Desulfurivibrio spp. mediate sulfur-oxidation coupled to Sb(V) reduction, a novel biogeochemical process

Differential Mechanisms of Microbial As(III) and Sb(III) Oxidation and Their Contribution to Tailings Reclamation

Mine tailings are extremely oligotrophic environments frequently contaminated with elevated As and Sb, making As(III) and Sb(III) oxidation potentially important energy sources for the tailing microbiome. Although they have been proposed to share similar metabolic pathways, a systemic comparison of the As(III) and Sb(III) oxidation mechanisms and energy utilization efficiencies requires further elucidation. In this study, we employed a combination of physicochemical, molecular, and bioinformatic analyses to compare the kinetic and genetic mechanisms of As(III) and Sb(III) oxidation as well as their respective energy efficiencies for fueling the key nutrient acquisition metabolisms. Thiobacillus and Rhizobium spp. were identified as functional populations for both As(III) and Sb(III) oxidation in mine tailings by DNA-stable isotope probing. However, these microorganisms mediated As(III) and Sb(III) oxidation via different metabolic pathways, resulting in preferential oxidation of Sb(III) over As(III). Notably, both As(III) and Sb(III) oxidation can facilitate nitrogen fixation and phosphate solubilization in mine tailings, with Sb(III) oxidation being more efficient in powering these processes. Thus, this study provided novel insights into the microbial As(III) and Sb(III) oxidation mechanisms and their respective nutrient acquisition efficiencies, which may be critical for the reclamation of mine tailings.

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.

Can Sb(III)-oxidizing prokaryote also oxidize As(III) under aerobic and anaerobic conditions, and vice versa?

Sb(III) and As(III) share similar chemical features and coexist in the environment. However, their oxidase enzymes have completely different sequences and structures. This raises an intriguing question: Could Sb(III)-oxidizing prokaryotes (SOPs) also oxidize As(III), and vice versa? Regarding this issue, previous investigations have yielded unclear, incorrect and even conflicting data. This work aims to address this matter. First, we prepared an enriched population of SOPs that comprises 55 different AnoA genes, lacking AioAB and ArxAB genes. We found that these SOPs can oxidize both Sb(III) and As(III) with comparable capabilities. To further confirm this finding, we isolated three cultivable SOP strains that have AnoA gene, but lack AioAB and ArxAB genes. We observed that they also oxidize both Sb(III) and As(III) under both anaerobic and aerobic conditions. Secondly, we obtained an enriched population of As(III)-oxidizing prokaryotes (AOPs) from As-contaminated soils, which comprises 69 different AioA genes, lacking AnoA gene. We observed that the AOP population has significant As(III)-oxidizing activities, but lack detectable Sb(III)-oxidizing activities under both aerobic and anaerobic conditions. Therefore, we convincingly show that SOPs can oxidize As(III), but AOPs cannot oxidize Sb(III). These findings clarify the previous ambiguities, confusion, errors or contradictions regarding how SOPs and AOPs oxidize each other's substrate.

Effects of biodegradable microplastics on arsenic migration and transformation in paddy soils: a comparative analysis with conventional microplastics

The combined pollution of microplastics (MPs) and arsenic (As) in paddy soils has attracted more attention worldwide. However, there are few comparative studies on the effects of biodegradable and conventional MPs on As migration and transformation. Therefore, conventional (polystyrene, polyethylene, polyvinyl chloride) and biodegradable (polybutadiene styrene, polylactic acid, polybutylene adipate terephthalate) MPs were selected to explore and demonstrate their influences and mechanism on As migration from paddy soils to overlying water and As speciation transformation through microcosmic experiment with measuring the changes of As chemical distribution, physicochemical indexes and microbial community in paddy soils. The results showed that biodegradable MPs enhanced As migration and transformation more effective than conventional MPs during 60 d. Biodegradable MPs indirectly increased the content of As(Ⅲ) and bioavailable As by changing the microbial community structure and affecting the biogeochemical cycles of carbon, nitrogen, sulfur and iron in soils, and promoted the As migration and transformation. PBS showed the strongest promoting effect, transforming to more As(Ⅲ) (11.43%) and bioavailable As (4.28%) than control. This helps to a better understanding of the effects of MPs on As biogeochemical cycle and to clarify the ecological and food safety risks of their combined pollution in soils.

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.

