Microbial community profiles in soils adjacent to mining and smelting areas: Contrasting potentially toxic metals and co-occurrence patterns

Harnessing plant-beneficial bacterial encapsulation: A sustainable strategy for facilitating cadmium bioaccumulation in Medicago sativa

Plant-beneficial bacteria (PBB) have emerged as a promising approach for assisting phytoremediation of heavy metal (HM)-contaminated soils. However, their colonization efficiency is often challenged by complex soil environments. In this study, we screened one rhizobacterium (Klebsiella variicola Y38) and one endophytic bacterium (Serratia surfactantfaciens Y15) isolated from HM-contaminated soils and plants for their high resistance to Cd and strong growth-promoting abilities. These strains were encapsulated individually or in combination with alginate and applied with Medicago sativa in Cd-contaminated soil pot experiments. The effectiveness of different bacterial formulations in promoting plant growth and enhancing Cd bioconcentration in M. sativa was evaluated. Results showed that PBB application enhanced plant growth and antioxidant capacity while reducing oxidative damage. Encapsulated formulations outperformed unencapsulated ones, with combined formulations yielding superior results to individual applications. Quantitative PCR indicated enhanced PBB colonization in Cd-contaminated soils with alginate encapsulation, potentially explaining the higher efficacy of alginate-encapsulated PBB. Additionally, the bacterial agents modified Cd speciation in soils, resulting in increased Cd bioaccumulation in M. sativa by 217-337 %. The alginate-encapsulated mixed bacterial agent demonstrated optimal effectiveness, increasing the Cd transfer coefficient by 3.2-fold. Structural equation modeling and correlation analysis elucidated that K. variicola Y38 promoted Cd bioaccumulation in M. sativa roots by reducing oxidative damage and enhancing root growth, while S. surfactantfaciens Y15 facilitated Cd translocation to shoots, promoting shoot growth. The combined application of these bacteria leveraged the benefits of both strains. These findings contribute to diversifying strategies for effectively and sustainably remediating Cd-contaminated soils, while laying a foundation for future investigations into bacteria-assisted phytoremediation.

Impact of soil physicochemical factors and heavy metals on co-occurrence pattern of bacterial in rural simple garbage dumping site

Rural waste accumulation leads to heavy metal soil pollution, impacting microbial communities. However, knowledge gaps exist regarding the distribution and occurrence patterns of bacterial communities in multi-metal contaminated soil profiles. In this study, high-throughput 16 S rRNA gene sequencing technology was used to explore the response of soil bacterial communities to various heavy metal pollution in rural simple waste dumps in karst areas of Southwest China. The study selected three habitats in the center, edge, and uncontaminated areas of the waste dump to evaluate the main factors driving the change in bacterial community composition. Pollution indices reveal severe contamination across all elements, except for moderately polluted lead (Pb); contamination severity ranks as follows: Mn > Cd > Zn > Cr > Sb > V > Cu > As > Pb. Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteriota predominate, collectively constituting over 60% of the relative abundance. Analysis of Chao and Shannon indices demonstrated that the waste dump center boasted the greatest bacterial richness and diversity. Correlation data indicated a predominant synergistic interaction among the landfill's bacterial community, with a higher number of positive associations (76.4%) compared to negative ones (26.3%). Network complexity was minimal at the dump's edge. RDA analysis showed that Pb(explained:46%) and Mn(explained:21%) were the key factors causing the difference in bacterial community composition in the edge area of the waste dump, and AK(explained:42.1%) and Cd(explained:35.2%) were the key factors in the center of the waste dump. This study provides important information for understanding the distribution patterns, co-occurrence networks, and environmental response mechanisms of bacterial communities in landfill soils under heavy metal stress, which helps guide the formulation of rural waste treatment and soil remediation strategies.

Polymetallic contamination drives indigenous microbial community assembly dominated by stochastic processes at Pb-Zn smelting sites

Indigenous microbial communities in smelting areas are crucial for maintaining fragile ecosystem functions. However, the community assembly process and their responses to polymetallic pollution are poorly understood, especially the taxa in each bin from the amplicons that contributed to the assembly process. Herein, microbial diversity, co-occurrence patterns, assembly process and the intrinsic mechanisms across contamination gradients at a typical PbZn smelting site were systematically unravelled by high-throughput sequencing. The results showed a consistent compositional profile among the indigenous communities across sampling sites, wherein genera KD4-96 from Chloroflexi and Sphingomonas from Proteobacteria emerged as the most abundant taxa. Network modularity of the high- and middle-contaminated communities at Pb and Zn smelting sites was >0.44, indicating that community populations were clustered into modules to resist high heavy metal stress. Stochastic processes dominated the community assembly, with the greatest contribution from drift (DR), which was significantly correlated with Pb, Zn, Cr and Cu contents. What's particular was that the DR-controlled bins were dominated by Proteobacteria (typical r-strategists), while the HoS-controlled bins were by Chloroflexi (typical K-strategists). Furthermore, the proportion of DR in the bins dominated by Sphingomonadaceae (phylum Proteobacteria) increased gradually with the increase of heavy metal contents. These discoveries provide essential insights for community control in restoring and mitigating soil degradation at PbZn smelting sites.

