Responses of soil fungal and archaeal communities to environmental factors in an ongoing antimony mine area

Diazotrophic community difference between specialists and generalists in response to arsenic and antimony contaminations

Diazotrophs are pivotal in bioremediation, particularly in environments contaminated by metal(loid)s. Despite their significance, the specific impacts of such contamination on the diverse functional groups of soil diazotrophs, including both generalists and specialists, are not well understood. Our study examines the influences of antimony and arsenic contamination on the ecological functions of these diazotrophic groups in areas with high (HC) and low (LC) contamination. Utilizing geochemical analyses, nitrogenase gene (nifH) sequencing, and robust statistical approaches, we assessed the composition and distribution patterns of diazotrophs across different contamination levels. Our results show consistent alpha diversity among diazotrophic subcommunities in both HC and LC sites, highlighting their resilience to metal-induced stress. Generalists exhibited significant compositional shifts between HC and LC sites, whereas specialists remained stable. Network analyses revealed that specialists more frequently occupy central roles than generalists, yet metal stress displaces both groups from these positions within the networks. Deterministic processes were identified as the dominant factors influencing community assembly for both subcommunities. While MST values suggested a similar balance of deterministic and stochastic processes between HC and LC sites, the findings indicate that metal(loid) contamination may still contribute to ecological selection, particularly through Sb and As influencing generalist and specialist composition. These results provide valuable insights into the differential responses of generalist and specialist subcommunities to metal contamination, informing improved ecosystem management and bioremediation strategies.

Cobalt regulation biocathode with sulfate-reducing bacteria for enhancing the reduction of antimony and the removal of sulfate in a microbial electrolysis cell simultaneously

Antimony (Sb) contamination in water resources poses a critical environmental and health challenge globally. Sulfate reducing bacteria (SRB) are employed to reduce SO42- to S2- for removing Sb in a microbial electrolysis cell (MEC). Yet, the reduction efficiency of reducing SO42- and Sb(V) through SRB remains relatively low, and the underlying mechanism remains elusive. Herein, the MEC reactor modified with Co-based or Fe-based MOF materials was served to enhance the electron transfer between the aqueous environment and the microorganisms to enhance the operational efficiency of the bio-electrochemical system (MEC-SRB). This study highlights the central role of removal efficiency as a critical performance metric and its direct correlation with material properties and mechanisms. The results demonstrate that the ZIF-8@Co electrode significantly outperformed other materials, achieving 98.7% sulfate and 93.1% total Sb removal over multiple cycles. Electrochemical analysis revealed that the superior performance of ZIF-8@Co electrode is attributed to rapid electron transfer and low electronic impedance. The charge transfer resistance of the ZIF-8@Co group was 155 Ω, significantly lower than that of the ZIF-8@Fe group (1724 Ω) and the ZIF-8@CoFe group (427 Ω). These findings demonstrate that the material's ability to facilitate electron transfer directly governs the pollutant removal efficiency. Fluorescence analysis revealed that the ZIF-8@Co electrode supported a denser biofilm and enhanced microbial activity. Mechanistic studies confirmed that Sb(V) was reduced and deposited as Sb2S3 precipitate, which was further characterized and analyzed by methods such as XRD and XPS. This research elucidates the potential and underlying mechanisms of an electrically stimulated SRB bio-electrochemical system for effective Sb-containing wastewater treatment. Our findings provide crucial insights for developing high-efficiency, sustainable remediation technologies for heavy metal contamination, with significant potential for real-world application in water treatment and environmental protection.

Interactive effects of microplastics and cadmium on soil properties, microbial communities and bok choy growth