Biological oxidation of As(III) and Sb(III) by a novel bacterium with Sb(III) oxidase rather than As(III) oxidase under anaerobic and aerobic conditions

Sb and As are chemically similar, but the sequences and structures of Sb(III) and As(III) oxidase are totally distinct. It is thus interesting to explore whether Sb(III) oxidase oxidizes As(III), and if so, how microbial oxidations of Sb(III) and As(III) influence one another. Previous investigations have yielded ambiguous or even erroneous conclusions. This study aimed to clarify this issue. Firstly, we prepared a consortium of Sb(III)-oxidizing prokaryotes (SOPs) by enrichment cultivation. Metagenomic analysis reveals that SOPs with the Sb(III) oxidase gene, but lacking the As(III) oxidase gene are predominant in the SOP community. Despite this, SOPs exhibit comparable Sb(III) and As(III)-oxidizing activities in both aerobic and anaerobic conditions, indicating that at the microbial community level, Sb(III) oxidase can oxidize As(III). Secondly, we isolated a representative cultivable SOP, Ralstonia sp. SbOX with Sb(III) oxidase gene but without As(III) oxidase gene. Genomic analysis of SbOX reveals that this SOP strain has a complete Sb(III) oxidase (AnoA) gene, but lacks As(III) oxidase (AioAB or ArxAB) gene. It is interesting to discover that, besides its Sb(III) oxidation activities, SbOX also exhibits significant capabilities in oxidizing As(III) under both aerobic and anaerobic conditions. Moreover, under aerobic conditions and in the presence of both Sb(III) and As(III), SbOX exhibited a preference for oxidizing Sb(III). Only after the near complete oxidation of Sb(III) did SbOX initiate rapid oxidation of As(III). In contrast, under anaerobic conditions and in the presence of both Sb(III) and As(III), Sb(III) oxidation notably inhibited the As(III) oxidation pathway in SbOX, while As(III) exhibited minimal effects on the Sb(III) oxidation. These findings suggest that SOPs can oxidize As(III) under both aerobic and anaerobic conditions, exhibiting a strong preference for Sb(III) over As(III) oxidation in the presence of both. This study unveils a novel mechanism of interaction within the Sb and As biogeochemical cycles.

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.

Microbial-mediated oxidative dissolution of orpiment and realgar in circumneutral aquatic environments

Arsenic (As) is a toxic metalloid that causes severe environmental contamination worldwide. Upon exposure to aqueous phases, the As-bearing minerals, such as orpiment (As2S3) and realgar (As4S4), undergo oxidative dissolution, in which biotic and abiotic activities both contributed significant roles. Consequently, the dissolved As and S are rapidly discharged through water transportation to broader regions and contaminate surrounding areas, especially in aquatic environments. Despite both orpiment and realgar are frequently encountered in carbonate-hosted neutral environments, the microbial-mediated oxidative dissolution of these minerals, however, have been primarily investigated under acidic conditions. Therefore, the current study aimed to elucidate microbial-mediated oxidative dissolution under neutral aquatic conditions. The current study demonstrated that the dissolution of orpiment and realgar is synergistically regulated by abiotic (i.e., specific surface area (SSA) of the mineral) and biotic (i.e., microbial oxidation) factors. The initial dissolution of As(III) and S2- from minerals is abiotically impacted by SSA, while the microbial oxidation of As(III) and S2- accelerated the overall dissolution rates of orpiment and realgar. In As-contaminated environments, members of Thiobacillus and Rhizobium were identified as the major populations that mediated oxidative dissolution of orpiment and realgar by DNA-stable isotope probing. This study provides novel insights regarding the microbial-mediated oxidative dissolution process of orpiment and realgar under neutral conditions.

Pyrrhotite-dependent microbial reduction and magnetic separation for efficient vanadium detoxification and recovery in contaminated aquifer

Microbial reduction under anaerobic condition is a promising method for remediating vanadate [V(V)] contamination in aquifers, while V(V) may be re-generated with redox fluctuations. The inability to remove vanadium after remediation has become a key issue limiting bioremediation. In this study, we proposed the use of pyrrhotite, a natural mineral with magnetic properties, to immobilize V(V) to insoluble V(IV) under microbial action and remove vanadium from the aquifer using a magnetic field, which could avoid the problem of V(V) recontamination under redox fluctuating conditions. Up to 49.0 ± 4.7 % of vanadium could be removed from the aquifer by the applied magnetic field, and the vanadium in the aquifer after the reaction was mainly in the acid-extractable and reducible states. pH had a strong effect on the magnetic recovery of V(V), while the influence of initial V(V) concentration was weak. Microbial community structure analysis showed that Thiobacillus, Proteiniphilum, Fermentimonas, and Desulfurivibrio played key roles for V(V) reduction and pyrrhotite oxidation. Structural equation model indicated the positive correlation between these genera with the magnetic recovery of vanadium. Real time-qPCR confirmed the roles of functional genes of V(V) reduction (napA and nirK) and SO42- reduction (dsrA) in such biological processes. This study provides a novel route to sustainable V(V) remediation in aquifers, with synchronous recovery of vanadium resources without rebound.