The roles of rare and abundant microbial species in the primary succession of biological soil crusts are differentiated in metal tailings ponds with different states

Tailings ponds formed by long-term accumulation of mineral processing waste have become a global environmental problem. Even worse, tailings ponds are often simply abandoned or landfilled after they cease to be used. This allows pollution to persist and continue to spread in the environment. The significance of primary succession mediated by biological soil crusts for tailings pond remediation has been illustrated by previous studies. However, the process of primary succession may not be the same at different stages during the lifetime of tailings ponds. Therefore, we investigated the environmental differences and the successional characteristics of microbial communities in the primary successional stage of tailings ponds at three different states. The results showed that the primary succession process positively changed the environment of tailings ponds in any state of tailings ponds. The primary successional stage determined the environmental quality more than the state of the tailings pond. In the recently abandoned tailings ponds, abundant species were more subjected to heavy metal stress, while rare species were mainly limited by nutrient content. We found that as the succession progressed, rare species gradually acquired their own community space and became more responsive to environmental stresses. Rare species played an important role in microbial keystone species groups.

Ecotoxicological effects of polyethylene microplastics and lead (Pb) on the biomass, activity, and community diversity of soil microbes

Microplastics and heavy metals are ubiquitous and persistent contaminants that are widely distributed worldwide, yet little is known about the effects of their interaction on soil ecosystems. A soil incubation experiment was conducted to investigate the individual and combined effects of polyethylene microplastics (PE-MPs) and lead (Pb) on soil enzymatic activities, microbial biomass, respiration rate, and community diversity. The results indicate that the presence of PE-MPs notably reduced soil pH and elevated soil Pb bioavailability, potentially exacerbated the combined toxicity on the biogeochemical cycles of soil nutrients, microbial biomass carbon and nitrogen, and the activities of soil urease, sucrase, and alkaline phosphatase. Soil CO2 emissions increased by 7.9% with PE-MPs alone, decreased by 46.3% with single Pb, and reduced by 69.4% with PE-MPs and Pb co-exposure, compared to uncontaminated soils. Specifically, the presence of PE-MPs and Pb, individually and in combination, facilitated the soil metabolic quotient, leading to reduced microbial metabolic efficiency. Moreover, the addition of Pb and PE-MPs modified the composition of the microbial community, leading to the enrichment of specific taxa. Tax4Fun analysis showed the effects of Pb, PE-MPs and their combination on the biogeochemical processes and ecological functions of microbes were mainly by altering amino acid metabolism, carbohydrate metabolism, membrane transport, and signal transduction. These findings offer valuable insights into the ecotoxicological effects of combined PE-MPs and Pb on soil microbial dynamics, reveals key assembly mechanisms and environmental drivers, and highlights the potential threat of MPs and heavy metals to the multifunctionality of soil ecosystems.

High-proportions of tailwater discharge alter microbial community composition and assembly in receiving sediments

The tailwater from wastewater treatment plants serves as an important water resource in arid regions, alleviating the conflict between supply and demand. However, the effects of different tailwater discharge proportions on microbial community dynamics remain unclear. In this study, we investigated the effects of different tailwater discharge proportions on the water quality and microbial community characteristics of sediments in receiving water bodies under controlled conditions (WF-1, WF-2, WF-3, WF-4, and WF-5, containing 0% tailwater + 100% natural water, 25% tailwater + 75% natural water, 50% tailwater + 50% natural water, 75% tailwater + 25% natural water, and 100% tailwater + 0% natural water, respectively). Microbial co-occurrence networks and structural equation model were used to unveil the relationship between microbial communities and their shaping factors. Results showed that distinct microbial community compositions were found in the sediments with low- (< 50%) and high- (> 50%) proportions of tailwater. Specifically, WCHB1-41 and g_4-29-1, which are involved in organic degradation-related functions, were the key genera in the high-proportion cluster. A total of 21 taxa were more abundant in the low-proportion (< 50%) cluster than that in high-proportion (> 50%). Moreover, higher modularity was observed in the low-proportion. Total phosphorus directly affected while ammonia nitrogen indirectly affected the microbial community structure. Our findings support the distinct heterogeneity of microbial communities driven by tailwater discharge in receiving water bodies, and further confirmed that high-proportion tailwater depletes sensitive microbial communities, which may be avoided through scientific management.

Adaptation strategies and functional transitions of microbial community in pyrene-contaminated soils promoted by lead with Pseudomonas veronii and its extracellular polymeric substances

Pyrene was designated as a remediation target in this study, and low contamination of lead (Pb) was set to induce heavy metal stress. Pseudomonas veronii and its extracellular polymeric substances (EPSs) were chosen for biofortification, with the aim of elucidating the structural, metabolic, and functional responses of soil microbial communities. Community analysis of soil microorganisms using high-throughput sequencing showed that the co-addition of P. veronii and EPSs resulted in an increase in relative abundance of phyla associated with pyrene degradation, and formed a symbiotic system dominated by Firmicutes and Proteobacteria, which involved in pyrene metabolism. Co-occurrence network analysis revealed that the module containing P. veronii was the only one exhibiting a positive correlation between bacterial abundance and pyrene removal, indicating the potential of bioaugmentation in enriching functional taxa. Biofortification also enhanced the abundance of functional gene linked to EPS production (biofilm formation-Pseudomonas aeruginosa) and pyrene degradation. Furthermore, 17 potential functional bacteria were screened out using random forest algorithm. Lead contamination further promoted the growth of Proteobacteria, intensified cooperative associations among bacteria, and increased the abundance of bacteria with positive correlation with pyrene degradation. The results offer novel perspectives on alterations in microbial communities resulting from the synergistic impact of heavy metal stress and biofortification.