The simultaneous presence of microplastics (MPs) and cadmium (Cd) in soil environments has raised concerns regarding their potential interactive effects on soil-plant ecosystems. This study explores how polyethylene (PE) at concentrations of 0.5 % (w/w), 1 % (w/w), and 2 % (w/w), and Cd at concentrations of 3 mg kg-1 and 12 mg kg-1, either alone or combined, impact soil physicochemical properties, microbial community structures, and bok choy growth through a 40-day pot experiment. Our findings reveal that the addition of 2 % (w/w) PE significantly increased soil organic carbon (SOC). However, when 2 % PE coexisted with Cd, SOC levels decreased, potentially due to a reduction in enzyme activity (β-1,4-glucosidase). PE increased the proportion of 1-2 mm soil aggregates, while the coexistence of 2 % PE and Cd significantly increased the content of soil aggregates larger than 2 mm. The coexistence of PE and Cd increased available potassium (AK) in the soil by approximately 13 % to 41 %. Regarding bok choy growth, the aboveground biomass under 2 % PE was approximately 210 % of that under 0.5 % PE, possibly because of the enhancement in soil nutrients. The presence of Cd, however, reduced the chlorophyll content of bok choy by approximately 18 % to 34 %. Notably, the coexistence of high PE concentration (2 % w/w) and low Cd concentration (3 mg kg-1) resulted in the highest aboveground biomass among all coexistence treatments. Furthermore, the addition of PE and Cd significantly altered the structure of soil bacterial and fungal communities, with fungi showing a greater response. Bacteria were significantly associated with soil inorganic N content and plant growth. This study provides new insights into the interactions of microplastics and Cd within microbial-soil-plant systems.

Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria

The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.

The Diversity and Community Composition of Three Plants' Rhizosphere Fungi in Kaolin Mining Areas

Mining activities in the kaolin mining area have led to the disruption of the ecological health of the mining area and nearby soils, but the effects on the fungal communities in the rhizosphere soils of the plants are not clear. Three common plants (Conyza bonariensis, Artemisia annua, and Dodonaea viscosa) in kaolin mining areas were selected and analyzed their rhizosphere soil fungal communities using ITS sequencing. The alpha diversity indices (Chao1, Shannon, Simpson, observed-species, pielou-e) of the fungal communities decreased to different extents in different plants compared to the non-kauri mining area. The β-diversity (PCoA, NMDS) analysis showed that the rhizosphere soil fungal communities of the three plants in the kaolin mine area were significantly differentiated from those of the control plants grown in the non-kaolin mine area, and the extent of this differentiation varied among the plants. The analysis of fungal community composition showed that the dominant fungi in the rhizosphere fungi of C. bonariensis and A. annua changed, with an increase in the proportion of Mycosphaerella (genus) by about 20% in C. bonariensis and A. annua. An increase in the proportion of Didymella (genus) by 40% in D. viscosa was observed. At the same time, three plant rhizosphere soils were affected by kaolin mining activities with the appearance of new fungal genera Ochrocladosporium and Plenodomus. Predictive functional potential analysis of the samples revealed that a significant decrease in the potential of functions such as biosynthesis and glycolysis occurred in the rhizosphere fungal communities of kaolin-mined plants compared to non-kaolin-mined areas. The results show that heavy metals and plant species are the key factors influencing these changes, which suggests that selecting plants that can bring more abundant fungi can adapt to heavy metal contamination to restore soil ecology in the kaolin mining area.

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.

Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia

Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.

Response of soil microbial activities and ammonia oxidation potential to environmental factors in a typical antimony mining area

Mining, smelting and tailing deposition activities can cause metal(loid) contamination in surrounding soils, threatening ecosystems and human health. Microbial indicators are sensitive to environmental factors and have a crucial role in soil ecological risk assessment. Xikuangshan, the largest active antimony (Sb) mine in the world, was taken as the research area. The soil properties, metal(loid) contents and microbial characteristics were investigated and their internal response relationships were explored by multivariate statistical analysis. The assessment of the single pollution index and Nemerow synthetic pollution index (P_N) showed that the soils were mainly polluted by Sb, followed by Cd and As, in which sampling site S1 had a slight metal(loid) pollution and the other sampling sites suffered from severe synthetic metal(loid) pollution. The microbial characteristics were dissimilar among sampling points at different locations from the mining area according to hierarchical cluster analysis. The correlation analysis indicated that fluorescein diacetate hydrolase, acid phosphatase, soil basal respiration and microbial biomass carbon were negatively correlated with P_N, indicating their sensitivity to combined metal(loid) contamination; that dehydrogenase was positively correlated with pH; and that urease, potential ammonia oxidation and abundance of ammonia-oxidizing bacteria and archaea were correlated with N (nitrogen) contents. However, β-glucosidase activity had no significant correlations with physicochemical properties and metal(loid) contents. Principal components analysis suggested bioavailable Sb and pH were the dominant factors of soil environment in Xikuangshan Sb mining area. Our results can provide a theoretical basis for ecological risk assessment of contaminated soil.

