing salicylic acid (13.2 %) and abscisic acid (13.7 %) contents in plants. Bio-SiNPs augmented Si deposition on root surfaces, preserving normal ultrastructure in leaf cells. Additionally, 16S rRNA gene sequencing demonstrated that Bio-SiNPs treatment favorably reshaped structure and abundance of specific bacterial groups (Proteobacteria, Actinobacteriota, and Acidobacteriota) in the rhizosphere. Notably, Bio-SiNPs application significantly modulated the key metabolites (phenylacetaldehyde, glycitein, maslinic acid and methylmalonic acid) under both normal and Cd stress conditions. Overall, this study highlights that bio-nanoremediation using Bio-SiNPs enhances tolerance to Cd stress in bayberry plants by beneficially modulating biochemical, microbial, and metabolic attributes.

Heavy metals drive microbial community assembly process in farmland with long-term biosolids application

Biosolids are considered an alternative to chemical fertilizers due to their rich nutrients. However, long-term biosolids application can lead to heavy metals accumulation, which severely affects soil microbial community compositions. The factors influencing soil microbial community assembly were explored under a 16-year long-term experiment with biosolids applications. Our results indicated that biosolids application significantly increased fungal richness while not for bacterial and arbuscular mycorrhizal (AM) fungal richness. Besides, biosolids application significantly affected soil bacterial, fungal compositions and AM fungal community. Soil microorganisms were clustered into different modules with bacterial and AM fungal communities were affected by both organic matter and heavy metals, while fungal communities were affected by heavy metals (Cr, Ni, and As). The soil bacterial community assembly was dominated by stochastic processes while the fungal and AM fungal community assemblies were mainly driven by deterministic processes. Random forest analysis showed that heavy metals were identified as major drivers (Hg, Cu, Cd, and Zn for bacteria, Pb and Cr for fungi, and As and Ni for AM fungi) of the community assembly process. Overall, our study highlights the significant role of heavy metals in shaping microbial community dynamics and gives a guide for controlling biosolids application.

Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites

Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.

The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters

Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe2+ transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.

Selenium and Bacillus proteolyticus SES increased Cu-Cd-Cr uptake by ryegrass: highlighting the significance of key taxa and soil enzyme activity

Many studies have focused their attention on strategies to improve soil phytoremediation efficiency. In this study, a pot experiment was carried out to investigate whether Se and Bacillus proteolyticus SES promote Cu-Cd-Cr uptake by ryegrass. To explore the effect mechanism of Se and Bacillus proteolyticus SES, rhizosphere soil physiochemical properties and rhizosphere soil bacterial properties were determined further. The findings showed that Se and Bacillus proteolyticus SES reduced 23.04% Cu, 36.85% Cd, and 9.85% Cr from the rhizosphere soil of ryegrass. Further analysis revealed that soil pH, organic matter, soil enzyme activities, and soil microbial properties were changed with Se and Bacillus proteolyticus SES application. Notably, rhizosphere key taxa (Bacteroidetes, Actinobacteria, Firmicutes, Patescibacteria, Verrucomicrobia, Chloroflexi, etc.) were significantly enriched in rhizosphere soil of ryegrass, and those taxa abundance were positively correlated with soil heavy metal contents (P < 0.01). Our study also demonstrated that in terms of explaining variations of soil Cu-Cd-Cr content under Se and Bacillus proteolyticus SES treatment, soil enzyme activities (catalase and acid phosphatase) and soil microbe properties showed 42.5% and 12.2% contributions value, respectively. Overall, our study provided solid evidence again that Se and Bacillus proteolyticus SES facilitated phytoextraction of soil Cu-Cd-Cr, and elucidated the effect of soil key microorganism and chemical factor.

Microbial Removal of Heavy Metals from Contaminated Environments Using Metal-Resistant Indigenous Strains

Contamination of soil with heavy metals has become a matter of global importance due to its impact on agriculture, environmental integrity, and therefore human health and safety. Several microbial strains isolated from soil contaminated by long-term chemical and petrochemical activities were found to manifest various levels of tolerance to Cr, Pb, and Zn, out of which Bacillus marisflavi and Trichoderma longibrachiatum exhibited above-moderate tolerance. The concentrations of target heavy metals before and after bioremediation were determined using electrochemical screen-printed electrodes (SPE) modified with different nanomaterials. The morpho-structural SEM/EDX analyses confirmed the presence of metal ions on the surface of the cell, with metal uptake being mediated by biosorption with hydroxyl, carboxyl, and amino groups as per FTIR observations. T. longibrachiatum was observed to pose a higher bioremediation potential compared to B. marisflavi, removing 87% of Cr and 67% of Zn, respectively. Conversely, B. marisflavi removed 86% of Pb from the solution, compared to 48% by T. longibrachiatum. Therefore, the fungal strain T. longibrachiatum could represent a viable option for Cr and Zn bioremediation strategies, whereas the bacterial strain B. marisflavi may be used in Pb bioremediation applications.