Effects of coal-fired power plants on soil microbial diversity and community structures

Long-term deposition of atmospheric pollutants emitted from coal combustion and their effects on the eco-environment have been extensively studied around coal-fired power plants. However, the effects of coal-fired power plants on soil microbial communities have received little attention through atmospheric pollutant deposition and coal-stacking. Here, we collected the samples of power plant soils (PS), coal-stacking soils (CSS) and agricultural soils (AS) around three coal-fired power plants and background control soils (BG) in Huainan, a typical mineral resource-based city in East China, and investigated the microbial diversity and community structures through a high-throughput sequencing technique. Coal-stacking significantly increased (p < 0.05) the contents of total carbon, total nitrogen, total sulfur and Mo in the soils, whereas the deposition of atmospheric pollutants enhanced the levels of V, Cu, Zn and Pb. Proteobacteria, Actinobacteria, Thaumarchaeota, Thermoplasmata, Ascomycota and Basidiomycota were the dominant taxa in all soils. The bacterial community showed significant differences (p < 0.05) among PS, CSS, AS and BG, whereas archaeal and fungal communities showed significant differences (p < 0.01) according to soil samples around three coal-fired power plants. The predominant environmental variables affecting soil bacterial, archaeal and fungal communities were Mo-TN-TS, Cu-V-Mo, and organic matter (OM)-Mo, respectively. Certain soil microbial genera were closely related to multiple key factors associated with stacking coal and heavy metal deposition from power plants. This study provided useful insight into better understanding of the relationships between soil microbial communities and long-term disturbances from coal-fired power plants.

Comparison of microbial communities in unleached and leached ionic rare earth mines

The leaching of ionic rare earth elements has caused serious environmental pollution and ecological damage. Microorganisms play a crucial role in soil ecosystems and are one of the most important components of these systems. However, there are fewer studies related to the changes that occur in microbial community structure and diversity before and after leaching in ionic rare earth mines. In this study, Illumina high-throughput sequencing was used to examine the diversity and composition of soil microorganisms on the summit, hillside, and foot valley surfaces of unleached and leached mines after in situ leaching. The results showed that microbial diversity and abundance in the surface soil of the unleached mine were higher than those in the leached mine, and leaching had a significant impact on the microbial community of mining soil. pH was the main factor affecting the microbial community. Proteobacteria, Actinobacteriota, and Chloroflexi were phyla that showed high abundance in the soil. Network analysis showed that microbial interactions can improve microbial adaptation and stability in harsh environments. PICRUSt2 predictions indicate functional changes and linkages in soil microbial communities.

Arsenic biogeochemical cycling association with basin-scale dynamics of microbial functionality and organic matter molecular composition

Geogenic arsenic (As)-contaminated groundwater is a sustaining global health concern that is tightly constrained by multiple interrelated biogeochemical processes. However, a complete spectrum of the biogeochemical network of high-As groundwater remains to be established, concurrently neglecting systematic zonation of groundwater biogeochemistry on the regional scale. We uncovered the geomicrobial interaction network governing As biogeochemical pathways by merging in-field hydrogeochemical monitoring, metagenomic analyses, and ultrahigh resolution mass spectrometry (FT-ICR MS) characterization of dissolved organic matter. In oxidizing to weakly reducing environments, the nitrate-reduction and sulfate-reduction encoding genes (narGHI, sat) inhibited the dissolution of As-bearing iron minerals, leading to lower As levels in groundwater. In settings from weakly to moderately reducing, high abundances of sulfate-reduction and iron-transport encoding genes boosted iron mineral dissolution and consequent As release. As it evolved to strongly reducing stage, elevated abundance of methane cycle-related genes (fae, fwd, fmd) further enhanced As mobilization in part by triggering the formation of gaseous methylarsenic. During redox cycling of N, S, Fe, C and As in groundwater, As migration to groundwater and immobilization in mineral particles are geochemically constrained by basin-scale dynamics of microbial functionality and DOM molecular composition. The study constructs a theoretical model to summarize new perspectives on the biogeochemical network of As cycling.

Physiological tolerance of black locust (Robinia pseudoacacia L.) and changes of rhizospheric bacterial communities in response to Cd and Pb in the contaminated soil