Remedial effect and operating status of a decommissioned uranium mill tailings (UMT) repository: A micro-ecological perspective based on bacterial community

From a radioecological perspective, increasing attention has been paid to the long-term stabilisation of decommissioned uranium mill tailings (UMT) repositories. However, little is known about the evaluation of decommissioning and remedial effects of UMT repositories from a microecological perspective based on bacterial communities. Here, we analysed the distribution and structure of soil community assemblies along different vertical soil profiles in a decommissioned UMT repository and explored the impact of soil properties, including physicochemical parameters, metal(loid)s, and radionuclides, on the bacterial assemblage. We found that the α diversity of the bacterial community was unaffected by variations in different soil profiles and taxa were classified at the phylum level with small significant differences. In contrast, the bacterial community structure in and around the UMT repository showed significant differences; however, this difference was significantly affected by soil metal(loid)s and physicochemical properties rather than soil radionuclides. In addition, seven bacterial genera with significant differences between the inner and surrounding regions of the repository could be used as potential indicators to further investigate the remedial effects on soil environmental quality. These findings provide novel insights into the construction of an assessment system and in situ biomonitoring of UMT repositories from a microecological perspective based on bacterial communities.

Disentangling biogeographic and underlying assembly patterns of fungal communities in metalliferous mining and smelting soils

Elucidating community assembly and their relevance to environmental variables are fundamental for understanding microbial diversity and functioning in terrestrial ecosystems, yet the geographical diversity and assembly patterns of the fungal community in metalliferous ecospheres associated with mining and smelting activities have received penurious understandings. Here, the fungal communities collected from three groups of soils around the mining and smelting sites were profiled by Internal Transcribed Spacer (ITS) sequencing, in order to understand the geographical distributions of fungal community diversities, structures, compositions, assembly processes and the occurrence patterns. The results suggested obvious biogeographic distribution patterns of fungal compositions among the three groups of soils. Among them, 15 fungal phyla including Ascomycota, Basidiomycota and Mortierellomycota were recognized across the samples. 12 abundant classes showing significantly different in relative abundances among the three groups of soils. Total metal(loid)s and level significantly decreased the fungal abundances and diversities. The community similarity demonstrated distance-decay pattern among the three sites. Metal(loid)s explained relatively higher fungal community variations (4.16 %) relative to other factors (1.89 %) and geography (1.21 %), though 83.32 % of the variations could not be explained. Stochastic dispersal limitation and undominated fraction were dominated relative to deterministic heterogeneous selection in total and individual site, respectively. These results highlighted the stochastic processes in governing the biogeography of fungal communities in mining and smelting ecospheres.

Rhizosphere Microbial Communities and Geochemical Constraining Mechanism of Antimony Mine Waste-Adapted Plants in Southwestern China

Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste—Sb mine tailing, waste rocks, and smelting slag—and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.

Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soil

Bacterial communities in antimony (Sb) polluted soils have been well addressed, whereas the important players fungal communities are far less studied to date. Here, we report different responses of bacterial and fungal communities to Sb contamination and the ecological processes controlling their community assembly. Soil samples in the Xikuangshan mining area were collected and subjected to high through-put sequencing of 16S rRNA and ITS1 to investigate bacterial and fungal communities, respectively, along an Sb gradient. Sb speciation in the soil samples and other physicochemical parameters were analyzed as well. Bacterial communities were dominated by Deltaproteobacteria in the soil with highest Sb concentration, whereas Chloroflexi were dominant in the soil with lowest Sb concentration. Fungal communities in high-Sb soils were predominated by unclassified Fungi, whilst Leotiomycetes were dominant in low-Sb soil samples. Multivariate analysis indicated that Sb, pH and soil texture were the main drivers to strongly impact microbial communities. We further identified Sb-resistant microbial groups via correlation analysis. In total, 18 bacterial amplicon sequence variants (ASVs) were found to potentially involve in biogeochemical cycles such as Sb oxidation, sulfur oxidation or nitrate reduction, whereas 12 fungal ASVs were singled out for potential heavy metal resistance and plant growth promotion. Community assembly analysis revealed that variable selection contributed 100% to bacterial community assembly under acidic or high Sb concentration conditions, whereas homogeneous selection dominated fungal community assembly with a contribution over 78.9%. The community assembly of Sb-resistant microorganisms was mainly controlled by stochastic process. The results offer new insights into microbial ecology in Sb-contaminated soils, especially on the different responses of microbial communities under identical environmental stress and the different ecological processes underlining bacterial and fungal community assembly.