Evaluating the role of rhizosphere microbial home-field advantage in Betula luminifera adaptation to antimony mining areas

It has been established that the coevolution of plants and the rhizosphere microbiome in response to abiotic stress can result in the recruitment of specific functional microbiomes. However, the potential of inoculated rhizosphere microbiomes to enhance plant fitness and the inheritance of adaptive traits in subsequent generations remains unclear. In this study, cross-inoculation trials were conducted using seeds, rhizosphere microbiome, and in situ soil collected from areas of Betula luminifera grown in both antimony mining and control sites. Compared to the control site, plants originating from mining areas exhibited stronger adaptive traits, specifically manifested as significant increases in hundred-seed weight, specific surface area, and germination rate, as well as markedly enhanced seedling survival rate and biomass. Inoculation with mining microbiomes could enhance the fitness of plants in mining sites through a "home-field advantage" while also improving the fitness of plants originating from control sites. During the initial phase of seedling development, bacteria play a crucial role in promoting growth, primarily due to their mechanisms of metal resistance and nutrient cycling. This study provided evidence that the outcomes of long-term coevolution between plants and the rhizosphere microbiome in mining areas can be passed on to future generations. Moreover, it has been demonstrated that transgenerational inheritance and rhizosphere microbiome inoculation are important factors in improving the adaptability of plants in mining areas. The findings have important implications for vegetation restoration and ecological environment improvement in mining areas.

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.

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.

Bacterial diversity and community structure of salt pans from Goa, India

In Goa, salt production from the local salt pans is an age-old practice. These salt pans harbor a rich diversity of halophilic microbes with immense biotechnological applications, as they tolerate extremely harsh conditions. Detecting the existence of these microbes by a metabarcoding approach could be a primary step to harness their potential. Three salt pans viz. Agarwado, Curca, and Nerul adjoining prominent estuaries of Goa were selected based on their unique geographical locations. The sediments of these salt pans were examined for their bacterial community and function by 16S rRNA amplicon-sequencing. These salt pans were hypersaline (400-450 PSU) and alkaline (pH 7.6-8.25), with 0.036-0.081 mg/L nitrite, 0.0031-0.016 mg/L nitrate, 6.66-15.81 mg/L sulfate, and 20.8-25.6 mg/L sulfide. The relative abundance revealed that the Pseudomonadota was dominant in salt pans of Nerul (13.9%), Curca (19.6%), and Agarwado (32.4%). The predominant genera in Nerul, Curca, and Agarwado salt pan sediments were Rhodopirellula (1.12%), Sulfurivermis (1.28%), and Psychrobacter (25.5%) respectively. The highest alpha diversity (Shannon-diversity Index) was observed in the Nerul salt pan (4.8) followed by Curca (4.3) and Agarwado (2.03). Beta diversity indicated the highest dissimilarity between Agarwado and the other two salt pans (0.73) viz. Nerul and Curca and the lowest dissimilarity was observed between Nerul and Curca salt pans (0.48). Additionally, in the Agarwado salt pan, 125 unique genera were detected, while in Nerul 119, and in Curca 28 distinct genera were noted. The presence of these exclusive microorganisms in a specific salt pan and its absence in the others indicate that the adjacent estuaries play a critical role in determining salt pan bacterial diversity. Further, the functional prediction of bacterial communities indicated the predominance of stress adaptation genes involved in osmotic balance, membrane modification, and DNA repair mechanisms. This is the first study to report the bacterial community structure and its functional genes in these three salt pans using Next-Generation Sequencing. The data generated could be used as a reference by other researchers across the world for bioprospecting these organisms for novel compounds having biotechnological and biomedical potential.

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.

Community ecological study on the reduction of soil antimony bioavailability by SRB-based remediation technologies

Sulfate-reducing bacteria (SRB) were effective in stabilizing Sb. However, the influence of electron donors and acceptors during SRB remediation, as well as the ecological principles involved, remained unclear. In this study, Desulfovibrio desulfuricans ATCC 7757 was utilized to stabilize soil Sb within microcosm. Humic acid (HA) or sodium sulfate (Na2SO4) were employed to enhance SRB capacity. The SRB+HA treatment exhibited the highest Sb stabilization rate, achieving 58.40%. Bacterial community analysis revealed that SRB altered soil bacterial diversity, community composition, and assembly processes, with homogeneous selection as the predominant assembly processes. When HA and Na2SO4 significantly modified the stimulated microbial community succession trajectories, shaped the taxonomic composition and interactions of the bacterial community, they showed converse effect in shaping bacterial community which were both helpful for promoting dissimilatory sulfate reduction. Na2SO4 facilitated SRB-mediated anaerobic reduction and promoted interactions between SRB and bacteria involved in nitrogen and sulfur cycling. The HA stimulated electron generation and storage, and enhanced the interactions between SRB and bacteria possessing heavy metal tolerance or carbohydrate degradation capabilities.

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.