Archaea are better adapted to antimony stress than their bacterial counterparts in Xikuangshan groundwater

Archaea are important ecological components of microbial communities in various environments, but are currently poorly investigated in antimony (Sb) contaminated groundwater particularly on their ecological differences in comparison with bacteria. To address this issue, groundwater samples were collected from Xikuangshan aquifer along an Sb gradient and subjected to 16S rRNA gene amplicon sequencing and bioinformatic analysis. The results demonstrated that bacterial communities were more susceptibly affected by elevated Sb concentration than their archaeal counterparts, and the positive stimulation of Sb concentration on bacterial diversity coincided with the intermediate disturbance hypothesis. Overall, the balance of environmental variables (Sb, pH, and EC), competitive interactions, and stochastic events jointly regulated bacterial and archaeal communities. Linear fitting analysis revealed that Sb significantly drove the deterministic process (heterogeneous selection) of bacterial communities, whereas stochastic process (dispersal limitation) contributed more to archaeal community assembly. In contract, the assembly of Sb-resistant bacteria and archaea was dominated by the stochastic process (undominated), which implied the important role of diversification and drift instead of selection. Compared with Sb-resistant microorganisms, bacterial and archaeal communities showed lower niche width, which may result from the constraints of Sb concentration and competitive interaction. Moreover, Sb-resistant archaea had a higher niche than that of Sb-resistant bacteria via investing on flexible metabolic pathways such as organic metabolism, ammonia oxidation; and carbon fixation to enhance their competitiveness. Our results offered new insights into the ecological adaptation mechanisms of bacteria and archaea in Sb-contaminated groundwater.

Reuse and Mechanochemical Processing of Ore Dressing Tailings Used for Extracting Pb and Zn

The increasing accumulation of rock waste obtained due to ore processing and its environmental impacts, such as acid mine drainage and elevated concentrations of heavy metals in soils, necessitates the transformation of mining technologies based on the concept of circular waste management. The research is aimed at improving the parameters of the mechanical activation effect produced on technogenic georesources, as well as at expanding the application scope of disintegrators in the field of using the partial backfill of the mined-out space when developing stratified deposits. In this regard, the research purpose was to substantiate the parameters of extracting metals from enrichment tailings using their mechanochemical activation to ensure cyclic waste management. The research involved the application of three-dimensional interpolation methods used for processing the data and the graphical representation. As a result, the following was found to be characteristic of the waste of the Sadonsky mine management. The degree of extracting zinc from pre-activated tailings increases logarithmically when the H2SO4 concentration and the NaCl proportion decrease 3.5 times. The degree of extracting lead from the activated tailings increases according to the Fourier law when decreasing the NaCl mass concentration, and an optimal range of the H2SO4 (0.38-0.51%) proportion decreases six times. One of the key results of the research is the justification of expanding the scope of applying disintegrators in the case of a directed activation influence exerted on the components of the stowing strips. The obtained results expand the understanding of the mechanism of the influence of the mechanochemical activation of dry tailings on the reactivity unevenness when extracting several metals from them.

Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary

To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.

Increased Tolerance of Massion's pine to Multiple-Toxic-Metal Stress Mediated by Ectomycorrhizal Fungi