Antimony Immobilization in Primary-Explosives-Contaminated Soils by Fe-Al-Based Amendments

Soils at primary explosives sites have been contaminated by high concentrations of antimony (Sb) and co-occurring heavy metals (Cu and Zn), and are largely overlooked and neglected. In this study, we investigated Sb concentrations and species and studied the effect of combined Fe- and Fe-Al-based sorbent application on the mobility of Sb and co-occurring metals. The content of Sb in soil samples varied from 26.7 to 4255.0 mg/kg. In batch experiments, FeSO4 showed ideal Sb sorption (up to 97% sorption with 10% FeSO4·7H2O), whereas the sorptions of 10% Fe0 and 10% goethite were 72% and 41%, respectively. However, Fe-based sorbents enhanced the mobility of co-occurring Cu and Zn to varying levels, especially FeSO4·7H2O. Al(OH)3 was required to prevent Cu and Zn mobilization. In this study, 5% FeSO4·7H2O and 4% Al(OH)3 mixed with soil was the optimal combination to solve this problem, with Sb, Zn, and Cu stabilizations of 94.6%, 74.2%, and 82.2%, respectively. Column tests spiked with 5% FeSO4·7H2O, and 4% Al(OH)3 showed significant Sb (85.85%), Zn (83.9%), and Cu (94.8%) retention. The pH-regulated results indicated that acid conditioning improved Sb retention under alkaline conditions. However, no significant difference was found between the acidification sets and those without pH regulation. The experimental results showed that 5% FeSO4·7H2O + 4% Al(OH)3 without pH regulation was effective for the stabilization of Sb and co-occurring metals in primary explosive soils.

Quantifying the contribution rates of sulfonamide antibiotics removal mechanisms in constructed wetlands using multivariate statistical analysis

The removal of antibiotics in subsurface flow constructed wetlands is performed through various removal mechanisms, such as adsorption, hydrolysis, microbial degradation and plant uptake. However, the contribution rates of the removal mechanisms in constructed wetlands are still not well studied. This study conducted a series of experiments and used multivariate statistical analysis to determine contribution rates for substrate adsorption, hydrolysis, and microbial degradation. Multiple stepwise regression analysis indicated that specific surface area and salt content were the main factors influencing sulfonamide adsorption, while temperature and pH were the main factors influencing sulfonamide hydrolysis. Variance partitioning analysis showed that the influence of physical-chemical factors was greater than that of nutrients on the microbial community. Partial least squares path analysis showed that the path coefficients of microbial degradation, adsorption and hydrolysis for sulfonamides removal in vertical subsurface flow constructed wetlands were 0.6339, 0.3608 and 0.0351, respectively, while the corresponding path coefficient were 0.5658, 0.4707 and 0.1079 in horizontal subsurface flow constructed wetlands, respectively. This means that microbial degradation contributes the most to the removal of sulfonamides in subsurface flow constructed wetlands. Enhanced microbial degradation may be a powerful measure to improve the removal of sulfonamides. These results will be helpful for understanding the removal mechanism of antibiotics and will provide a definite direction for pertinently improving sulfonamide removal efficiency in constructed wetlands.

Soil Fungal Community in Grazed Inner Mongolian Grassland Adjacent to Coal-Mining Activity

Coal mining results in reduced soil quality and makes environments less stable. Soil fungi are suitable indicators of soil quality for monitoring purposes. Here, the objective was therefore to investigate the effects of grazing and mining on the composition of the soil fungal community at the periphery of an opencast coal-mine dump in the Shengli mining area, Xilingol League, Inner Mongolia. A total of 2,110 fungal operational taxonomic units were identified and subdivided into 81 orders and nine categories, based on trophic modes. The sensitive factor to mining was soil pH, and that to grazing were soil nitrate-nitrogen and alkaline phosphatase activity. According to the Pearson correlation and Mantel test, we propose interactions between grazing and coal-mining exist a co-effect and could regulate edaphic variables to alter the behavior of soil fungal community. Moreover, compared with coal-mining, grazing has a greater impact on it. The results provide a basis to further clarify soil fungal ecological functions, and may also contribute to the practice of soil remediation and environmental management in coal-mining areas.