Arsenic (As) oxidation by core endosphere microbiome mediates As speciation in Pteris vittata roots

Pteris vittata is an arsenic(As)-hyperaccumulator that may be employed in phytoremediation of As-contaminated soils. P. vittata-associated microbiome are adapted to elevated As and may be important for host survival under stresses. Although P. vittata root endophytes could be critical for As biotransformation in planta, their compositions and metabolisms remain elusive. The current study aims to characterize the root endophytic community composition and As-metabolizing potentials in P. vittata. High As(III) oxidase gene abundances and rapid As(III) oxidation activity indicated that As(III) oxidation was the dominant microbial As-biotransformation processes compared to As reduction and methylization in P. vittata roots. Members of Rhizobiales were the core microbiome and the dominant As(III) oxidizers in P. vittata roots. Acquasition of As-metabolising genes, including both As(III) oxidase and As(V) detoxification reductase genes, through horizontal gene transfer was identified in a Saccharimonadaceae genomic assembly, which was another abundant population residing in P. vittata roots. Acquisition of these genes might improve the fitness of Saccharimonadaceae population to elevated As concentrations in P. vittata. Diverse plant growth promoting traits were encoded by the core root microbiome populations Rhizobiales. We propose that microbial As(III) oxidation and plant growth promotion are critical traits for P. vittata survival in hostile As-contaiminated sites.

Removal of toilet paper fibers from residential wastewater: a life cycle assessment

Toilet paper has been reported as one of the major insoluble pollutant components in the influent of wastewater treatment plants. Toilet paper fibers contribute to a large production of sewage sludge, resulting in a high treatment cost and high energy consumption. To find energy-efficient, cost-effective, and environment-friendly technologies for fiber removal and resource recovery from wastewater, a life-cycle assessment (LCA) was performed to analyze the wastewater treatment processes, including a sieving process for removing and recovering suspended solids before the biodegradation units. Based on the LCA results, it was estimated that the sieve screening process saved 8.57% of energy consumption. The construction phase of sieving consumed 1.31% energy cost compared with the operation phase. Environmental impact analysis showed that sieving reduced the impacts of climate change, human toxicity, fossil depletion, and particulate matter formation, which reduced the total normalized environmental impacts by 9.46%. The life-cycle analysis of the removal of toilet paper fibers from wastewater revealed the need to use more efficient methods to enhance the recovery of cellulose fibers.

New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing

Autochthonous fungal bioaugmentation (AFB) is considered a reliable bioremediation approach for polycyclic aromatic hydrocarbon (PAH) contamination, but little is known about its mechanisms in contaminated soils. Here, a microcosm experiment was performed to explore the AFB mechanisms associated with two highly efficient phenanthrene degrading agents of fungi (with laccase-producing Scedosporium aurantiacum GIG-3 and non-laccase-producing Aspergillus fumigatus LJD-29), using stable-isotope-probing (SIP) and high-throughput sequencing. The results showed that each fungus markedly improved phenanthrene removal, and microcosms with both fungi exhibited the best phenanthrene removal performance among all microcosms. Additionally, AFB markedly shifted the composition of the microbial community, particularly the phenanthrene-degrading bacterial taxa. Interestingly, based on SIP results, strains GIG-3 and LJD-29 did not assimilate phenanthrene directly during AFB, but instead played key roles in the preliminary decomposition of phenanthrene though secretion of different extracellular enzymes to oxidize the benzene ring (GIG-3 bioaugmentation with laccase, and LJD-29 bioaugmentation with manganese and lignin peroxidases). In addition, all functional degraders directly involved in phenanthrene assimilation were indigenous bacteria, while native fungi rarely participated in the direct phenanthrene mineralization. Our findings provide a new mechanism of AFB with multiple fungi, and support AFB as a promising strategy for the in situ bioremediation of PAH-contaminated soil.

Anaerobic selenite-reducing bacteria and their metabolic potentials in Se-rich sediment revealed by the combination of DNA-stable isotope probing, metagenomic binning, and metatranscriptomics

Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (Se^IVRB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative Se^IVRB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative Se^IVRB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment.

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

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

Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils

Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.

Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria

Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.

Dynamics of vanadium and response of inherent bacterial communities in vanadium-titanium magnetite tailings to beneficiation agents, temperature, and illumination