Pinus massoniana (Massion's pine), a pioneer tree species, exhibits restoration potential in polluted mining areas. However, the physiological and molecular mechanisms of ectomycorrhizal (ECM) fungi in Massion's pine adaptability to multiple-toxic-metal stress are still unclear. Hence, Massion's pine seedlings inoculated with two strains of C. geophilum, which were screened and isolated from a polluted mine area, were cultivated in mine soil for 90 days to investigate the roles of EMF in mediating toxic metal tolerance in host plants. The results showed that compared with the non-inoculation control, C. geophilum (CG1 and CG2) significantly promoted the biomass, root morphology, element absorption, photosynthetic characteristics, antioxidant enzyme activities (CAT, POD, and SOD), and proline content of Massion's pine seedlings in mine soil. C. geophilum increased the concentrations of Cr, Cd, Pb, and Mn in the roots of Massion's pine seedlings, with CG1 significantly increasing the concentrations of Pb and Mn by 246% and 162% and CG2 significantly increasing the concentrations of Cr and Pb by 102% and 78%. In contrast, C. geophilum reduced the concentrations of Cr, Cd, Pb, and Mn in the shoots by 14%, 33%, 27%, and 14% on average, respectively. In addition, C. geophilum significantly reduced the transfer factor (TF) of Cr, Cd, Pb, and Mn by 32-58%, 17-26%, 68-75%, and 18-64%, respectively, and the bio-concentration factor (BF) of Cd by 39-71%. Comparative transcriptomic analysis demonstrated that the differently expressed genes (DEGs) were mainly encoding functions involved in "transmembrane transport", "ion transport", "oxidation reduction process", "oxidative phosphorylation", "carbon metabolism", "glycolysis/gluconeogenesis", "photosynthesis", and "biosynthesis of amino acids." These results indicate that C. geophilum is able to mitigate toxic metals stress by promoting nutrient uptake, photosynthesis, and plant growth, thereby modulating the antioxidant system to reduce oxidative stress and reducing the transport and enrichment of toxic metals from the root to the shoot of Massion's pine seedlings.

Microbial community composition and cooccurrence patterns driven by co-contamination of arsenic and antimony in antimony-mining area

In the current study, a typical Sb mine was selected to explore the microbial community composition and assembly driven by the cocontamination of As/Sb with geographic distance. Our results showed that environmental parameters, especially pH, TOC, nitrate, total and bioavailable As/Sb contents largely affected the microbial community diversity and composition. The total and bioavailable As/Sb levels were significantly positively correlated with the relative abundance of Zavarzinella, Thermosporothrix and Holophaga, while the pH presented a significant negative correlation with the three genera, potentially implying they are important taxonomic groups in acid-mining soils. The cooccurrence network analysis indicated the environmental stress dominated by pH and As/Sb co-contamination affected the microbial modularity and interaction. Meanwhile, Homogeneous selection (HoS, 26.4-49.3%), and drift and others (DR, 27.1∼40.2%) were the most important assembly processes for soil bacterial, and the importance of HoS decreased and the DR increased with geographic distance to the contamination source respectively. Soil pH, nutrient availability, total and bioavailable As/Sb contents significantly affected the HoS and DR processes. This study provides theoretical support for microbial remediation in metal(loid)-contaminated soils.

Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide

Monitoring of the microbial community in bioleaching system is essential for control process parameters and enhance the leaching efficiency. Due to the difficulty of sampling, microbial distribution, community succession and bioleaching activity along the vertical depth of bioleaching heaps remain unresolved. This study investigated the geochemical parameters and microbial community structure along a depth profile in a bioleaching heap and leachate. 80 ore samples at different heap depths and 9 leaching solution samples from three bioheaps of Zijin Copper Mine were collected. Microbial composition, mineral types and geochemical parameters of these samples were analyzed by 16S rRNA high-throughput sequencing and a series of chemical measurement technologies. The results revealed that the pH, Cu, Fe and the total sulfur contents were the major factors shaping the composition of the microbial communities in the bioleaching system. The extent of mineral oxidation increased as the sample depth increases, followed by the increasing of sulfur oxidizers. The abundance of sulfur and iron oxidizers including members of Acidithiobacillus, Sulfobacillus and Acidiferrobacter were significantly higher in the leaching heap than in the leaching solution, meanwhile, they showed strong positive interactions with other members within the same genera and iron oxidizer Leptospirillum and Ferroplasma. Besides, Acidithiobacillus negatively interacted with heterotrophs such as Sphingobium, Exiguobacterium, Brevundimonas and so on. On the contrast, members of Leptospirillum and unclassified Archaea were significantly abundant in the leaching solution and revealed strong interactions with members of Thermoplasmatales. The main conclusion of this study, especially the leaching potential of microorganisms prevailing in bioheaps and their relationships with geochemical factors, provides theoretical guidance for future process design such as the control of processing parameters and microbial community in heap leaching.

