Arsenic and antimony co-contamination influences on soil microbial community composition and functions: Relevance to arsenic resistance and carbon, nitrogen, and sulfur cycling

Effects of arsenic and trace metals on bacterial denitrification process from estuarine sediments and associated nitrous oxide emission

Coastal ecosystems currently face significant challenges due to nutrient enrichment and trace metal contamination. However, the effects of arsenic (As) and other trace metals (copper, lead, zinc, cadmium, mercury) on denitrification processes and nitrous oxide (N2O) emissions in estuarine sediments remain poorly understood. Here, we examined the influence of As and other trace metals on denitrification and N2O emissions in a single denitrifying strain, Marinobacter sp. MSD-1, isolated from metal-contaminated estuarine sediments based on its As(III)-oxidizing and denitrifying abilities and functional microbial composition. The results showed that As did not significantly affect the denitrification or N2O emission of MSD-1. However, Cd(II) at concentrations of 5-10 mg/L significantly induced the accumulation of N2O, while not significantly affecting the reduction of nitrate (NO3-) and nitrite (NO2-). The presence of As(III) further inhibited the N2O reduction under Cd exposure, but it had no significant effect on the N2O reduction after exposure to other trace metals. A negative correlation was observed between N2O reductase (NO2R) activity and N2O emissions, indicating that Cd(II) inhibits the reduction process of N2O mainly by suppressing the activity of NO2R. This study highlights the detrimental effects of cadmium on microbial denitrification and subsequent emissions of the greenhouse gas N2O, thereby improving our understanding of how estuarine and coastal ecosystems respond and adapt to trace metal pollution.

Release and Redistribution of Arsenic Associated with Ferrihydrite Driven by Aerobic Humification of Exogenous Soil Organic Matter

Humification of exogenous soil organic matter (ESOM) remodels the organic compositions and microbial communities of soil, thus exerting potential impacts on the biogeochemical transformation of iron (hydr)oxides and associated trace metals. Here, we conducted a 70-day incubation experiment to investigate how aerobic straw humification influenced the repartitioning of arsenic (As) associated with ferrihydrite in paddy soil. Results showed that the humification was characterized by rapid OM degradation (1-14 days) and subsequent slow maturation (14-70 days). During the degradation stage, considerable As (13.1 mg·L-1) was released into the aqueous phase, which was reimmobilized to the solid phase in the maturation stage. Meanwhile, the low-crystalline structural As/Fe was converted to a more stable species, with a subtle crystalline phase transformation. The generated highly unsaturated and phenolic compounds and enriched Enterobacter and Sphingomonas induced ferrihydrite (∼3.1%) and As(V) reduction, leading to As release during the degradation stage. In the maturation stage, carboxylic-rich alicyclic molecules facilitated the aqueous As reimmobilization. Throughout the humification process, organo-mineral complexes formed between OM and ferrihydrite via C-O-Fe bond contributed to the solid-phase As/Fe stabilization. Collectively, this work highlighted the ESOM humification-driven iron (hydr)oxide transformation and associated As redistribution, advancing our understanding of the coupled biogeochemical behaviors of C, Fe, and As in soil.

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.

Diverse adaptation strategies of generalists and specialists to metal and salinity stress in the coastal sediments

Understanding the distinct roles and responses of bacterial community to environmental stressors is crucial for effective ecosystem management and conservation. Despite this, there is limited research on how environmental gradients specifically impact generalist and specialist subcommunities. This study investigates these subcommunities in the sediments of Jinzhou Bay, highlighting their distinct responses to environmental gradients. Generalists thrive in disturbed environments due to their broad ecological tolerances, while specialists show higher diversity in the stable, less contaminated upstream areas. At the genus level, Porphyrobacter and Subgroup_23 were identified as the dominant taxa of generalists, while Woeseia and Lutibacter were the dominant species of specialists. Physicochemical parameters, especially metals and salinity, significantly influence subcommunity composition. Generalists are adaptable to a wider range of factors, whereas specialists are affected by specific parameters, reflecting their narrower niches. The generalists exhibit a greater abundance of salinity tolerance genes compared to the specialists; however, this trend does not extend to metal resistance genes. Keystone taxa, primarily specialists, play crucial roles in maintaining community stability. Our results underscore the importance of considering both generalists and specialists in ecological assessments, offering insights for the management and conservation of bacterial microbial diversity in coastal ecosystems.

Reduction of antimony bioavailability with the application of stable exogenous organic matter: a comparative study between rice straw and manure compost

Considering the widespread use of organic amendments to improve soil quality and enhance soil carbon sequestration, it is crucial to understand their impact on the bioavailability of metalloids in soils. Antimony (Sb), a priority pollutant, is particularly impacted by organic matter, yet the effects of different organic amendments-varying in stability and composition-on Sb bioavailability remain unclear. This study investigates the influence of different organic amendments, rice straw and compost, on Sb bioavailability in the rice-soil system, with rice ingestion being a major Sb exposure pathway in humans. Results show that while both amendments increased dissolved organic carbon in soil solution, their effects on Sb bioavailability differed markedly. Rice straw increased CDGT-SbIII by 13.24 %-66.63 %, whereas compost decreased CDGT-SbIII by 32.47 %-43.51 %. These differences were also reflected in Sb accumulation in rice shoots, where compost application resulted in lower Sb content. This reduction may be attributed to increased microbial genera such as Ramlibacter and Sphingomonas, which are associated with SbIII oxidation. Conversely, organic matter with low stability, prone to rapid degradation, could promote reducing soil conditions, thereby increasing SbIII concentrations. Our findings suggest that stable exogenous organic matter, such as pre-decomposed compost, is preferable for managing Sb-contaminated soils.

The influences of heavy metals on soil microbial C, N, P cycling and heavy metal resistance under different fertilization regimes

Heavy metal pollution changes microbial heavy metal resistance and ecological functions of carbon (C), nitrogen (N), phosphorus (P), sulfur (S) cycling, although the connections between these changes have been insufficiently explored. The study investigated the effects of varying levels of heavy metal pollution and nutrient on microbial heavy metal resistance and C, N, P, S cycling in soils. The results indicated that heavy metal pollution significantly enhanced microbial metabolic potentials, such as denitrification, Dissimilatory nitrate reduction (DNRA), P uptake and transport, as well as resistance to Cu, Cd, Pb, and As. Heavy metals and pH were identified as major factors affecting these microbial functions. The diversity and evenness of host microorganisms carrying functional genes and heavy metal resistance genes (MRGs) were significantly affected by heavy metal pollution, but this effect was alleviated with the nutrient increased. In low-nutrient soils, a strong correlation between nitrogen degradation and Zn resistance was observed due to heavy metal pollution. As nutrients increased, the close correlations between hemicellulose, P uptake and transport, nitrogen degradation and Zn resistance were also observed. Bradyrhizobium, Nitrospira, Steroidobacter, and Luteitalea might play important roles in regulating C, N, P cycling and heavy metal resistance. This study revealed the adjustment mechanisms of microbial heavy metals resistance and ecological functions under heavy metal pollution and identified the primary host microorganisms.