Vanadium-titanium (V-Ti) magnetite tailings contain toxic metals that could potentially pollute the surrounding environment. However, the impact of beneficiation agents, an integral part of mining activities, on the dynamics of V and the microbial community composition in tailings remains unclear. To fill this knowledge gap, we compared the physicochemical properties and microbial community structure of V-Ti magnetite tailings under different environmental conditions, including illumination, temperature, and residual beneficiation agents (salicylhydroxamic acid, sodium isobutyl xanthate, and benzyl arsonic acid) during a 28-day reaction. The results revealed that beneficiation agents exacerbated the acidification of the tailings and the release of V, among which benzyl arsonic acid had the greatest impact. The concentration of soluble V in the leachate of tailings with benzyl arsonic acid was 6.4 times higher than that with deionized water. Moreover, illumination, high temperatures, and beneficiation agents contributed to the reduction of V in V-containing tailings. High-throughput sequencing revealed that Thiobacillus and Limnohabitans adapted to the tailings environment. Proteobacteria was the most diverse phylum, and the relative abundance was 85.0%-99.1%. Desulfovibrio, Thiobacillus, and Limnohabitans survived in the V-Ti magnetite tailings with residual beneficiation agents. These microorganisms could contribute to the development of bioremediation technologies. The main factors affecting the diversity and composition of bacteria in the tailings were Fe, Mn, V, SO₄^2-, total nitrogen, and pH of the tailings. Illumination inhibited microbial community abundance, while the high temperature (39.5 °C) stimulated microbial community abundance. Overall, this study strengthens the understanding of the geochemical cycling of V in tailings influenced by residual beneficiation agents and the application of inherent microbial techniques in the remediation of tailing-affected environments.

Microbiological mechanism for "production while remediating" in Cd-contaminated paddy fields: A field experiment

Security utilization measures (SUMs) for "production while remediating" in moderate and mild Cd-polluted paddy fields had been widely used. To investigate how SUMs drove rhizosphere soil microbial communities and reduced soil Cd bioavailability, a field experiment was conducted using soil biochemical analysis and 16S rRNA high-throughput sequencing. Results showed that SUMs improved rice yield by increasing the number of effective panicles and filled grains, while also inhibiting soil acidification and enhancing disease resistance by improving soil enzyme activities. SUMs also reduced the accumulation of harmful Cd in rice grains and transformed it into FeMn oxidized Cd, organic-bound Cd, and residual Cd in rhizosphere soil. This was partly due to the higher degree of soil DOM aromatization, which helped complex the Cd with DOM. Additionally, the study also found that microbial activity was the primary source of soil DOM, and that SUMs increased the diversity of soil microbes and recruited many beneficial microbes (Arthrobacter, Candidatus_Solibacter, Bryobacter, Bradyrhizobium, and Flavisolibacter) associated with organic matter decomposition, plant growth promotion, and pathogen inhibition. Besides, special taxa (Bradyyrhizobium and Thermodesulfovibrio) involved in sulfate/sulfur ion generation and nitrate/nitrite reduction pathway were observably enriched, which effectively reduced the soil Cd bioavailability through adsorption and co-precipitation. Therefore, SUMs not only changed the soil physicochemical properties (e.g., pH), but also drove rhizosphere microbes to participate in the chemical species transformation of soil Cd, thus reducing Cd accumulation in rice grains.

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.

Thallium adsorption on three iron (hydr)oxides and Tl isotopic fractionation induced by adsorption on ferrihydrite

Thallium (Tl) is an extraordinarily toxic metal, which is usually present with Tl(I) and highly mobile in aquatic environment. Limited knowledge is available on the adsorption and isotopic variations of Tl(I) to Fe-(hydr)oxides. Herein, the adsorption behavior and mechanism of Tl(I) on representative Fe-(hydr)oxides, i.e. goethite, hematite, and ferrihydrite, were comparatively investigated kineticly and isothermally, additional to crystal structure modelling and Tl isotope composition (²⁰⁵Tl/²⁰³Tl). The results showed that ferrihydrite exhibited overall higher Tl(I) adsorption capacity (1.11-10.86 mg/kg) than goethite (0.21-1.83 mg/kg) and hematite (0.14-2.35 mg/kg), and adsorption by the three prevalent Fe-minerals presented strong pH and ionic strength dependence. The magnitude of Tl isotopic fractionation during Tl(I) adsorption to ferrihydrite (α_{solid-solution} ≈ 1.00022-1.00037) was smaller than previously observed fractionation between Mn oxides and aqueous Tl(I) (α_{solid-solution} ≈ 1.0002-1.0015). The notable difference is likely that whether oxidation of Tl(I) occurred during Tl adsorption to the mineral surfaces. This study found a small but detectable Tl isotopic fractionation during Tl(I) adsorption to ferrihydrite and heavier Tl isotope was slightly preferentially adsorbed on surface of ferrihydrite, which was attributed to the formation of inner-sphere complex between Tl and ≡Fe-OH. The findings offer a new understanding of the migration and fate of ²⁰⁵Tl/²⁰³Tl during Tl(I) adsorption to Fe (hydr)oxides.