Effect of metal pollution on the distribution and co-occurrence pattern of bacterial, archaeal and fungal communities throughout the soil profiles

Metal pollution has raised negative impact on microbes, but little is known about the distribution and co-occurrence pattern of bacterial, fungal and archaeal communities along the soil profiles at multiple metal contamination sites. Here, we characterized the variations of metal concentrations and microbial communities with soil depth along five deep bores at the Tanghe Sewage Reservoir, a typical metal contamination area on the North China Plain. Co, Cd, Mg, Se, and Li were identified as the major contaminants in this area, and the pollution load index was 1.88, 1.54 and 1.62 in the shallow layer (0-0.6 m), deep layer (>2.0 m) and middle layer (0.6-2.0 m), respectively. The diversities and compositions of bacterial, archaeal and fungal communities varied significantly along the soil profiles. Deterministic process played a crucial role in shaping the difference of microbial community compositions among different soil layers, in which metal levels contributed more than soil physiochemical parameters. Furthermore, the interspecific co-occurrence network was most complex in the middle layer, indicating that metal pollution could decrease microbial network complexity. Bacterial keystone species in the co-occurrence networks showed both positive and negative correlations with polluted metals, whereas most archaeal and fungal keystone species were negatively related to multiple metals. These findings increased our understanding of distribution patterns, co-occurrence networks and environmental drivers of microbial communities in metal pollution soils.

Tailings Utilization and Zinc Extraction Based on Mechanochemical Activation

The significant containment of the global mining industry is caused by the problem of the transition to sustainable metal extraction and the integrated use of technogenic raw materials from the tailings of ore processing. The modeling of metal leaching processes using mechanical activation of polymetallic raw material components is particularly important in expanding the application of mining tailings as inert fillers of filling mixtures. This study is aimed at detecting the rotor speed factor on the chemical and mechanochemical effect of zinc yield growth from polymetallic tailings of the mining industry. In this regard, the purpose of this study was to improve the modeling of metal leaching processes using mechanical activation by improving the compositions of the filling mixtures. The methodology of the work included several comprehensive studies: the mechanical activation of tailings during zinc leaching from pulp in the DESI-11 disintegrator; the activation of enrichment tailings and the formation of a filling mass with different parameters of the component composition; the curing of cubic samples and their testing on the IP-1250 press. The Vi Improved text editor was used to prepare the algorithms for deterministic methods of three-dimensional interpolation in the Python language. The experimental results were graphically displayed using Gnuplot. The study of the agitation leaching of the waste obtained from the Sadonskiy mining district results in the fact that the NaCl mass concentration decreased from 13 to 1% and the H₂SO₄ concentration stabilization within 0.5 to 0.6% led to a 3-time increase in the zinc yield from the pulp, according to the polynomial law (from 28 to 91%). The obtained results expand the idea of the mechanism of the strength gain by the filling mass under mechanical activation on the components of the filling mixture, as well as changes in the efficiency of zinc leaching at different ratios of two types of lixiviants (sulphuric acid and sodium chloride) in the leaching solution.

Characteristics and DGT Based Bioavailability of Cadmium in the Soil-Crop Systems from the East Edge of the Dongting Lake, China

Contamination of heavy metals (including the cadmium, Cd) in agricultural soils has become an increased issue, posing a threat to the crop safety and human health. In order to evaluate the contamination characteristics and bioavailability of Cd in the soil−crop systems from the East edge of the Dongting Lake, four kinds of agricultural products for typical crops (rice, peanut, sweet potato, and corn) and corresponding rhizosphere soils were collected and analyzed for the Cd concentrations. The technique of diffusive gradients in thin-films (DGT) was applied to evaluate the Cd bioavailability in the rhizosphere soils. Concentrations of Cd ranged from 0.04 to 2.95 mg/kg (average 0.24 mg/kg) with 73.9% sites above the background levels, especially for paddy soils. Cd concentrations in the agricultural products ranged from 0.01 to 2.19 mg/kg (average 0.18 mg/kg), with Cd enrichment observed in the peanut samples. No obvious correlations (R2 < 0.25) were observed between the Cd concentrations in the agricultural products and total Cd concentrations in the rhizosphere soils, this indicated that the total Cd concentrations in the soils cannot predict the concentrations in the agricultural products of crops. While the DGT measured Cd concentrations showed good correlations (R2 = 0.64−0.90) with the concentrations in the most agricultural products of crops, which may be used to evaluate the safety of the soil and further safety of the agricultural products of crops. Overall, DGT showed a good potential for prediction of heavy metal bioavailability in soil since the DGT technique can simulate the sustained supply of heavy metals from solid to liquid in the soils.