The Bacterial Antimonite Oxidase AnoA: Unexpected Diversity and Environmental Widespread Occurrence

The growing contamination of urban areas by antimony (Sb) has sparked interest in microbial processes that modulate Sb speciation in ecosystems. The bacterial antimonite oxidase AnoA is the only oxidase known so far whose gene expression is specifically induced by Sb(III), but its annotation in public databases is currently lacking. Here, the computational search for AnoA orthologs predicted an unexpected phylogenetic distribution across the Pseudomonadota and Actinomycetota. Putative orthologs were identified in both known Sb(III)-oxidisers (e.g., Shinella, Hydrogenophaga, Bosea, Cupriavidus and Pseudomonas) and taxa not previously linked to the Sb cycle (e.g., Bradyrhizobium, Mesorhizobium, Methylobacterium and Paraburkholderia). The anoA gene is single-copy in most Proteobacterial genomes, but is often detected in multiple copies in the Actinomycetota. Furthermore, sequence evolutionary distances suggest that it is mainly inherited vertically, with horizontal transfer events, in particular towards the Gammaproteobacteria. Using the constructed database, new PCR primers were designed and outperformed existing strain-specific primers in amplifying the anoA gene from samples with varying Sb levels and microbial profiles. Sequencing and quantification of PCR amplicons revealed a diverse range of sequences in sediments and natural biofilms, indicating that the oxidase is more environmentally diverse and widespread than previously thought and may play a significant role in Sb(III) detoxification.

Standardized framework for assessing soil quality at antimony smelting site by considering microbial-induced resilience and heavy metal contamination

Antimony smelting activities damage the soil and vegetation surroundings while generating economic value. However, no standardized methods are available to diagnose the extent of soil degradation at antimony smelting sites. This study developed a standardized framework for assessing soil quality by considering microbial-induced resilience and heavy metal contamination at Xikuangshan antimony smelting site. The soil resilience index (SRI) and soil contamination index (SCI) were calculated by Minimum Data Set and geo-accumulation model, respectively. After standardized by a multi-criteria quantitative procedure of modified Nemerow's pollution index (NPI), the integrated assessment of soil quality index (SQI), which is the minimum of SRINPI and SCINPI, was achieved. The results showed that Sb and As were the prominent metal(loid) pollutants, and significant correlations between SQI and SRI indicated that the poor soil quality was mainly caused by the low level of soil resilience. The primary limiting factors of SRI were Fungi in high and middle contaminated areas, and Skermanella in low contaminated area, suggesting that the weak soil resilience was caused by low specific microbial abundances. Microbial regulation and phytoremediation are greatly required to improve the soil quality at antimony smelting sites from the perspectives of pollution control and resilience improvement. This study improves our understanding of ecological effects of antimony smelting sites and provides a theoretical basis for ecological restoration and sustainable development of mining areas.

Arsenic efflux and bioremediation potential of Klebsiella oxytoca via the arsB gene

Arsenic-resistant Klebsiella oxytoca strain AT-02 was isolated from the ground water of the Multan region of Pakistan. The strain displayed high arsenite and arsenate resistance as minimal inhibitory concentration (MIC) was 600ppm and 10,000ppm respectively. The high tolerance of the isolated strain towards arsenate can be postulated due to significant increase in biofilm in response to arsenate. The bacterial strain exposed to 1/2 and 3/4 MIC showed a significant 10 and 12 folds increase in expression of the arsenite efflux gene arsB. Sequential and structural comparison of the arsB gene showed the presence of conserved arsenic binding residues. Arsenic remediation by AT-02 biomass was 50% after 0.5 hours of incubation and 66% in 2 hours. the increase in remediation efficiency with the increase in incubation time indicates its biosorption potential. the arsenic sensitive strain NK11 showed only 4-5% arsenic remediation. Fourier transform infrared spectroscopy (FTIR) analysis confirmed interaction of arsenate and arsenite with functional groups (aromatic amino acid residues) on the cell surface leading to characteristic peak shifts. Thus, the isolated AT-02 has the potential to remediate both arsenite and arsenate from contaminated environmental sites.

Mechanism of extracellular electron transport and reactive oxygen mediated Sb(III) oxidation by Klebsiella aerogenes HC10

Microbial oxidation and the mechanism of Sb(III) are key governing elements in biogeochemical cycling. A novel Sb oxidizing bacterium, Klebsiella aerogenes HC10, was attracted early and revealed that extracellular metabolites were the main fractions driving Sb oxidation. However, linkages between the extracellular metabolite driven Sb oxidation process and mechanism remain elusive. Here, model phenolic and quinone compounds, i.e., anthraquinone-2,6-disulfonate (AQDS) and hydroquinone (HYD), representing extracellular oxidants secreted by K. aerogenes HC10, were chosen to further study the Sb(III) oxidation mechanism. N2 purging and free radical quenching showed that oxygen-induced oxidation accounted for 36.78% of Sb(III) in the metabolite reaction system, while hydroxyl free radicals (·OH) accounted for 15.52%. ·OH and H2O2 are the main driving factors for Sb oxidation. Radical quenching, methanol purification and electron paramagnetic resonance (EPR) analysis revealed that ·OH, superoxide radical (O2•-) and semiquinone (SQ-•) were reactive intermediates of the phenolic induced oxidation process. Phenolic-induced ROS are one of the main oxidants in metabolites. Cyclic voltammetry (CV) showed that electron transfer of quinone also mediated Sb(III) oxidation. Part of Sb(V) was scavenged by the formation of the secondary Sb(V)-bearing mineral mopungite [NaSb(OH)6] in the incubation system. Our study demonstrates the microbial role of oxidation detoxification and mineralization of Sb and provides scientific references for the biochemical remediation of Sb-contaminated soil.

Biotransformation of chloramphenicol by enriched bacterial consortia and the newly isolated bacterial strain Bordetella sp. C3: Detoxifying biotransformation pathway and its potential application in agriculture

Limited sources of consortia/pure cultures that degrade chloramphenicol (CAP) and the incomplete biodegradation profiles of CAP hinder the remediation of CAP pollution. In this study, two CAP-degrading consortia (designated as CM and PM) were obtained after long-term acclimation, and Alcaligenaceae and Enterobacteriaceae enriched in CM and PM, respectively. Notably, Bordetella sp. C3, a new isolate belonging to the family Alcaligenaceae, was isolated from CM and capable of degrading 85.7 % 10 mg/L CAP at 30 ℃ and pH 7 in 10 d. The biotransformation of CAP by Bordetella sp. C3 was proposed as a detoxification process, including a novel initial degradation pathway: dechlorination of CAP into AP. Strain C3 can also function as a plant growth-promoting bacterium that solubilizes inorganic phosphate and produces siderophores and indole-3-acetic acid (IAA). This study expands our knowledge of the migration and transformation pathways of CAP and microbial community profiles during acclimatization.

Ecological influences of sulfadiazine on rhizosphere soil microbial communities in ryegrass (Lolium perenne L.)-soil potting systems: Perspectives on diversity, co-occurrence networks, and assembly processes

Microorganisms in the soil are crucial constituents of land ecosystems, significantly influencing their structure and functionality. However, the accumulation of antibiotics in agricultural practices may negatively affect these microbial communities. The objective of this study was to explore the ecological effects of the sulfonamide drug sulfadiazine (SDZ) on the rhizosphere soil microbial communities of ryegrass (Lolium perenne L.). A potting system experiment was constructed by exposing for 45 days after treatments with different initial concentrations of SDZ (0, 1, 10, and 30 mg/kg) to assess the effects of SDZ on soil microbial diversity, bacterial-fungal co-occurrence networks, and community assembly processes. The findings indicated that SDZ treatment significantly altered the community composition, especially for bacteria in the phylum Proteobacteria and Gemmatimonadota and fungi in the phylum Mortierellomycota and Aphelidiomycota. Network analysis revealed that SDZ stress caused alterations in microbial interaction patterns, especially at high treatment concentrations, and reduced network connectivity. In addition, SDZ significantly affected microbial community assembly processes, where stochastic processes were enhanced in bacterial communities, while fungal communities showed a balance of stochastic and deterministic processes. Analysis of environmental variables revealed that the presence of SDZ may disrupt the link between soil microorganisms and soil nitrogen compounds. The results provide new perspectives for understanding the ecological impacts of antibiotic residues in agroecosystems and provide a scientific basis for soil health management.