Soil microbial responses to simultaneous contamination of antimony and arsenic in the surrounding area of an abandoned antimony smelter in Southwest China

Soil contamination with heavy metal(loid)s may influence microbial activities in the soil, and consequently jeopardize soil health. Microbial responses to soil contamination play an important role in ecological risk assessment. This study investigated the effect of heavy metal(loid)s contamination on microbial community structure and abundance in the surrounding soil of an abandoned antimony (Sb) smelter in Qinglong county, Guizhou province, Southwest China. A total of 46 soil samples were collected from ten sampling sites (labelled as A-I, and CK) across the study area at depths of 0-2, 2-10, 10-20, 20-30, 30-40, and 40-50 cm. The soil samples were analyzed for total and bioavailable heavy metal(loid) concentrations, bacterial, fungal, and archaeal community structures, diversities, and functions, together with soil basic physicochemical properties. Much greater ecological risk of Sb and arsenic (As) was present in the surface soil (0-2 cm) compared to that in the subsoils. The activities of dominant microorganisms tended to be associated with soil pH and heavy metal(loid)s (i.e., Sb, As, lead (Pb), cadmium (Cd), and chromium (Cr)). Bacteria associated with IMCC26256, Rhizobiales, Burkholderiales, and Gaiellales, and archaea associated with Methanocellales were estimated to be tolerant to high concentrations of Sb and As in the soil. In addition, the magnitude of soil microbial responses to Sb and As contamination was in the order of archaea > bacteria > fungi. In contrast to the negligible response of fungi and negative response of bacteria to Sb and As contamination, there was a strongly positive correlation between archaeal activity and total Sb and As concentrations in the soil. Our findings provide a theoretical basis for the remediation of Sb smelter-affected soil.

Elevated antimony concentration stimulates rare taxa of potential autotrophic bacteria in the Xikuangshan groundwater

Microbial communities composed of few abundant and many rare species are widely involved in the biogeochemical cycles of elements. Yet little is known about the ecological roles of rare taxa in antimony (Sb) contaminated groundwater. Groundwater samples were collected along an Sb concentration gradient in the Xikuangshan antimony mine area and subjected to high through-put sequencing of 16S rRNA genes to investigate the bacterial communities. Results suggested that both abundant and rare sub-communities were dominated by Betaproteobacteria, Gammaproteobacteria, and Alphaproteobacteria, whereas rare sub-communities showed higher alpha-diversities. Multivariate analysis showed that both the abundant and rare taxa were under the stress of Sb, but the impact on rare taxa was greater. Nitrate explained a large part for the variation of the abundant sub-communities, indicating the critical role of nitrate for their activities under anoxic conditions. In contrast, bicarbonate significantly impacted rare sub-communities, suggesting their potential autotrophic characteristics. To further explore the role of rare taxa in the communities and the mechanism of affecting the community composition, a network was constructed to display the co-occurrence pattern of bacterial communities. The rare taxa contributed most of the network nodes and served as keystone species to maintain the stability of community. Abiotic factors (mainly Sb and pH) and bacterial interspecific interactions (interactions between keystone species and other bacterial groups) jointly affect the community dynamics. Functional prediction was performed to further reveal the ecological function of rare taxa in the Sb-disturbed groundwater environment. The results indicated that the rare taxa harbored much more diverse functions than their abundant counterparts. Notably, elevated Sb concentration promoted some potential autotrophic functions in rare taxa such as the oxidation of S-, N-, and Fe(II)-compounds. These results offer new insights into the roles of rare species in elemental cycles in the Sb-impacted groundwater.

Antimony toxicity upon microorganisms from aerobic and anaerobic environments

Antimony (Sb) is a toxic and carcinogenic metalloid that can be present in contaminated water generated by mining operations and other industrial activities. The toxicity of Sb (III) and Sb (V) to aerobic microorganisms remains limited and unexplored for anaerobic microorganisms involved in hydrogen (H₂) and methane (CH₄) production. This study aimed to evaluate the toxicity of Sb (III) and Sb (V) upon aerobic and anaerobic microorganisms important in biological wastewater treatment systems. Sb (III) was more toxic than Sb (V) independently of the test and environment evaluated. Under aerobic conditions maintained in the Microtox assay, Sb (V) was not toxic to Allivibrio fischeri at concentrations as high as 500 mg/L, whereas Sb (III) caused just over 50% inhibition at concentration of 250 mg/L after 5 min of exposure. In the respirometry test, for the specific oxygen uptake rate, the concentrations of Sb (III) and Sb (V) displaying 50% inhibition were 0.09 and 56.2 mg/L, respectively. Under anaerobic conditions, exposure to Sb (III) and Sb (V) led to a decrease in microorganisms activity of fermentative and methanogenic processes. The results confirm that the microbial toxicity of Sb depends on its speciation and Sb (III) displays a significantly higher inhibitory potential than Sb (V) in both aerobic and anaerobic environments.

Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils

As(III) oxidation-dependent biological nitrogen fixing (As-dependent BNF) bacteria use a novel biogeochemical process observed in tailings recently. However, our understanding of microorganisms responsible for As-dependent BNF is limited and whether such a process occurs in As-contaminated soils is still unknown. In this study, two contrasting types of soils (surface soils versus river sediments) heavily contaminated by As were selected to study the occurrence of As-dependent BNF. BNF was observed in sediments and soils amended with As(III), whereas no apparent BNF was found in the cultures without As(III). The increased abundances of the nitrogenase gene (nifH) and As(III) oxidation gene (aioA) suggest that an As-dependent BNF process was catalyzed by microorganisms harboring nifH and aioA. In addition, DNA-SIP demonstrated that Thiobacillus spp. and Anaeromyxobacter spp. were putative As-dependent BNF bacteria in As-contaminated soils and sediments, respectively. Metagenomic analysis further suggested that these taxa contained genes responsible for BNF, As(III) oxidation, and CO₂ fixation, demonstrating their capability for serving as As-dependent BNF. These results indicated the occurrence of As-dependent BNF in various As-contaminated habitats. The contrasting geochemical conditions in different types of soil suggested that these conditions may enrich different As-dependent BNF bacteria (Thiobacillus spp. for soils and Anaeromyxobacter spp. for sediments).

Distribution fractions and potential ecological risk assessment of heavy metals in mangrove sediments of the Greater Bay Area

The restoration of mangrove in coastal wetlands of China has been started since the 1990s. However, various pollutants, especially for heavy metals (HMs), contained in wastewater might present a significant risk to mangrove forests during the restoration. In this study, sediments of five typical mangrove wetlands with varying restoration years and management measures in the Greater Bay Area were collected to evaluate the distribution fractions and potential ecological risk of HMs. Cd (0.2-1.6 mg/kg) was found in high concentrations in the exchangeable fraction (37.8-71.5%), whereas Cu (54.2-94.8 mg/kg), Zn (157.6-332.6 mg/kg), Cr (57.7-113.6 mg/kg), Pb (36.5-89.9 mg/kg), and Ni (29.7-69.5 mg/kg) primarily presented in residual fraction (30.8-91.9%). According to the geo-accumulation index (I_geo) analysis, sediment Cd presented a high level of pollution (3 ≤ I_geo ≤ 4), while Zn and Cu were associated with moderately pollution (1 ≤ I_geo ≤ 2). Besides, high ecological risk of Cd was found in sediments of five mangroves, with risk assessment code (RAC) ranging from 45.9 to 84.2. Redundancy analysis revealed that the content of NO₃^--N was closely related to that of HMs in sediments and, pH value and NO₃^--N concentration affected the distribution of HMs geochemical fractions. High concentration of HMs in QA and NS sampling sites was caused by the formerly pollutants discharge, resulting in these sediments still with a higher HM pollution level after the plant of mangrove for a long period. Fortunately, strict drainage standards for industrial activities in Shenzhen significantly availed for decreasing HMs contents in mangrove sediments. Therefore, future works on mangrove conversion and restoration should be linked to the water purification in the GBA.

Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats

Nitrogen (N) deficiency in mining-contaminated habitats usually hinders plant growth and thus hampers tailing revegetation. Biological N fixation (BNF) is an essential biogeochemical process that contributes to the initial accumulation of N in oligotrophic mining-contaminated regions. Previous studies reported that chemolithotrophic rather than heterotrophic diazotrophs frequently dominated in the mining-contaminated regions. Chemolithotrophic diazotrophs may utilize elements abundant in such habitats (e.g., sulfur (S), arsenic (As), and antimony (Sb)) as electron donors to fix N₂. BNF fueled by the oxidation of S and As has been detected in previous studies. However, BNF fueled by Sb(III) oxidation (Sb-dependent BNF) has never been reported. The current study observed the presence of Sb-dependent BNF in slurries inoculated from Sb-contaminated habitats across the South China Sb belt, suggesting that Sb-dependent BNF may be widespread in this region. DNA-stable isotope probing identified bacteria associated with Rhodocyclaceae and Rhizobiaceae as putative microorganisms responsible for Sb-dependent BNF. Furthermore, metagenomic-binning demonstrated that Rhodocyclaceae and Rhizobiaceae contained essential genes involved in Sb(III) oxidation, N₂ fixation, and carbon fixation, suggesting their genetic potential for Sb-dependent BNF. In addition, meta-analysis indicated that these bacteria are widespread among Sb-contaminated habitats with different niche preferences: Rhodocyclaceae was enriched in river sediments and tailings, while Rhizobiaceae was enriched only in soils. This study may broaden our fundamental understanding of N fixation in Sb-mining regions.