Woody plants possess great potential for phytoremediation of heavy metal-contaminated soil. A pot trial was conducted to study growth, physiological response, and Cd and Pb uptake and distribution in black locust (Robinia pseudoacacia L.), as well as the rhizosphere bacterial communities in Cd and Pb co-contaminated soil. The results showed that R. pseudoacacia L. had strong physiological regulation ability in response to Cd and Pb stress in contaminated soil. The total chlorophyll, malondialdehyde (MDA), soluble protein, and sulfhydryl contents, as well as antioxidant enzymes (superoxide dismutase, peroxidase, catalase) activities in R. pseudoacacia L. leaves under the 40 mg·kg-1 Cd and 1000 mg·kg-1 Pb co-contaminated soil were slightly altered. Cd uptake in R. pseudoacacia L. roots and stems increased, while the Pb content in the shoots of R. pseudoacacia L. under the combined Cd and Pb treatments decreased in relative to that in the single Pb treatments. The bacterial α-diversity indices (e.g., Sobs, Shannon, Simpson, Ace, and Chao) of R. pseudoacacia L. rhizosphere soil under Cd and Pb stress were changed slightly relative to the CK treatment. However, Cd and Pb stress could significantly (p < 0.05) alter the rhizosphere soil microbial communities. According to heat map and LEfSe (Linear discriminant analysis Effect Size) analysis, Bacillus, Sphingomonas, Terrabacter, Roseiflexaceae, Paenibacillus, and Myxococcaceae at the genus level were notably (p < 0.05) accumulated in the Cd- and/or Pb-contaminated soil. Furthermore, the MDA content was notably (p < 0.05) negatively correlated with the relative abundances of Isosphaeraceae, Gaiellales, and Gemmatimonas. The total biomass of R. pseudoacacia L. was positively (p < 0.05) correlated with the relative abundances of Xanthobacteraceae and Vicinamibacreraceae. Network analysis showed that Cd and Pb combined stress might enhance the modularization of bacterial networks in the R. pseudoacacia L. rhizosphere soil. Thus, the assembly of the soil bacterial communities in R. pseudoacacia L. rhizosphere may improve the tolerance of plants in response to Cd and/or Pb stress.

Gut microbiota-driven metabolic alterations reveal gut-brain communication in Alzheimer's disease model mice

The gut microbiota (GM) and its metabolites affect the host nervous system and are involved in the pathogeneses of various neurological diseases. However, the specific GM alterations under pathogenetic pressure and their contributions to the "microbiota - metabolite - brain axis" in Alzheimer's disease (AD) remain unclear. Here, we investigated the GM and the fecal, serum, cortical metabolomes in APP/PS1 and wild-type (WT) mice, revealing distinct hub bacteria in AD mice within scale-free GM networks shared by both groups. Moreover, we identified diverse peripheral - central metabolic landscapes between AD and WT mice that featured bile acids (e.g. deoxycholic and isodeoxycholic acid) and unsaturated fatty acids (e.g. 11Z-eicosenoic and palmitoleic acid). Machine-learning models revealed the relationships between the differential/hub bacteria and these metabolic signatures from the periphery to the brain. Notably, AD-enriched Dubosiella affected AD occurrence via cortical palmitoleic acid and vice versa. Considering the transgenic background of the AD mice, we propose that Dubosiella enrichment impedes AD progression via the synthesis of palmitoleic acid, which has protective properties against inflammation and metabolic disorders. We identified another association involving fecal deoxycholic acid-mediated interactions between the AD hub bacteria Erysipelatoclostridium and AD occurrence, which was corroborated by the correlation between deoxycholate levels and cognitive scores in humans. Overall, this study elucidated the GM network alterations, contributions of the GM to peripheral - central metabolic landscapes, and mediatory roles of metabolites between the GM and AD occurrence, thus revealing the critical roles of bacteria in AD pathogenesis and gut - brain communications under pathogenetic pressure.

A critical review on the migration and transformation processes of heavy metal contamination in lead-zinc tailings of China

The health risks of lead-zinc (Pb-Zn) tailings from heavy metal (HMs) contamination have been gaining increasing public concern. The dispersal of HMs from tailings poses a substantial threat to ecosystems. Therefore, studying the mechanisms of migration and transformation of HMs in Pb-Zn tailings has significant ecological and environmental significance. Initially, this study encapsulated the distribution and contamination status of Pb-Zn tailings in China. Subsequently, we comprehensively scrutinized the mechanisms governing the migration and transformation of HMs in the Pb-Zn tailings from a geochemical perspective. This examination reveals the intricate interplay between various biotic and abiotic constituents, including environmental factors (EFs), characteristic minerals, organic flotation reagents (OFRs), and microorganisms within Pb-Zn tailings interact through a series of physical, chemical, and biological processes, leading to the formation of complexes, chelates, and aggregates involving HMs and OFRs. These interactions ultimately influence the migration and transformation of HMs. Finally, we provide an overview of contaminant migration prediction and ecological remediation in Pb-Zn tailings. In this systematic review, we identify several forthcoming research imperatives and methodologies. Specifically, understanding the dynamic mechanisms underlying the migration and transformation of HMs is challenging. These challenges encompass an exploration of the weathering processes of characteristic minerals and their interactions with HMs, the complex interplay between HMs and OFRs in Pb-Zn tailings, the effects of microbial community succession during the storage and remediation of Pb-Zn tailings, and the importance of utilizing process-based models in predicting the fate of HMs, and the potential for microbial remediation of tailings.

Distribution heterogeneity of sediment bacterial community in the river-lake system impacted by nonferrous metal mines: Diversity, composition and co-occurrence patterns

Metal(loid) pollution caused by mining activities can affect microbial communities. However, knowledge of the diversity, composition, and co-occurrence patterns of bacterial communities in aquatic systems impacted by nonferrous metal mines. Here, the metal(loid) contents and bacterial communities in sediments from the Zijiang River (tributary to mainstream) to Dongting Lake were investigated by geochemical and molecular biology methods. The results indicated that the river sediments had lower pH and higher ecological risk of metal(loid)s than the lake sediment. The diversity and composition of bacterial communities in river sediments significantly (p < 0.05) differed from those in lake sediments, showing distributional heterogeneity. The biomarkers of tributary, mainstream, and lake sediments were mainly members of Deltaproteobacteria, Firmicutes, and Nitrospirae, respectively, reflecting species sorting in different habitats. Multivariate statistical analysis demonstrated that total and bioavailable Sb, As, and Zn were positively correlated with bacterial community richness. pH, TOC, TN, and Zn were crucial factors in shaping the distribution difference of bacterial communities. Environment-bacteria network analysis indicated that pH, SO42-, and total and bioavailable As and Sb greatly influenced the bacterial composition at the genus level. Bacteria-bacteria network analysis manifested that the co-occurrence network in mainstream sediments with a higher risk of metal(loid) pollution exhibited higher modularity and connectivity, which might be the survival mechanism for bacterial communities adapted to metal(loid) pollution. This study can provide a theoretical basis for understanding the ecological status of aquatic systems.