Interactions between arsenic and nitrogen regulate nitrogen availability and arsenic mobility in flooded paddy soils

In paddy soils, arsenic (As) stress influences nitrogen (N) transformation while application of N fertilizers during rice cropping affects As transformation. However, specific interactive effects between As and N in flooded paddy soils on As mobility and N availability were unclear. Here, we examined N and As dynamics in flooded paddy soils treated with four As levels (0, 30, 80 and 150 mg kg-1) and three urea additions (0, 4 and 8 mmol N kg-1). Arsenic contamination inhibited diazotrophs (nifH) and fungi but promoted AOA and denitrification genes (narG, nirK, nirS), decreasing dissolved organic N, NH4+-N and NO3--N. Besides, urea application stimulated As- and Fe-reducing bacteria (arrA and Geo) coupled with anammox. On Day 28, the addition of 8 mmol N kg-1 increased total As concentrations in solutions of soils treated with 30 and 80 mg As kg-1 by 2.4 and 1.8 times compared with the nil-N control. In contrast, at 150 mg As kg-1, it decreased the total As concentration in soil solution by 63 % through facilitating As(III) oxidation coupled with NO3--N reduction. These results indicate that As contamination decreases N availability, but urea application affects As mobility, depending on As contamination level.

Alteration of soil microbiomes in an arsenic and antimony co-contamination zone after dam failure

Arsenic (As) and antimony (Sb), two toxic metal(loid)s, behave similarly and commonly occur in mine tailings. Yet, responses of microbes to As and Sb co-contamination in tailings dam failure-affected area remain limited. Herein, soil microbiomes (archaea, bacteria and fungi) across two contrasting sites (tailing-contaminated farmland and nearby undisturbed forestland) at a Sb-Au mining district in Chizhou, China were investigated by high-throughput sequencing. Results showed that As and Sb occurred mainly in the residual form, accounting for 55.82 % and 52.04 %, respectively. The bioavailable form was 12.77 % and 10.39 % in contaminated farmland compared to 13.31 % and 11.66 % in undisturbed forestland, respectively. Contrary to archaea and fungi, bacterial alpha-diversity significantly increased in contaminated farmland. The taxa-taxa interactions in archaea were most robust, followed by bacteria; and fungi were the weakest, which was corresponding to the habitat niche breadth. Microbial communities were affected by the deterministic processes with a modified stochasticity ratio (MST) value of 36.36 %, whereas more stochasticity (MST = 49.71 %) was raised in contaminated farmland than in undisturbed forestland (MST = 36.98 %). The microbial function based on taxonomy-based inference indicated that nitrogen and carbon metabolisms associated with archaea and bacteria increased in contaminated farmland, as well as plant pathogen, wood saprotroph and endophyte related with fungi. The turnover of soil microbiomes was tightly correlated with As and Sb speciation. Collectively, this study reveals that the soil microbial survival strategies to As-Sb co-contamination after dam failure, providing guidance for the development of bioremediation and tailings management strategies.

Antimony resistant bacteria isolated from Budúcnosť adit (Pezinok-Kolársky vrch deposit) in western Slovakia

Potentially toxic elements (PTE), such as antimony (Sb), are dangerous putative contaminants for ground and surface waters around abandoned mines and ore deposits in Slovakia. Nearby mines antimony is commonly coprecipitated in ochre sediments precipitated from Fe-rich drainage waters and, therefore, these sites function as natural scavengers of this metalloid. Bacteria are well known to contribute to the process of redox state maintenance, biosorption and bioaccumulation of antimony and, consequently, to antimony precipitation or release from iron oxides complexes. Here we isolated 48 bacterial strains from circumneutral hydrous ferric oxides (HFO) rich iron ochres accumulated in the waters running from tailing pounds nearby Budúcnosť mine, Pezinok, Slovakia and polluted with high, but fluctuating, concentrations of antimony (130 μg/l Sb in water and 2317 mg/kg Sb in iron ochre in average). The isolated strains were V1-V9 16S rRNA sequenced and the resulting taxonomic affiliations of isolated strains were compared with taxonomy assignments obtained by V4 16S rRNA next generation sequencing approach, including two independent NGS analysis pipelines and different taxonomy classifiers ((IDTAXA (RDP, GTDB, SILVA, CONTAX), MEGAN (NCBI), RDP a SILVAngs). A Sb resistant subgroup of isolated strains (Pseudomonas A60B, Pseudomonas A59, Pseudomonas A28, Aeromonas A21, Aeromonas A13, Aeromonas A60A, Acinetobacter A14, Buttiauxella A58, Shewanella A20A a Yersinia A68), well growing at high Sb concentration (300 mg/l Sb), was tested for an ability of the strains to retain Sb from cultivation media. Based on ICP-MS measurements of the dried biomasses we concluded that all the strains can retain antimony from growth media to some extent, with strains Shewanella A20A, Buttiauxella A58, Yersinia A68 and Aeromonas A60A being the most effective.

Biochemical transformation and bioremediation of thallium in the environment

Thallium (Tl) is a toxic element associated with minerals, and its redistribution is facilitated by both geological and anthropogenic activities. In the natural environment, the transformation and migration of Tl mediated by (micro)organisms have attracted increasing attention. This review presents an overview of the biochemical transformation of Tl and the bioremediation strategies for Tl contamination. In the environment, Tl exists in various forms and originates from diverse sources. The global distribution characteristics of Tl in various media are summarized here, while its speciation and toxicity mechanism to organisms are elucidated. Interactions between (micro)organisms and Tl are commonly observed in the environment. Microbial response mechanisms to typical Tl exposure are analyzed at both species and gene levels, and the possibility of microorganisms as bio-indicators for monitoring Tl contamination is also highlighted. The processes and mechanisms involved in the microbial and benthic mediated transformation of Tl, as well as its enrichment by plants, are discussed. Additionally, in situ bioremediation strategies for Tl contamination and bio-treatment techniques for Tl-containing wastewater are summarized. Finally, the existing knowledge gaps and future research challenges are emphasized, including Tl distribution characteristics in the atmosphere and ocean, the key molecular mechanisms underlying Tl transformation by organisms, the screening of potential Tl oxidizing microorganisms and hyperaccumulators, as well as the revelation of global biogeochemical cycling pathways of Tl.

Using Sediment Bacterial Communities to Predict Trace Metal Pollution Risk in Coastal Environment Management: Feasibility, Reliability, and Practicability

The distribution of trace metals (TMs) in a continuous water body often exhibits watershed attributes, but the tidal gates of the coastal rivers may alter their transformation and accumulation patterns. Therefore, a tidal gate-controlled coastal river was selected to test the distribution and accumulation risks of Al, As, Cr, Cu, Fe, Mn, Ni, Sr, and Zn in the catchment area (CA), estuarine area (EA), and offshore area (OA). Associations between TMs and bacterial communities were analyzed to assess the feasibility of using bacterial parameters as ecological indicators. The results showed that As and Cr were the key pollutants due to the higher enrichment factor and geoaccumulation index, reaching slight to moderate pollution levels. The Nemero index was highest in EAs (14.93), indicating a higher pollution risk in sediments near tide gates. Although the TM dynamics can be explained by the metal-indicating effects of Fe and Mn, they have no linear relationships with toxic metals. Interestingly, the metabolic abundance of bacterial communities showed good correlations with different TMs in the sediment. These results highlight bacterial community characteristics as effective biomarkers for assessing TM pollution and practical tools for managing pollution control in coastal environment.