A Critical Review of Resistance and Oxidation Mechanisms of Sb-Oxidizing Bacteria for the Bioremediation of Sb(III) Pollution

Antimony (Sb) is a priority pollutant in many countries and regions due to its chronic toxicity and potential carcinogenicity. Elevated concentrations of Sb in the environmental originating from mining and other anthropogenic sources are of particular global concern, so the prevention and control of the source of pollution and environment remediation are urgent. It is widely accepted that indigenous microbes play an important role in Sb speciation, mobility, bioavailability, and fate in the natural environment. Especially, antimony-oxidizing bacteria can promote the release of antimony from ore deposits to the wider environment. However, it can also oxidize the more toxic antimonite [Sb(III)] to the less-toxic antimonate [Sb(V)], which is considered as a potentially environmentally friendly and efficient remediation technology for Sb pollution. Therefore, understanding its biological oxidation mechanism has great practical significance to protect environment and human health. This paper reviews studies of the isolation, identification, diversity, Sb(III) resistance mechanisms, Sb(III) oxidation characteristics and mechanism and potential application of Sb-oxidizing bacteria. The aim is to provide a theoretical basis and reference for the diversity and metabolic mechanism of Sb-oxidizing bacteria, the prevention and control of Sb pollution sources, and the application of environment treatment for Sb pollution.

Synergistic effects of antimony and arsenic contaminations on bacterial, archaeal and fungal communities in the rhizosphere of Miscanthus sinensis: Insights for nitrification and carbon mineralization

The impacts of metal(loids) on soil microbial communities are research focuses to understand nutrient cycling in heavy metal-contaminated environments. However, how antimony (Sb) and arsenic (As) contaminations synergistically affect microbially-driven ecological processes in the rhizosphere of plants is poorly understood. Here we examined the synergistic effects of Sb and As contaminations on bacterial, archaeal and fungal communities in the rhizosphere of a pioneer plant (Miscanthus sinensis) by focusing on soil carbon and nitrogen cycle. High contamination (HC) soils showed significantly lower levels of soil enzymatic activities, carbon mineralization and nitrification potential than low contamination (LC) environments. Multivariate analysis indicated that Sb and As fractions, pH and available phosphorus (AP) were the main factors affecting the structure and assembly of microbial communities, while Sb and As contaminations reduced the microbial alpha-diversity and interspecific interactions. Random forest analysis showed that microbial keystone taxa provided better predictions for soil carbon mineralization and nitrification under Sb and As contaminations. Partial least squares path modeling indicated that Sb and As contaminations could reduce the carbon mineralization and nitrification by influencing the microbial biomass, alpha-diversity and soil enzyme activities. This study enhances our understanding of microbial carbon and nitrogen cycling affected by Sb and As contaminations.

Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas

Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.

Responses of fungal communities along a chronosequence succession in soils of a tailing dam with reclamation by Heteropogon contortus