New insights on the effect of non-ferrous metal mining and smelting activities on microbial activity characteristics and bacterial community structure

Mining and smelting activities have brought potentially serious heavy metal(loid)s pollution to their surrounding locale. However, studies on microbial metabolic activities, community structure, and adaptation in soils proximal to non-ferrous metal mining and smelting areas are still lacking. Here the effects of biotic and abiotic characteristics of soil taken from sites surrounding inactive and active non-ferrous metal mine smelting facilities on microbial enzyme activity, microcalorimetry, and high-throughput sequencing of 16S rRNA gene barcoding were studied. Data indicated that the soils were heavily polluted by toxic metal(loid)s, of which As and Cd were the main contaminants. Microbial acid phosphatase activity and microcalorimetric total heat value were sensitive metabolic indicators in the studied areas. Actinobacteriota had the highest relative abundance, followed by Proteobacteria, Chloroflexi, and Acidobacteria. Microbial metabolic activity, bacterial community structure and phenotype varied between inactive and active sites (p < 0.05). Such analyses indicated that electrical conductivity, total As, Cu, and Mn contents, and bioavailable As, Cu, Cd, and Mn concentrations were key factors determining microbial activities, bacterial community structure, and phenotypes. Knowledge of microbial adaptation to heavy metal stressors is important for better understanding the aerial transfer of fugitive heavy metal(loid)s (and possibly microbes) and for designing future strategies for improved soil bioremediation.

Pollution caused by mining reshaped the structure and function of bacterial communities in China's largest ion-adsorption rare earth mine watershed

Ion-adsorption rare earth mining results in the production of high levels of nitrogen, multiple metals, and strong acidic mine drainage (AMD), the impacts of which on microbial assembly and ecological functions remain unclear. To address this knowledge gap, we collected river sediments from the watershed of China's largest ion-adsorption rare earth mine and analyzed the bacterial community's structure, function, and assembly mechanisms. Results showed that bacterial community assembly was weakly affected by spatial dispersion, and dispersal limitation and homogeneous selection were the dominant ecological processes, with the latter increasing with pollution gradients. Bacterial alpha diversity decreased with pollution, which was mainly influenced by lead (Pb), pH, rare earth elements (REEs), and electrical conductivity (EC). However, bacteria developed survival strategies (i.e., enhanced acid tolerance and interspecific competition) to adapt to extreme environments, sustaining species diversity and community stability. Community structure and function showed a consistent response to the polluted environment (r = 0.662, P = 0.001). Enhanced environmental selection reshaped key microbial-mediated biogeochemical processes in the mining area, in particular weakening the potential for microbial denitrification. These findings provide new insights into the ecological response of microbes to compound pollution and offer theoretical support for proposing effective remediation and management strategies for polluted areas.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Impacts of high-quality coal mine drainage recycling for replenishment of aquatic ecosystems in arid regions of China: Bacterial community responses

Coal mine water is usually recycled as supplementary water for aquatic ecosystems in arid and semiarid mining regions of China. To ensure ecosystem health, the coal mine water is rigorously treated using several processes, including reverse osmosis, to meet surface water quality standards. However, the potential environmental impacts of this management pattern on the ecological function of receiving water bodies are unclear. In this study, we built several microcosm water ecosystems to simulate the receiving water bodies. High-quality treated coal mine drainage was mixed into the model water bodies at different concentrations, and the sediment bacterial community response and functional changes were systematically investigated. The results showed that the high-quality coal mine drainage could still shape bacterial taxonomic diversity, community composition and structure, with a concentration threshold of approximately 50%. Moreover, both the Mantel test and the structural equation model indicated that the salinity fluctuation caused by the receiving of coal mine drainage was the primary factor shaping the bacterial communities. 10 core taxa in the molecular ecological network influenced by coal mine drainage were identified, with the most critical taxa being patescibacteria and g_Geothermobacter. Furthermore, the pathway of carbohydrate metabolism as well as signaling molecules and interactions was up-regulated, whereas amino acid metabolism showed the opposite trend. All results suggested that the complex physical-chemical and biochemical processes in water ecosystems may be affected by the coal mine drainage. The bacterial community response and underlying functional changes may accelerate internal nutrient cycling, which may have a potential impact on algal bloom outbreaks.