Bacterial community composition and function vary with farmland type and soil depth around a mining area

Heavy metal pollution can have adverse impacts on microorganisms, plants and even human health. To date, the impact of heavy metals on bacteria in farmland has yielded poor attention, and there is a paucity of knowledge on the impact of land type on bacteria in mining area with heavy metal pollution. Around a metal-contaminated mining area, two soil depths in three types of farmlands were selected to explore the composition and function of bacteria and their correlations with the types and contents of heavy metals. The compositions and functions of bacterial communities at the three different agricultural sites were disparate to a certain extent. Some metabolic functions of bacterial community in the paddy field were up-regulated compared with those at other site. These results observed around mining area were different from those previously reported in conventional farmlands. In addition, bacterial community composition in the top soils was relatively complex, while in the deep soils it became more unitary and extracellular functional genes got enriched. Meanwhile, heavy metal pollution may stimulate the enrichment of certain bacteria to protect plants from damage. This finding may aid in understanding the indirect effect of metal contamination on plants and thus putting forward feasible strategies for the remediation of metal-contaminated sites. MAIN FINDINGS OF THE WORK: This was the first study to comprehensively explore the influence of heavy metal pollution on the soil bacterial communities and metabolic potentials in different agricultural land types and soil depths around a mining area.

Effective co-immobilization of arsenic and cadmium in contaminated soil by sepiolite-modified nano-zero-valent iron and its impact on the soil bacterial community

Sepiolite-modified nano-zero-valent iron (S-nZVI) is used as an amendment and incubated to remediate As-Cd-contaminated soil under three different soil‒water management conditions [moderately wet (MW), continuously flooded (CF) and alternately wet and dry (AWD)]. The results showed that soil pH is in the order of CF > AWD > MW. The soil pH increased approximately 0.5 to 1 unit by 3% and 5% doses after 36 d of incubation. Soil pH was negatively correlated with available As-Cd content under the three water regimes (p < 0.01). All doses of S-nZVI significantly reduced soil available As-Cd under the three soil moistures by 45-80% for As and 5-45% for Cd. Moreover, S-nZVI addition also promoted the transformation of As-Cd in the acid-extracted fraction, oxidation fraction, and reduced fraction to a more stable residue fraction. High-throughput sequencing results showed that high doses of S-nZVI had a significant adverse effect on soil bacterial diversity and richness. After 36 d of incubation, the Chao1 index and the Shannon index were significantly decreased in MW, CF, and AWD, respectively. Decreasing the S-nZVI dose and increasing the incubation time simultaneously reduced As-Cd availability and S-nZVI ecotoxicity in the soil, thereby effectively maintaining the survivability of the original dominant bacteria, increasing the soil pH, and promoting the interaction between dominant bacteria and soil factors in As-Cd cocontaminated soil.

Sulfate-reducing consortium HQ23 stabilizes metal(loid)s and activates biological N-fixation in mixed heavy metal-contaminated soil

Sulfate-reducing bacteria (SRB) are used in the remediation of mine pollution; however, the mechanism of stabilizing multiple heavy metal(loid)s by the SRB consortium under low oxygen conditions needs further study. Indigenous microflora were extracted from non-ferrous metal-contaminated soil co-inoculated with enriched SRB consortium and assembled as the HQ23 consortium. The presence of Desulfovibrio (SRB) in HQ23 was confirmed by 16S rRNA sequencing and qPCR. The effects of culture media, dissolved oxygen (DO), SO42¯, and pH on the HQ23 growth rate, and the SO42¯-reducing activity were examined. Data indicates that the HQ23 sustained SRB function under low DO conditions (3.67 ± 0.1 mg/L), but the SRB activity was inhibited at high DO content (5.75 ± 0.39 mg/L). The HQ23 can grow from pH 5 to pH 9 and can decrease mobile or bioavailable Cr, Cu, and Zn concentrations in contaminated soil samples. FTIR revealed that Cu and Cr adsorbed to similar binding sites on bacteria, likely decreasing bacterial Cu toxicity. Increased abundances of DSV (marker for Desulfovibrio) and nifH (N-fixation) genes were observed, as well as an accumulation of nitrate-N content in soils suggesting that HQ23 stimulates the biological N-fixation in soils. This study strongly supports the future application of SRB for the bioremediation of heavy metal-polluted sites.

Coupled redox cycling of arsenic and sulfur regulates thioarsenate enrichment in groundwater

High‑arsenic groundwater is influenced by a combination of processes: reductive dissolution of iron minerals and formation of secondary minerals, metal complexation and redox reactions of organic matter (OM), and formation of more migratory thioarsenate, which together can lead to significant increases in arsenic concentration in groundwater. This study was conducted in a typical sulfur- and arsenic-rich groundwater site within the Datong Basin to explore the conditions of thioarsenate formation and its influence on arsenic enrichment in groundwater using HPLC-ICPMS, hydrogeochemical modeling, and fluorescence spectroscopy. The shallow aquifer exhibited a highly reducing environment, marked by elevated sulfide levels, low concentrations of Fe(II), and the highest proportion of thioarsenate. In the middle aquifer, an optimal ∑S/∑As led to the presence of significant quantities of thioarsenate. In contrast, the deep aquifer exhibited low sulfide and high Fe(II) concentration, with arsenic primarily originating from dissolved iron minerals. Redox fluctuations in the sediment driven by sulfur‑iron minerals generated reduced sulfur, thereby facilitating thioarsenate formation. OM played a crucial role as an electron donor for microbial activities, promoting iron and sulfate reduction processes and creating conditions conducive to thioarsenate formation in reduced and high‑sulfur environments. Understanding the process of thioarsenate formation and the influencing factors is of paramount importance for comprehending the migration and redistribution of arsenic in groundwater systems.

Combined toxicity of Cd and aniline to soil bacteria varying with exposure sequence

Joint toxicity of organic-metal co-contamination can vary depending on organisms, toxicants, and even the sequence of exposure. This study examines how the combined toxicity of aniline (An) and cadmium (Cd) to soil bacteria in microcosms changes when the order of contaminant introduction is altered. Through analyzing biodiversity, molecular ecological network, functional redundancy, functional genes and pathways, we find the treatment of Cd followed by An brings about the strongest adverse impact to the bacterial consortium, followed by the reverse-ordered exposure and the simple mixture of the two chemicals. On the level of individual organisms, exposure sequence also affects the bacteria that are otherwise resistant to the standalone toxicity of both An and Cd. The dynamic behavior of aniline-cadmium composite is interpreted by considering the tolerance of organisms to individual chemicals, the interactions of the two toxicants, the recovery time, as well as the priority effect. The overall effect of the composite contamination is conceptualized by treating the chemicals as environmental filters screening the growth of the community.

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.

Pioneer plants enhance soil multifunctionality by reshaping underground multitrophic community during natural succession of an abandoned rare earth mine tailing

Spontaneous natural succession in metal mine tailings is fundamental to the rehabilitation of bare tailing. Here, an abandoned rare earth element (REE) mine tailing with spontaneous colonisation by pioneer plants with different functional traits was selected. Soil nutrient cycling, fertility, organic matter decomposition as well as underground organismal communities and their multitrophic networks were investigated. Compared with the bare tailing, the colonisation with Lycopodium japonicum, Miscanthus sinensis, and Dicranopteris dichotoma increased soil multifunction by 222%, 293%, and 525%, respectively. This was accompanied by significant changes in soil bacterial and protistan community composition and increased soil multitrophic network complexity. Rhizospheres of different plant species showed distinct microbial community composition compared to that of bare tailing. Some WPS-2, Chloroflexi, and Chlorophyta were mainly present in the bare tailing, while some Proteobacteria and Cercozoa were predominantly seen in the rhizosphere. Pearson correlation and Random Forest revealed the biotic factors driving soil multifunction. Structural equation modelling further revealed that pioneer plants improved soil multifunction primarily by decreasing the microbial biodiversity and increasing the multitrophic network complexity. Overall, this highlights the importance of subterrestrial organisms in accelerating soil rehabilitation during natural succession and provides options for the ecological restoration of degraded REE mining areas.