Phytoremediation can obviously change the fungal communities in the soils, which will significantly impact carbon (C) and nitrogen (N) cycling in ecological system. So far, the relationship between soil fungal communities and environmental factors is still poorly understood along a long chronosequence. In this study, fungal communities in the surface and rhizosphere soils of a tailing dam with Heteropogon contortus phytoremediation were investigated to explore the evolution of fungal community in a span of 50 years. The results showed that microbial community diversity increases along with time series of Heteropogon contortus phytoremediation. The dominant Dothideomycetes (20.86%), Agaricomycetes (18.09%), and Arthoniomycetes (1.69%) in rhizosphere soils were relatively higher than those in topsoil (13.9%, 2.65%, and 0.20%) at class level. Spearman correction analysis by phylum level was conducted to detect whether microflora was related to soil Physico-chemical properties, which affecting the composition of fungal communities along with the Heteropogon contortus phytoremediation. The nitrogen cycle indicators represented good linear correlations as chronosequence goes on, the indexes in the rhizosphere soil were much higher than those in the surface soils and the highest level has occurred in the 47-year-old Heteropogon contortus phytoremediation. The relative abundance of plant pathogen, wood saprotroph, dung saprotroph, and Arbuscular Mycorrhizal showed an upward tendency in rhizosphere soils along with the Heteropogon contortus phytoremediation. The highest soil fungal communities abundance and diversity were possibly attributed to the high-quality Heteropogon contortus litter returning to the ground and artificial disturbance treatments. Such changes in soil fungal communities might demonstrate a significant step forward and provided theoretical support for the biological governance of Heteropogon contortus phytoremediation in 50 years. Our study provides an insight on microbial communities connecting with soil C, N, P and S cycles and community functions in a complex plant-fungal-soil system along a long chronosequence in mine micro-ecology.

The response of microbial community structure and sediment properties to anthropogenic activities in Caohai wetland sediments

This study aimed to investigate the response of sediment microbial communities (including bacteria and archaeal groups) in Caohai Lake to anthropogenic activities. The sediment samples were collected from the regions with high anthropogenic interference and low anthropogenic interference. Their physicochemical properties and enzyme activities were analyzed, and the bacterial and archaeal communities were investigated using high-throughput sequencing technology. The results showed that the physicochemical characters changed by anthropogenic activities were the important factors that influenced enzyme activities, alpha diversity, key functional taxa, and community structure. And the impact of anthropogenic activities on microbial communities might follow a non-linear pattern. Furthermore, few significant differences of alpha indices between the high and low disturbed areas, but clear differences of microbial community composition analysis and beta-diversity analysis were observed. The hypothesis was proved that the intensity of anthropogenic impacts in Caohai had not reached the potential thresholds. The best distinguish biomarkers between the two areas and the most related key nodes among the network did not always have a high microbial abundance. The anthropogenic activities might influence the microbial community by affecting a small number of the key taxon in the ecological network. These findings provided a valuable understanding of how sediment microorganisms respond to anthropogenic activities in Caohai Lake.

Distribution and speciation of Sb and toxic metal(loid)s near an antimony refinery and their effects on indigenous microorganisms

Although several studies have investigated the effects of Sb contamination on surrounding environments and indigenous microorganisms, little is known about the effect of co-contamination of Sb and toxic metal(loid)s. In this study, the occurrence of Sb and other toxic metal(loid)s near an operating Sb refinery and near-field landfill site were investigated. Topsoil samples near the refinery had high Sb levels (∼3250 mg kg^-1) but relatively low concentrations of other toxic metal(loid)s. However, several soil samples taken at greater depth from the near-field landfill site contained high concentrations of As and Pb, as well as extremely high Sb contents (∼21,400 mg kg^-1). X-ray absorption fine structure analysis showed that Sb in the soils from both sites was present as Sb(V) in the form of tripuhyite (FeSbO₄), a stable mineral. Three-dimensional principal coordinate analysis showed that microbial community compositions in samples with high toxic metal(loid)s concentrations were significantly different from other samples and had lower microbial populations (∼10⁴ MPN g^-1). Sequential extraction results revealed that Sb is present primarily in the stable residual fraction (∼99 %), suggesting low Sb bioavailability. However, microbial redundancy analysis suggested that the more easily extractable Pb might be the major factor controlling microbial community compositions at the site.

Changes in microbial community structure due to chronic trace element concentrations in different sizes of soil aggregates

Studies on the effects of trace elements (TEs) (e.g. Cu, Cd, Zn) on soil microbial communities have provided useful information on the toxicity of TEs to microbes. However, previous studies mainly focused on the effects of TEs on microbial community structure in intact soil, while there are few studies on the impact of TEs on microbial community structure in soil aggregates. In this study, soils previously polluted for 20 years, and now containing low and high TE concentrations derived from, now abandoned, metal smelters were sampled from the surface layer (0-15 cm) of two adjacent Chinese paddy fields. The aim was to determine the effects of TEs on the soil microbial biomass and community structure in different sized soil aggregates. Long-term high TE pollution decreased microbial biomass concentration and species, changed the proportion of bacteria and fungi and decreased the diversity of bacteria in the different sized aggregates. The microbial communities in soil aggregates became clustered with increasing TE concentrations.