Out of site, out of mind: Changes in feather moss phyllosphere microbiota in mine offsite boreal landscapes

Plant-microbe interactions play a crucial role in maintaining biodiversity and ecological services in boreal forest biomes. Mining for minerals, and especially the emission of heavy metal-enriched dust from mine sites, is a potential threat to biodiversity in offsite landscapes. Understanding the impacts of mining on surrounding phyllosphere microbiota is especially lacking. To investigate this, we characterized bacterial and fungal communities in the phyllosphere of feather moss Pleurozium schreberi (Brid). Mitt in boreal landscapes near six gold mine sites at different stages of the mine lifecycle. We found that (1) both mining stage and ecosystem type are drivers of the phyllosphere microbial community structure in mine offsite landscapes; (2) Bacterial alpha diversity is more sensitive than fungal alpha diversity to mining stage, while beta diversity of both groups is impacted; (3) mixed and deciduous forests have a higher alpha diversity and a distinct microbial community structure when compared to coniferous and open canopy ecosystems; (4) the strongest effects are detectable within 0.2 km from operating mines. These results confirmed the presence of offsite effects of mine sites on the phyllosphere microbiota in boreal forests, as well as identified mining stage and ecosystem type as drivers of these effects. Furthermore, the footprint was quantified at 0.2 km, providing a reference distance within which mining companies and policy makers should pay more attention during ecological assessment and for the development of mitigation strategies. Further studies are needed to assess how these offsite effects of mines affect the functioning of boreal ecosystems.

The relationships between heavy metals and bacterial communities in a coal gangue site

Coal is the main source of energy for China's economic development, but coal gangue dumps are a major source of heavy metal pollution. Bacterial communities have a major effect on the bioremediation of heavy metals in coal gangue dumps. The effects of different concentrations of heavy metals on the composition of bacterial communities in coal gangue sites remain unclear. Soil bacterial communities from four gangue sites that vary in natural heavy metal concentrations were investigated using high-throughput sequencing in this study. Correlations among bacterial communities, heavy metal concentrations, physicochemical properties of the soil, and the composition of dissolved organic matter of soil in coal gangue dumps were also analyzed. Our results indicated that Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota were the bacterial taxa most resistant to heavy metal stress at gangue sites. Heavy metal contamination may be the main cause of changes in bacterial communities. Heavy metal pollution can foster mutually beneficial symbioses between microbial species. Microbial-derived organic matter was the main source of soil organic matter in unvegetated mining areas, and this could affect the toxicity and transport of heavy metals in soil. Polar functional groups such as hydroxyl and ester groups (A_226-400) play an important role in the reaction of cadmium (Cd) and lead (Pb), and organic matter with low molecular weight (S_R) tends to bind more to mercury (Hg). In addition to heavy metals, the content of nitrogen (N), phosphorus (P), and total organic carbon (TOC) also affected the composition of the bacterial communities; TOC had the strongest effect, followed by N, SOM, and P. Our findings have implications for the microbial remediation of heavy metal-contaminated soils in coal gangue sites and sustainable development.

Dynamic network modeling of gut microbiota during Alzheimer's disease progression in mice

The intimate association between the gut microbiota (GM) and the central nervous system points to potential intervention strategies for neurological diseases. Nevertheless, there is currently no theoretical framework for selecting the window period and target bacteria for GM interventions owing to the complexity of the gut microecosystem. In this study, we constructed a complex network-based modeling approach to evaluate the topological features of the GM and infer the window period and bacterial candidates for GM interventions. We used Alzheimer's disease (AD) as an example and traced the GM dynamic changes in AD and wild-type mice at one, two, three, six, and nine months of age. The results revealed alterations of the topological features of the GM from a scale-free network into a random network during AD progression, indicating severe GM disequilibrium at the late stage of AD. Through stability and vulnerability assessments of the GM networks, we identified the third month after birth as the optimal window period for GM interventions in AD mice. Further computational simulations and robustness evaluations determined that the hub bacteria were potential candidates for GM interventions. Moreover, our GM functional analysis suggested that Lachnospiraceae UCG-001 - the hub and enriched bacterium in AD mice - was the keystone bacterium for GM interventions owing to its contributions to quinolinic acid synthesis. In conclusion, this study established a complex network-based modeling approach as a practical strategy for disease interventions from the perspective of the gut microecosystem.

Heavy metal(loid)s shape the soil bacterial community and functional genes of desert grassland in a gold mining area in the semi-arid region

Gold mining can create serious environmental problems, such as soil pollution by heavy metal (loid)s. In this study, we assessed the ecological risk of Hatu gold mining activities and synchronously investigated the bacterial community structure, distribution of soil nutrient-element cycling genes (CNPS) and heavy metal resistance genes (MRG) in adjacent desert grassland soil. The study area was above the moderate risk level, with the ecological risk index (RI) of each sampling site greater than 150. Arsenic, mercury and copper were the main pollutants. Proteobacteria, Actinobacteria and Firmicutes dominated the phyla of the bacterial communities. Species turnover rather than nestedness accounted for the significant differences in community structure among various regions in the mining area. In addition, the bioavailable heavy metal (loid)s (AHM) content had a strong correlation with beta diversity and species turnover of the bacterial community (p < 0.05). No clear difference was found in the total abundance of CNPS genes among various functional regions, but eight specific functional genes were identified from downwind grasslands with lower pollution levels. Among the MRGs, Hg MRG had the highest average total relative abundance, followed by Cu, Co/Zn/Cd and As. The mercury resistance gene subtype hgcAB was positively related to the diversity of the bacterial community, and the bacterial community of grassland soil showed congruency with the MRGs in the Hatu mining area. Total Hg (THg) showed the highest influence affecting the bacterial community, while NH₄⁺-N had the greatest effect on CNPS genes and MRGs. These results highlighted the role of heavy metal (loid)s in shaping the bacterial community and functional genes in arid and semiarid desert grassland soil in gold mining regions.