Effects of denitrification on speciation and redistribution of arsenic in estuarine sediments

Microbially-mediated redox processes involving arsenic (As) and its host minerals significantly contribute to the mobilization of As in estuarine sediments. Despite its significance, the coupling between As dynamics and denitrification processes in these sediments is not well understood. This study employed sequential sediment extractions and simultaneous monitoring of dissolved iron (Fe), nitrogen (N), and sulfur (S) to investigate the impact of nitrate (NO3-) on the speciation and redistribution of As, alongside changes in microbial community composition. Our results indicated that NO3- additions significantly enhance anaerobic arsenite (As(III)) oxidation, facilitating its immobilization by increased adsorption onto sediment matrices in As-contaminated estuarine settings. Furthermore, NO3- promoted the conversion of As bound to troilite (FeS) and pyrite (FeS2) into forms associated with Fe oxides, challenging the previously assumed stability of FeS/FeS2-bound As in such environments. Continuous NO3- additions ensured As and Fe oxidation, thereby preventing their reductive dissolution and stabilizing the process that reduces As mobility. Changes in the abundance of bacterial communities and correlation analyses revealed that uncultured Anaerolineaceae and Thioalkalispira may be the main genus involved in these transformations. This study underscores the critical role of NO3- availability in modulating the biogeochemical cycle of As in estuarine sediments, offering profound insights for enhancing As immobilization techniques and informing environmental management and remediation strategies in As-contaminated coastal regions.

Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes

Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4+, NO2- and SO42, while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.

Sb/As immobilization and soil function improvement under the combined remediation strategy of modified biochar and Sb-oxidizing bacteria at a smelting site

Antimony (Sb) and arsenic (As) lead to soil pollution and structural degradation at Sb smelting sites. However, most sites focus solely on Sb/As immobilization, neglecting the restoration of soil functionality. Here, we investigated the effectiveness of Fe/H2O2 modified biochar (Fe@H2O2-BC) and Sb-oxidizing bacteria (Bacillus sp. S3) in immobilizing Sb/As and enhancing soil functional resilience at an Sb smelting site. Over a twelve-month period, the leaching toxicity of As and Sb was reduced to 0.05 and 0.005 mg L-1 (GB3838-2002) respectively, with 1% (w/w) Fe@H2O2-BC and 2% (v/v) Bacillus sp. S3 solution. Compared to CK, the combination of Fe@H2O2-BC and Bacillus sp. S3 significantly reduced the bioavailable As/Sb by 98.00%/93.52%, whilst increasing residual As and reducible Sb fractions by 210.31% and 96.51%, respectively. The combined application generally improved soil aggregate structure, pore characteristics, and water-holding capacity. Fe@H2O2-BC served as a pH buffer and long-term reservoir of organic carbon, changing the availability of carbon substrates to bacteria. The inoculation of Bacillus sp. S3 facilitated the transformation of Sb(III)/As(III) to Sb(V)/As(V) and differentiated the composition and functional roles of bacterial communities in soils. The combination increased the abundance of soil saprotrophs by 164.20%, whilst improving the relative abundance of N- and S-cycling bacteria according to FUNGuild and FAPROTAX analysis. These results revealed that the integrated application was instrumental in As/Sb detoxification/immobilization and soil function restoration, which demonstrating a promising microbially-driven ecological restoration strategy at Sb smelting sites.

Arsenic stress on soil microbial nutrient metabolism interpreted by microbial utilization of dissolved organic carbon

In a 120-day microcosm incubation experiment, we investigated the impact of arsenic contamination on soil microbial nutrient metabolism, focusing on carbon cycling processes. Our study encompassed soil basal respiration, key enzyme activities (particularly, β-1,4-N-acetylglucosaminidase and phosphatases), microbial biomass, and community structure. Results revealed a substantial increase (1.21-2.81 times) in β-1,4-N-acetylglucosaminidase activities under arsenic stress, accompanied by a significant decrease (9.86%-45.20%) in phosphatase activities (sum of acid and alkaline phosphatases). Enzymatic stoichiometry analysis demonstrated the mitigation of microbial C and P requirements in response to arsenic stress. The addition of C-sources alleviated microbial C requirements but exacerbated P requirements, with the interference amplitude increasing with the complexity of the C-source. Network analysis unveiled altered microbial nutrient requirements and an increased resistance process of microbes under arsenic stress. Microbial carbon use efficiency (CUE) and basal respiration significantly increased (1.17-1.59 and 1.18-3.56 times, respectively) under heavy arsenic stress (500 mg kg-1). Arsenic stress influenced the relative abundances of microbial taxa, with Gemmatimonadota increasing (5.5-50.5%) and Bacteroidota/ Nitrospirota decreasing (31.4-47.9% and 31.2-63.7%). Application of C-sources enhanced microbial resistance to arsenic, promoting cohesion among microorganisms. These findings deepen our understanding of microbial nutrient dynamics in arsenic-contaminated areas, which is crucial for developing enzyme-based toxicity assessment systems for soil arsenic contamination.

The rhizosphere microbiome reduces the uptake of arsenic and tungsten by Blechnum orientale by increasing nutrient cycling in historical tungsten mining area soils

The growth of pioneer plants in metal mining area soil is closely related to their minimal uptake of toxic elements. Pioneer plants can inhibit the uptake of toxic elements by increasing nutrient uptake. However, few studies have focused on the mechanisms by which the rhizosphere microbiome affect nutrient cycling and their impact on the uptake of toxic elements by pioneer plants. In this study, we selected Blechnum orientale to investigate the potential roles of the rhizosphere microbiome in nutrient cycling and plant growth in a historical tungsten (W) mining area. Our results showed that while the arsenic (As) and W contents in the soil were relatively high, the enrichment levels of As and W in the B. orientale were relatively low. Furthermore, we found that the As and W contents in plants were significantly negatively correlated with soil nutrients (S, P and Mo), suggesting that elevated levels of these soil nutrients could inhibit As and W uptake by B. orientale. Importantly, we found that these nutrients were also identified as the most important factors shaping rhizosphere microbial attributes, including microbial diversity, ecological clusters, and keystone OTUs. Moreover, the genera, keystone taxa and microbial functional genes enriched in the rhizosphere soils from mining areas played a key role in nutrient (S, P and Mo) bioavailability, which could further increase the nutrient uptake by B. orientale. Taken together, our results suggest that rhizosphere microorganisms can improve pioneer plant growth by inhibiting toxic element accumulation via the increase in nutrient cycling in former W mining areas.

Impacts of o-cresol spill on composition and function of river sediment and soil microbial communities

o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.

Bacterial community in the metal(loid)-contaminated marine vertical sediments of Jinzhou Bay: Impacts and adaptations

Metal(loid) discharge has led to severe coastal contamination; however, there remains a significant knowledge gap regarding its impact on sediment profiles and depth-resolved bacterial communities. In this study, geochemical measurements (pH, nutrient elements, total and bioavailable metal(loid) content) consistently revealed decreasing nitrogen, phosphorus, and metal(loid) levels with sediment depth, accompanied by reduced alpha diversity. Principal coordinate analysis indicated distinct community compositions with varying sediment depths, suggesting a geochemical influence on diversity. Ecological niche width expanded with depth, favoring specialists over generalists, but both groups decreased in abundance. Taxonomic shifts emerged, particularly in phyla and families, correlated with sediment depth. Microbe-microbe interactions displayed intricate dynamics, with keystone taxa varying by sediment layer. Zinc and arsenic emerged as key factors impacting community diversity and composition using random forest, network analysis, and Mantel tests. Functional predictions revealed shifts in potential phenotypes related to mobile elements, biofilm formation, pathogenicity, N/P/S cycles, and metal(loid) resistance along sediment profiles. Neutral and null models demonstrated a transition from deterministic to stochastic processes with sediment layers. This study provides insights into the interplay between sediment geochemistry and bacterial communities across sediment depths, illuminating the factors shaping these ecosystems.