Low levels of salivary metals, oral microbiome composition and dental decay

Salivary microbiome composition can change following exposure to environmental toxicants, e.g., heavy metals. We hypothesized that levels of salivary nutrients and metals would correlate with salivary microbiome composition and be associated with dental decay. Here we assess the salivary concentrations of 5 essential minerals (cobalt, copper, manganese, molybdenum, and zinc), 4 metals with some evidence of normal physiological function (chromium, nickel, tungsten, and vanadium), and 12 with known toxicity (antimony, arsenic, barium, beryllium, cadmium, cesium, lead, mercury, platinum, thallium, tin, and uranium), and their associations with salivary microbiome composition and dental decay in 61 children and adults. 16 metals were detected in 54% of participants; 8 were found in all. Marked differences in salivary bacterial taxa were associated with levels of antimony, arsenic, and mercury, after adjusting for multiple testing. Further, antimony levels were associated with the presence of decayed teeth. Thus, salivary metal levels, even at low concentrations, may impact oral health.

Ecological Effects of Heavy Metal Pollution on Soil Microbial Community Structure and Diversity on Both Sides of a River around a Mining Area

The objectives of this study were to understand the characteristics of heavy metal pollution caused by mining activities on the two sides of the Shun'an river and the response of soil microorganisms to the habitats by different contamination levels and vegetation. This paper selected soil samples from the banks of the Shun'an River near the Shizishan mining area, which is at the left of the river, in Tongling, Anhui Province, China. Using Illumina MiSeq 2500 technology, we analyzed the relationship between environmental factors and microbial communities. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased. Additionally, the pollution severity and risk value of the left bank, where the mining area lies, were generally higher than those of the right bank. Because the symmetric sampling points on both banks of the river had similar planting types, their environmental factors and microbial community structure were similar and clustered. However, under different vegetation, the paddy soils tended to have a higher nutrient content and community richness and diversity than the vegetable fields or the abandoned land. It was found that soil microbial communities in this area were mostly affected by pH and Nemerow pollution index (P_N). The pH significantly affected the abundance and structure of most microorganisms. In addition, Proteobacteria, Acidobacteria, and Bacteroidetes had significant tolerance to Zn, Pb, and Cd. By exploring the potential use of these tolerant microorganisms, we seek to provide strains and the theoretical basis for the bioremediation of areas contaminated by heavy metal.

The Distribution of Bathyarchaeota in Surface Sediments of the Pearl River Estuary Along Salinity Gradient

Bathyarchaeota, a recently proposed archaeal phylum, is globally distributed and highly abundant in anoxic sediments. Metabolic pathways of the Bathyarchaeota members are diverse and, hence, this phylum has been proposed to play an important role in global biogeochemical cycles. Bathyarchaeota members are distributed in the estuarine environments. However, limited information is available about their detailed community structure, abundance, and functions in the Pearl River estuary (PRE). In the current study, we performed a comprehensive investigation of the archaeal community in the PRE surface sediments along a salinity gradient, with a focus on Bathyarchaeota. Bathyarchaeota was the dominant archaeal phylum, with the abundance of the bathyarchaeotal 16S rRNA gene ranging from 1.43 × 108 to 1.22 × 109 copies/g sediment dry weight (d.w.), and Bathy-8 was the dominant subgroup. Thaumarchaeota, Lokiarchaeota, and Euryarchaeota, including Thermoprofundales (MBG-D archaea), were the other major archaeal groups in the PRE. The differences of community distributions in the high- and low-salinity sediments were hence investigated. Statistical analysis revealed that besides salinity, ammonium, and total organic carbon were the most important environmental factors influencing the archaea community structure, including that of Bathyarchaeota, in the PRE. The archaeal network indicated the cooccurrence among Bathyarchaeota, Lokiarchaeota, and Euryarchaeota, while Bathy-6 presented unique correlations compared with other bathyarchaeotal subgroups. These observations indicate that Bathyarchaeota may play a role in ecosystem function through microbe-microbe interactions, revealing a possible different lifestyle for Bathy-6 in eutrophic estuarine sediments.