Occurrence of polycyclic aromatic compounds and potentially toxic elements contamination and corresponding interdomain microbial community assembly in soil of an abandoned gas station

Bacteria, archaea and fungi usually coexist in various soil habitats and play important roles in biogeochemical cycle and remediation of contamination. Despite their significance, their combined bioassembly pattern, ecological interactions and driving factors in contaminated soils still remain obscure. To fill the gap, a systemic investigation on the characteristics of microbial community including bacteria, archaea and fungi, assembly patterns and environmental driving factors was conducted in an abandoned gas station soils which were contaminated by polycyclic aromatic compounds and potentially toxic elements for decades. The results showed that the soils were contaminated excessively by benzo[a]pyrene (0.46-2.00 mg/kg) and Dibenz[a,h]anthracene (0.37-1.30 mg/kg). Multitudinous contaminant-degrading/resistant microorganisms and unigenes were detected, indicating potential of the soils to mitigate the pollution. Compared with fungi and archaea, the bacteria had higher community diversity and were more responsive to seasonal shifts. Functional genes (nidB, nahAb, nahAa, adhP, adh, adhC, etc.) involved in biodegradation were highly enriched in summer (1.96% vs 1.80%). The co-occurrence network analysis showed summer communities exhibit a more robust network structure and positive interactions than winter communities. The fungi Neocucurbitaria, Penicillium, Fusarium, Chrysosporium, Knufia, Filobasidium, Wallemia and Rhodotorula were identified as the keystone taxa, indicating that fungi also had important positions in the interdomain molecular ecological networks of both seasons. The network topological properties and |βNTI| (66.7%-93.3% greater than 2) results indicated the deterministic assembly processes of the microbial communities in the contaminated soil. Acenaphthylene, benzo[b]fluoranthene, indeno[1,2,3-cd]perylene, benzo[g,h,i]pyrene and 9-fluorenone were the key environmental factors driving the deterministic assembly processes of the interdomain microbial community in the contaminated soil. These findings extended our knowledge of interdomain microbial community assembly mechanisms and ecological patterns in natural attenuation and provide valuable guidance in associated bioremediation strategies.

A typical case study from smelter-contaminated soil: new insights into the environmental availability of heavy metals using an integrated mineralogy characterization

Mineralogy was an important driver for the environmental release of heavy metals. Therefore, the present work was conducted by coupling mineral liberation analyzer (MLA) with complementary geochemical tests to evaluate the geochemical behaviors and their potential environmental risks of heavy metals in the smelter contaminated soil. MLA analysis showed that the soil contained 34.0% of quartz, 17.15% of biotite, 1.36% of metal sulfides, 19.48% of metal oxides, and 0.04% of gypsum. Moreover, As, Pb, and Zn were primarily hosted by arsenopyrite (29.29%), galena (88.41%), and limonite (24.15%), respectively. The integrated geochemical results indicated that among the studied metals, Cd, Cu, Mn, Pb, and Zn were found to be more bioavailable, bioaccessible, and mobile. Based on the combined mineralogical and geochemical results, the environmental release of smelter-driven elements such as Cd, Cu, Mn, Pb, and Zn were mainly controlled by the acidic dissolution of minerals with neutralizing potential, the reductive dissolution of Fe/Mn oxides, and the partial oxidation of metal sulfide minerals. The present study results have confirmed the great importance of mineralogy analysis and geochemical approaches to explain the contribution of smelting activities to soil pollution risks.

Antibiotics and microbial community-induced antibiotic-resistant genes distribution in soil and sediment in the eastern coastline of China

The health risk of antibiotic-resistant genes (ARGs) has been a global concern, while the report on occurrence and prevalence of ARGs in coastal zone is relatively scarce. This study investigated typical ARGs in soil and sediment in coastal line of eastern China and assessed its relationship with antibiotics and heavy metals as well as microbial community. Results showed that eight ARGs were all detected in the samples, and β-lactam resistance gene blaTEM reached the highest absolute abundance (6.28 × 10⁷ ~ 6.48 × 10⁸ copies/g) and relative abundance (2.3 × 10^-2 copies/16S rRNA) among samples. Amoxicillin and tetracycline were most frequently detected with the average concentration of 2.28 μg/kg and 3.48 μg/kg, respectively. Cr and Zn were found to be most abundant heavy metals with average value of 82.1 and 59.1 mg/kg, respectively. Proteobacteria, Campilobacterota, Bacteroidota, and Firmicutes were dominant phyla in most samples, while bacterial community varied significantly among samples. Redundancy analyses (RDA) showed that microbial community and antibiotics (amoxicillin and tetracycline) were driving factors of ARGs distribution, while heavy metals were not significantly correlated with ARGs. This study is helpful to understand the fate of ARGs in coastal zone.