Metagenomic insights into the toxicity of carbamazepine to functional microorganisms in sludge anaerobic digestion

Contaminants of emerging concern (CECs) contained in sludge, such as carbamazepine, may be toxic to microorganisms and affect the biogenesis of methane during anaerobic digestion. In this study, different scales of anaerobic digesters were constructed to investigate the inhibitory effect of carbamazepine. Results showed that carbamazepine reduced methane production by 11.3 % and 62.1 % at concentrations of 0.4 and 2 mg/g TS, respectively. Carbamazepine hindered the dissolution of organic matter and the degradation of protein. Carbamazepine inhibited some fermentative bacteria, especially uncultured Aminicenantales, whose abundance decreased by 9.5-93.4 % under carbamazepine stress. It is worth noting that most prior studies investigated the effects of CECs only based on well-known microorganisms, ignoring the metabolisms of uncultured microorganisms. Genome-predicted metabolic potential suggested that 54 uncultured metagenome-assembled genomes (MAGs) associated with acidogenesis or acetogenesis. Therein, uncultured Aminicenantales related MAGs were proved to be acetogenic fermenters, their significant reduction may be an important reason for the decrease of methane production under carbamazepine stress. The toxicity of carbamazepine to microorganisms was mainly related to the overproduction of reactive oxygen species. This study elucidates the inhibition mechanism of carbamazepine and emphasizes the indispensable role of uncultured microorganisms in anaerobic digestion.

Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas

Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.

Efficient stabilization of arsenic migration and conversion in soil with surfactant-modified iron-manganese oxide: Environmental effects and mechanistic insights

The use of iron-manganese oxide (FMO) as a promising amendment for remediating arsenic (As) contamination in soils has gained attention, but its application is limited owing to agglomeration issues. This study aims to address agglomeration using surfactant-modified FMO and investigate their stabilization behavior towards As and resulting environmental changes upon amendments. The results confirmed the efficacy of surfactants and demonstrated that cetyltrimethylammonium-bromide-modified FMO significantly reduced the leaching concentration of As by 92.5 % and effectively suppressed the uptake of As by 85.8 % compared with the control groups. The ratio of the residual fraction increased from 30.5-41.6 % in unamended soil to 67.9-69.2 %. The number of active sites was through the introduction of surfactants and immobilized As via complexation, ion exchange, and redox reactions. The study also revealed that amendments and the concentration of As influenced the soil physicochemical properties and enriched bacteria associated with As and Fe reduction and changed the distribution of C, N, Fe, and As metabolism genes, which promoted the stabilization of As. The interactions among cetyltrimethylammonium bromide, FMO, and microorganisms were found to have the greatest effect on As immobilization.

Human-induced homogenization of microbial taxa and function in a subtropical river and its impacts on community stability

Combination of taxa and function can provide a more comprehensive picture on human-induced microbial homogenization. Here, we obtained 2.58 billion high-throughput sequencing reads and 479 high-quality metagenome-assembled genomes (MAGs) of planktonic microbial communities in a subtropical river for 5 years. We found the microbial taxa homogenization and functional homogenization were uncoupled. Although human activities in downstream sites significantly decreased the taxonomic diversity of non-abundant ASV communities (16S rRNA gene amplicon sequence variants), they did not significantly decrease the taxonomic diversity of abundant ASV and total observed MAG communities. However, the total observed MAG communities in downstream sites tended to homogenize into some specific taxa which encode human-activity-related functional genes, such as nutrient cycles, greenhouse gas emission, antibiotic and arsenic resistance. Those specific MAGs with high taxonomic diversity caused the weak heterogenization of total observed MAG communities in downstream sites. Moreover, functional homogenization promoted the synchrony among downstream MAGs, and these MAGs constructed some specific network modules might to synergistically execute or resist the human-activity-related functions. High synchrony also led to the tandem effects among MAGs and thus decreased community stability. Overall, our findings revealed the links of microbial taxa, functions and stability under human activity impacts, and provided a strong evidence to encourage us re-thinking biotic homogenization based on microbial taxa and their functional attributes.

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils

Microbial arsenic transformations play essential roles in controlling pollution and ameliorating risk. This study combined high-throughput sequencing and PCR-based approaches targeting both the 16 S rRNA and arsenic functional genes to investigate the temporal and spatial dynamics of the soil microbiomes impacted by high arsenic contamination (9.13 to 911.88 mg/kg) and to investigate the diversity and abundance of arsenic functional genes in soils influenced by an arsenic gradient. The results showed that the soil microbiomes were relatively consistent and mainly composed of Actinobacteria (uncultured Gaiellales and an unknown_67 - 14 bacterium), Proteobacteria, Firmicutes (particularly, Bacillus), Chloroflexi, and Acidobacteria (unknown_Subgroup_6). Although a range of arsenic functional genes (e.g., arsM, arsC, arrA, and aioA) were identified by shotgun metagenomics, only the arsM gene was detected by the PCR-based method. The relative abundance of the arsM gene accounted for 0.20%-1.57% of the total microbial abundance. Combining all analyses, arsenic methylation mediated by the arsM gene was proposed to be a key process involved in the arsenic biogeochemical cycle and mitigation of arsenic toxicity. This study advances our knowledge about arsenic mechanisms over the long-term in highly contaminated soils.

Reaction pathways and Sb(III) minerals formation during the reduction of Sb(V) by Rhodoferax ferrireducens strain YZ-1

Antimony (Sb), a non-essential metalloid, can be released into the environment through various industrial activities. Sb(III) is considered more toxic than Sb(V), but Sb(III) can be immobilized through the precipitation of insoluble Sb2S3 or Sb2O3. In the subsurface, Sb redox chemistry is largely controlled by microorganisms; however, the exact mechanisms of Sb(V) reduction to Sb(III) are still unclear. In this study, a new strain of Sb(V)-reducing bacterium, designated as strain YZ-1, that can respire Sb(V) as a terminal electron acceptor was isolated from Sb-contaminated soils. 16S-rRNA gene sequencing of YZ-1 revealed high similarity to a known Fe(III)-reducer, Rhodoferax ferrireducens. XRD and XAFS analyses revealed that bioreduction of Sb(V) to Sb(III) proceed through a transition from amorphous valentinite to crystalline senarmontite (allotropes of Sb2O3). Genomic DNA sequencing found that YZ-1 possesses arsenic (As) metabolism genes, including As(V) reductase arsC. The qPCR analysis showed that arsC was highly expressed during Sb(V)-reduction by YZ-1, and thus is proposed as the potential Sb(V) reductase in YZ-1. This study provides new insight into the pathways and products of microbial Sb(V) reduction and demonstrates the potential of a newly isolated bacterium for Sb bioremediation.