Multiple heavy metal distribution and microbial community characteristics of vanadium-titanium magnetite tailing profiles under different management modes

Vanadium-titanium (V-Ti) magnetite tailings have caused great concern due to their safety hazards and environmental risks. However, the microbial community structure and the key geochemical factors of V-Ti magnetite tailing profiles under different management modes remain unclear. Therefore, we investigated the heavy metal distribution and the microbial community structure of the soils and tailings at varied depths of V-Ti magnetite tailing profiles with and without soil coverage. The results indicated that the topsoil covering measures retarded the acidification of tailings during stockpiling. However, As, Mn, and V in tailings have the ability to migrate to the overlying soil. Based on 16S rRNA gene amplicon sequencing, Proteobacteria was the dominant genus in the topsoil-covered tailings, whereas the most abundant genus in the exposed tailings was Betaproteobacteria. Furthermore, Rhodobacter, Hydrogenophaga, Novosphingobium, and Geobacter enriched in tailings may potentially contribute to V(V) biotransformation and the development of mine bioreremediation technologies. RDA and Spearman correlation analysis showed that pH, EC, Cd, Mn, Pb, and V were the main influencing factors regulating microbial community composition. Overall, this study provides insights for evaluating the soil covering management mode and the engineering applications of microbial technologies to manage V-Ti magnetite tailings.

Biogeography, assembly processes and species coexistence patterns of microbial communities in metalloids-laden soils around mining and smelting sites

Microbes are important component in terrestrial ecosystem, which are believed to play vital roles in biogeochemical cycles of metalloids in mining and smelting surroundings. Many studies on microbial diversity and structures have been investigated around mining and smelting sites, whereas the ecological processes and co-occurrence patterns that influence the biogeographic distributions of microbial communities is yet poorly understood. Herein, microbial biogeography, assembly mechanism and co-occurrence pattern around mining and smelting zone were systematically unraveled using 16S rRNA gene sequencing. The 66 microbial phyla co-occurring across all the samples were dominated by Proteobacteria, Chloroflexi, Acidobacteria and Crenarchaeota. Obvious distance-decay (r = 0.3448, p < 0.001) of microbial community was observed across geographic distances. Differences in microbial communities were driven by the joint impacts of soil factors, spatial and metalloids levels. Dispersal limitation dominated the microbial assemblies in whole, SC and GX sites while homogeneous selection governed that in YN site. The changes in pH and Sb level significantly influenced the deterministic and stochastic processes of microbial communities. Network analysis suggested a typical module distribution, which had apparent ecological links among taxa in modules. This study provides first insight of the mechanism to maintain microbial diversity in metalloids-laden biospheres.

Metal(loid)s diffusion pathway triggers distinct microbiota responses in key regions of typical karst non-ferrous smelting assembly

Non-ferrous metal(loid)s in region with karst characteristic are highly diffusible, especially by runoff or atmospheric deposition. However, microbiota in response to the diffusing metal(loid)s is still to be understood. In this study, we focused on microbiota across metal(loid)s diffusion pathways around a non-ferrous smelting assembly. The microbial distribution and metal(loid)s-microbial interactions were analysed by 16S rRNA amplicon and multivariate statistical analysis. Although runoff and atmospheric deposition showed similar metal(loid)s diffusion contribution, different microbial compositions were revealed. The microbiota along the runoff transect (region3) was similar to those within the atmospheric deposition transect (region4), which significantly differed from those closer to the smelting assembly (region1 and region2; R² = 0.3866, p = 0.001). Random forest model indicated the negative impacts of bioavailable metal(loid)s on microbial diversity. Proteobacteria was predominant in region1 while Actinobacteriota dominated in the other regions. Twenty abundant genera were identified in metal(loid)s rich area, such as sulfur metabolizer Sulfurifustis and metal resistant Acinetobacter. Interactions between the geochemical parameters and the dominant taxa indicated that the main drivers were Al, Sb, As and their bioavailable fractions and sulfate. This study provides understandings of microbiota patterns towards different metal(loid)s diffusion pathways around non-ferrous smelting assembly with karst characteristic.

Microbial characteristics of the leachate contaminated soil of an informal landfill site

Because informal landfills are not constructed in a regulated manner, they will inevitably become a source of leachate pollution to the surrounding environment over time. Microbes are an important part of the soil system, playing a vital role in maintaining the normal functionality of soil. This study investigated the microbial composition and co-occurrence pattern in the leachate contaminated soil of an informal landfill site. The landfill leachate underwent horizontal and vertical migration through the contaminated soil, resulting in significant differences in the microbial compositions of horizontal surface soil (CS) and vertical subsurface soil (DS and ES) compared to uncontaminated soil (S). The microbial diversity of CS, DS, and ES was lower than that of S. Due to the migration of landfill leachate, the microbial composition of the surface soil was substantially changed. The dominant phyla in S included Proteobacteria (26.88%), Chloroflexi (23.68%), Actinobacteroita (17.36%), and Acidobacteroita (16.86%), but in contaminated soils, Firmicutes (35.27-86.68%) were the dominant bacteria. A network analysis indicated that Bacilli, Clostridia, and Thermacetogeniazai of the Firmicutes were the keystone taxa and played a vital role in maintaining the stability of the soil ecosystem. A functional annotation of prokaryotic taxa (FAPROTAX) analysis showed that the microbes involved in the C-, N-, and S-cycles in contaminated soil were significantly different to those in uncontaminated soil. The proportion of (aerobic)-chemoheterotrophy and cellulolysis functional communities in contaminated soils was significantly reduced, while there was an increase in functional communities, such as anammox and denitrification, which are not conducive to soil nitrogen fixation. This negatively affected the maintenance of normal soil ecological functions. This study identified the microbial characteristics in leachate contaminated soil and the results will be beneficial for the remediation of contaminated soil in informal landfill sites.