Remediation of arsenic-contaminated soil using nanoscale schwertmannite synthesized by persulfate oxidation with carboxymethyl cellulose stabilization

Schwertmannite (SCH) is a promising material for adsorbing inorganic arsenic (As). We synthesized SCH nanoparticles (nano-SCH) via a modified chemical oxidation method and investigated the application of nano-SCH for the remediation of As-contaminated soils. The production of nano-SCH was successfully prepared using the persulfate oxidation method with carboxymethyl cellulose stabilization. The spherical structure of the nano-SCH particles had an average hydrodynamic diameter of 296 nm with high specific surface areas (108.9 m2/g). Compared with SCH synthesized via the H2O2 oxidation method, the percentage of Fe3+ precipitation in nano-SCH synthesis increased from 63.2% to 84.1%. The inorganic As adsorption capacity of nano-SCH improved by 2.27 times at solution pH = 6. After remediation of heavily As-contaminated soils by using 5% nano-SCH, the leachability of inorganic As rapidly decreased to 0.01% in 30 d. Correspondingly, the immobilization efficiencies of inorganic As in soil reached >99.9%. The inorganic As fractions in treated soil shifted from specifically and nonspecifically bound forms to amorphous and crystalline hydrous oxide-bound fractions. After treatment with 5% nano-SCH for 60 d, soil pH slightly decreased from 5.47 to 4.94; by contrast, soil organic matter content increased by 20.9%. Simultaneously, dehydrogenase concentration in soil decreased by 22.4%-34.7% during the remediation process. These changes in soil properties and As immobilization jointly decreased microbial activity and initiated the re-establishment of bacterial communities in the soil. In summary, this study presents a novel and high-productivity technology for nano-SCH synthesis and confirms the high As immobilization effectiveness of nano-SCH in the remediation of As-contaminated soils.

Nano zero-valent iron and melatonin synergistically alters uptake and translocation of Cd and As in soil-rice system and mechanism in soil chemistry and microbiology

Nanoscale zero-valent iron (Fe) is a promising nanomaterial for remediating heavy metal-contaminated soils. Melatonin (MT) is essential to alleviate environmental stress in plants. However, the conjunction effects of Fe and MT (FeMT) on rice Cd, As accumulation and the mechanism of soil chemical and microbial factors interaction are unclear. Here, a pot experiment was conducted to evaluated the effects of the FeMT for rice Cd, As accumulation and underlying mechanisms. The findings showed that FeMT significantly reduced grains Cd by 92%-87% and As by over 90%, whereas improving grains Fe by over 213%. Soil available-Cd and iron plaques-Cd (extracted by dithionite-citrate-bicarbonate solution, DCB-Cd) significantly regulated roots Cd, thus affected Cd transport to grains. Soil pH significantly affected soil As and DCB-As, which further influenced roots As uptake and the transport to shoots and grains. The interactions between the soil bacterial community and soil Fe, available Fe, and DCB-Fe together affected root Fe absorption and transportation in rice. FeMT significantly influenced rhizosphere soil bacterial α- and β-diversity. Firmicutes as the dominant phylum exhibited a significant positive response to FeMT measure, and acted a key role in reducing soil Cd and As availability mainly by improving iron-manganese plaques. The increase of soil pH caused by FeMT was beneficial only for Actinobacteriota growth, which reduced Cd, As availability probably through complexation and adsorption. FeMT also showed greater potential in reducing human health and ecological risks by rice consumption and straw returning. These results showed the important role of both soil chemical and microbial factors in FeMT-mediated rice Cd, As reduction efficiency. This study opens a novel strategy for safe rice production and improvement of rice iron nutrition level in heavy-metals polluted soil, but also provides new insights into the intricate regulatory relationships among soil biochemistry, toxic elements, microorganism, and plants.

Heavy metal contamination impacts the structure and co-occurrence patterns of bacterial communities in agricultural soils

Heavy metal (HM) contamination caused by mining and smelting activities can be harmful to soil microbiota, which are highly sensitive to HM stress. Here, we explore the effects of HM contamination on the taxonomic composition, predicted function, and co-occurrence patterns of soil bacterial communities in two agricultural fields with contrasting levels of soil HMs (i.e., contaminated and uncontaminated natural areas). Our results indicate that HM contamination does not significantly influence soil bacterial α diversity but changes the bacterial community composition by enriching the phyla Gemmatimonadetes, Planctomycetes, and Parcubacteria and reducing the relative abundance of Actinobacteria. Our results further demonstrate that HM contamination can strengthen the complexity and modularity of the bacterial co-occurrence network but weaken positive interactions between keystone taxa, leading to the gradual disappearance of some taxa that originally played an important role in healthy soil, thereby possibly reducing the resistance of bacterial communities to HM toxicity. The predicted functions of bacterial communities are related to membrane transport, amino acid metabolism, energy metabolism, and carbohydrate metabolism. Among these, functions related to HM detoxification and antioxidation are enriched in uncontaminated soils, while HM contamination enriches functions related to metal resistance. This study demonstrated that microorganisms adapt to the stress of HM pollution by adjusting their composition and enhancing their network complexity and potential ecological functions.

Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments

Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.

Geochemical properties, heavy metals and soil microbial community during revegetation process in a production Pb-Zn tailings

Lead-zinc (Pb-Zn) tailings pose a significant environmental threat from heavy metals (HMs) contamination. Revegetation is considered as a green path for HM remediation. However, the interplay between HM transport processes and soil microbial community in Pb-Zn tailings (especially those in production) remain unclear. This study investigated the spatial distribution of HMs as well as the crucial roles of the soil microbial community (i.e., structure, richness, and diversity) during a three-year revegetation of production Pb-Zn tailings in northern Guangdong province, China. Prolonged tailings stockpiling exacerbated Pb contamination, elevating concentrations (from 10.11 to 11.53 g/kg) in long-term weathering. However, revegetation effectively alleviated Pb, reducing its concentrations of 9.81 g/kg. Through 16 S rRNA gene amplicon sequencing, the dominant genera shifted from Weissella (44%) to Thiobacillus (17%) and then to Pseudomonas (comprising 44% of the sequences) during the revegetation process. The structural equation model suggested that Pseudomonas, with its potential to transform bioavailable Pb into a more stable form, emerged as a potential Pb remediator. This study provides essential evidence of HMs contamination and microbial community dynamics during Pb-Zn tailings revegetation, contributing to the development of sustainable microbial technologies for tailings management.

Ammonium-Enhanced Arsenic Mobilization from Aquifer Sediments

Ammonium-related pathways are important for groundwater arsenic (As) enrichment, especially via microbial Fe(III) reduction coupled with anaerobic ammonium oxidation; however, the key pathways (and microorganisms) underpinning ammonium-induced Fe(III) reduction and their contributions to As mobilization in groundwater are still unknown. To address this gap, aquifer sediments hosting high As groundwater from the western Hetao Basin were incubated with 15N-labeled ammonium and external organic carbon sources (including glucose, lactate, and lactate/acetate). Decreases in ammonium concentrations were positively correlated with increases in the total produced Fe(II) (Fe(II)tot) and released As. The molar ratios of Fe(II)tot to oxidized ammonium ranged from 3.1 to 3.7 for all incubations, and the δ15N values of N2 from the headspace increased in 15N-labeled ammonium-treated series, suggesting N2 as the key end product of ammonium oxidation. The addition of ammonium increased the As release by 16.1% to 49.6%, which was more pronounced when copresented with organic electron donors. Genome-resolved metagenomic analyses (326 good-quality MAGs) suggested that ammonium-induced Fe(III) reduction in this system required syntrophic metabolic interactions between bacterial Fe(III) reduction and archaeal ammonium oxidation. The current results highlight the significance of syntrophic ammonium-stimulated Fe(III) reduction in driving As mobilization, which is underestimated in high As groundwater.

Dominant role of rare bacterial taxa rather than abundant taxa in driving the tailing primary succession

Primary ecological succession is imperative for tailing vegetation, driven notably by microbes that enhance tailing nutrient status. Yet, the roles of abundant and rare taxa in tailing primary succession remain underexplored. This study investigates these subcommunities across three succession stages (i.e., original tailing, biological crusts, grasslands). Throughout primary succession, alpha diversity and functional gene abundances of the rare taxa (RT) group consistently rise from bare tailings to grasslands. Conversely, the abundant taxa (AT) group displays an opposing trend. Intriguingly, employing co-occurrence networks, keystone taxa, mantel tests, similarity percentage analysis, and structural equation model, the study uncovers that RT wields a more pivotal role than AT in driving tailing primary succession. Community assembly analysis reveals stochastic control of AT and deterministic control of RT. Additionally, primary succession reinforces stochastic processes in AT, while RT's deterministic process remains unaffected. By unveiling these dynamics, the research enriches our understanding of primary ecological succession in tailings. Recognition of unique diversity patterns and community assembly mechanisms for rare and abundant subcommunities advances tailing ecosystem comprehension and informs ecological restoration strategies. This study thus contributes valuable insights to the complex interplay of microbial taxa during tailing primary succession.

Washing antimony and arsenic from agricultural soil with eco-friendly organic acids and the relevant bioavailability assessment

Antimony (Sb) and arsenic (As) contamination in agricultural soil poses human health risks through agricultural products. Soil washing with degradable low molecular weight organic acids (LMWOAs) is an eco-friendly strategy to remediate agricultural soils. In this study, three eco-friendly LMWOAs, oxalic acid (OA), tartaric acid (TA), and citric acid (CA), were used to treat Sb and As co-contaminated agricultural soil from Xikuangshan mine area. The OA, TA, and CA washed out 18.4, 16.8, and 26.6% of Sb and 15.3, 19.9, and 23.8% of As from the agricultural soil, with CA being the most efficient reagent for the soil washing. These organic acids also led to pH decline and macronutrients losses. Fraction analysis using a sequential extraction procedure showed that the three organic acids targeted and decreased the specifically sorbed (F2) (by 19.3-37.6% and 2.41-23.5%), amorphous iron oxide associated (F3) (by 49.1-61.2% and 51.2-70.2%), and crystallized iron oxide associated (F4) (by 12.3-26.0% and 26.1-29.1%) Sb and As. The leachability of Sb and As, as well as their concentrations and bioconcentration factor (BCF) in vegetables reduced due to the soil washing. It demonstrated that the bioavailability of both the elements was decreased by the organic acids washing. The concentrations of Sb and As in typical vegetable species cultivated in CA washed soil were less than the threshold value for consumption safety, while those in OA and TA washed soils were still higher than the value, suggesting that only CA is a potential washing reagent in soil washing for Sb- and As-contaminated agricultural soil.

Association of urinary arsenic metabolism with type 2 diabetes and glucose homeostasis: Cross-sectional and longitudinal associations

BACKGROUND

Previous researches have assessed the relationships of urinary arsenic metabolism with type 2 diabetes (T2D) and glucose-insulin homeostasis, but the results were controversial, and potential mechanisms remain largely unclear.

OBJECTIVES

This study aimed to investigate the cross-sectional and longitudinal associations of urinary arsenic metabolism with T2D prevalence and glucose changes in relatively higher arsenic exposure, and further to evaluate the underlying roles of oxidative damage in these relationships.

METHODS

We included 796 participants at baseline, among them 509 participants were followed up after 2 years. Logistic regression model and leave-one-out approach were applied to evaluate the associations of arsenic metabolism with T2D prevalence. Linear mixed model was conducted to estimate the relationship of arsenic metabolism with glycemic changes over two years. The associations between arsenic metabolism and indicators of oxidative stress were assessed with a linear regression model. We further performed mediation analysis to investigate the role of oxidative stress in the associations of arsenic metabolism with 2-year change of glucose levels.

RESULTS

Higher urinary MMA% increased T2D prevalence and baseline glucose levels. MMA% was positively associated with 2-year change of glucose levels. Moreover, we observed significant dose-response relationship between MMA% and 8-hydroxy-2-deoxyguanosine (8-OHdG). However, the mediating role of 8-OHdG in the association of MMA% and 2-year change of glucose levels was not observed in this population.

CONCLUSIONS

In this population exposure to relatively higher arsenic levels, higher MMA% contributed to increased T2D prevalence and glucose homeostasis disorder. Arsenic metabolism also affected oxidative stress levels, especially 8-OHdG. Further studies are required to investigate the potential mechanisms.

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.

Responses of Phragmites communis and its rhizosphere bacteria to different exposure sequences of molybdenum disulfide and levofloxacin

The effect of the molybdenum disulfide (MoS2)/levofloxacin (LVF) co-exposure was explored on Phragmites communis and rhizosphere soil bacterial communities. The sequence of MoS2/LVF exposure and the different MoS2 dosages (10 mg/kg and 100 mg/kg) contributed to different degrees of effect on the plant after 42 days of exposure. The treatment with priority addition of low dosage MoS2 significantly ameliorated P. communis growth, with root length growing up to 532.22 ± 46.29 cm compared to the sole LVF stress (200.04 ± 29.13 cm). Besides, MoS2 served as an alleviator and reduced the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA) in P. communis under LVF stress, and activated bacteria in rhizosphere soil. These rhizosphere soil microbes assisted in mitigating toxic pollution in the soil and inducing plant resistance to external stress, such as bacteria genera Bacillus, Microbacterium, Flavihumibacter and altererythrobacter. Potential functional profiling of bacterial community indicated the addition of MoS2 contributed to relieve the reduction in functional genes associated with amino acid metabolism and the debilitation of gram_negative and aerobic phenotypic traits caused by LVF stress. This finding reveals the effect of different exposure sequences of MoS2 nanoparticles and antibiotic for plant-soil systems.

Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation

Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass. Microbial community structures differed significantly among growth stages. Metabolisms such as benzenoids and carboxylic acids tended to be enriched in the early growth stage, while lipids and organic heterocyclic compounds dominated in the later stage. From SIP, eight BaP-degrading microbes were identified, and most of which such as Ilumatobacter and Singulisphaera were first linked with BaP biodegradation. Notably, the relationship between the differential metabolites and BaP degradation efficiency further suggested that BaP-degrading microbes might metabolize BaP directly to produce benzenoid metabolites (3-hydroxybenzo[a]pyrene), or utilize benzenoids (phyllodulcin) to stimulate the co-metabolism of BaP in early growth stage; some lipids and organic acids, e.g. 1-aminocyclopropane-1-carboxylic acid, might provide nutrients for the degraders to promote BaP metabolism in later stage. Accordingly, we determined that certain rhizospheric metabolites might regulate the rhizospheric microbial communities at different growth stages, and shift the composition and diversity of BaP-degrading bacteria, thereby enhancing in situ BaP degradation. Our study sheds light on POPs rhizoremediation mechanisms in petroleum-contaminated soils.

Contradictory Impacts of Nitrate on the Dissimilatory Arsenate-Respiring Prokaryotes-Induced Reductive Mobilization of Arsenic from Contaminated Sediments: Mechanism Insight from Metagenomic and Functional Analyses

Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be a key impetus of the reductive dissolution of solid-phase arsenic. However, little is known about the interaction between nitrate and DARPs so far. In this study, we showed that nitrate either inhibited or promoted the DARP population-catalyzed reductive mobilization of As in sediments. Metagenomic analysis of the microbial communities in the microcosms after seven days of As release assays suggested that microbes mainly consisted of: Type-I DARPs having potential to reduce NO3- into NO2- and Type-II DARPs having potential to reduce NO3- to NH4+. We further isolated two cultivable DARPs, Neobacillus sp. A01 and Paenibacillus sp. A02, which represent Type-I and -II DARPs, respectively. We observed that nitrate suppressed A01-mediated release of As(III) but promoted A02-mediated release of As(III). Furthermore, we demonstrated that this observation was due to the fact that nitrite, the end product of incomplete denitrification by Type-I DARPs, suppressed the arrA gene expression per cell and growth of all DARPs, whereas ammonium, the end product of dissimilatory nitrate reduction to ammonium (DNRA) by Type-II DARPs, enhanced the arrA gene expression per cell and significantly promoted the growth of all DARPs. These findings suggest that the actual effects of nitrate on DARP population-catalyzed reductive mobilization of arsenic, largely depend on the ratio of Type-I to Type-II DARPs in sediments.