Arsenic shapes the microbial community structures in tungsten mine waste rocks

Tungsten (W) is a critical material that is widely used in military applications, electronics, lighting technology, power engineering and the automotive and aerospace industries. In recent decades, overexploitation of W has generated large amounts of mine waste rocks, which generate elevated content of toxic elements and cause serious adverse effects on ecosystems and public health. Microorganisms are considered important players in toxic element migrations from waste rocks. However, the understanding of how the microbial community structure varies in W mine waste rocks and its key driving factors is still unknown. In this study, high-throughput sequencing methods were used to determine the microbial community profiles along a W content gradient in W mine waste rocks. We found that the microbial community structures showed clear differences across the different W levels in waste rocks. Notably, arsenic (As), instead of W and nutrients, was identified as the most important predictor influencing microbial diversity. Furthermore, our results also showed that As is the most important environmental factor that regulates the distribution patterns of ecological clusters and keystone ASVs. Importantly, we found that the dominant genera have been regulated by As and were widely involved in As biogeochemical cycling in waste rocks. Taken together, our results have provided useful information about the response of microbial communities to W mine waste rocks.

Response of soil protists to antimony and arsenic contamination

Microorganisms can mediate antimony (Sb) and arsenic (As) transformation and thus change their mobility and toxicity. Having similar geochemical behavior, Sb and As are generally considered to exert similar environmental pressure on microbiome. However, it needs further validation, especially for protists. In this study, the responses of protistan communities to Sb and As were investigated by collecting soils from Xikuangshan Sb mine and Shimen As mine in China. Antimony and As contamination taxonomically and functionally (consumer and phototroph) changed the alpha and beta diversities of protistan communities, but exerted different impacts on the parasitic community. Based on multiple statistical tools, As contamination had a greater impact on protistan communities than Sb. The ecological networks of highly contaminated sites were less complex but highly positively connected compared to less contaminated sites. High As contamination raised the ratio of consumers and decreased the ratio of phototrophs in ecological networks, while the opposite tendency was observed in Sb contaminated soils. High Sb and As contamination enriched different keystone taxa resistant to Sb and As. These results demonstrate that protistan community respond differently to Sb and As.

Effect of nitrate and sulfate coexistence on hydrogen autotrophic reduction of antimonate (Sb(V)) and microbial community structures

Hydrogen autotrophic bioreduction of antimonate (Sb(V)) to antimonite (Sb(III)) is an alternative approach for removing antimony (Sb) from water. This study investigated Sb(V) reduction kinetics and the effects of various parameters on the Sb(V) removal performance in a hydrogen autotrophic reaction system (HARS). Sb(V) reduction in the HARS was well fitted to the Michaelis-Menten model, showing a positive correlation between the reaction rate and biomass. The maximum specific substrate removal rates were 0.29-4.86 and 6.82-15.87 mg Sb(V)/(g·VSS·h) at initial Sb(V) concentrations of 500 μg/L and 10 mg/L, respectively. Coexisting nitrate significantly inhibited Sb(V) reduction, and the inhibition intensified with increasing nitrate concentration. However, coexisting sulfate had a positive effect on Sb(V) reduction, and the sulfate effectively enhanced total antimony (TSb) removal performance by generating sulfide from sulfate reduction. Illumina high-throughput sequencing technology was used to determine the changes in microbial community structure during different periods in the HARS, revealing the effects of co-existing ions on the dominant Sb(V) reducing bacteria. In the HARS, Longilinea and Terrimonas were the dominant genera in the presence of nitrate, and Longilinea was the dominant genus in the presence of sulfate, at initial Sb(V) concentration of 500 μg/L. When the concentration of Sb(V) was 10 mg/L, Longilinea and Thauera were the dominant genus in the HARS for treating water co-polluted with nitrate and sulfate, respectively. These results provide a theoretical basis of the application of HARS for the bio-remediation of Sb(V) contaminated water.

Mycobacteriaceae Mineralizes Micropolyethylene in Riverine Ecosystems

Microplastic (MP) contamination is a serious global environmental problem. Plastic contamination has attracted extensive attention during the past decades. While physiochemical weathering may influence the properties of MPs, biodegradation by microorganisms could ultimately mineralize plastics into CO₂. Compared to the well-studied marine ecosystems, the MP biodegradation process in riverine ecosystems, however, is less understood. The current study focuses on the MP biodegradation in one of the world's most plastic contaminated rivers, Pearl River, using micropolyethylene (mPE) as a model substrate. Mineralization of ¹³C-labeled mPE into ¹³CO₂ provided direct evidence of mPE biodegradation by indigenous microorganisms. Several Actinobacteriota genera were identified as putative mPE degraders. Furthermore, two Mycobacteriaceae isolates related to the putative mPE degraders, Mycobacterium sp. mPE3 and Nocardia sp. mPE12, were retrieved, and their ability to mineralize ¹³C-mPE into ¹³CO₂ was confirmed. Pangenomic analysis reveals that the genes related to the proposed mPE biodegradation pathway are shared by members of Mycobacteriaceae. While both Mycobacterium and Nocardia are known for their pathogenicity, these populations on the plastisphere in this study were likely nonpathogenic as they lacked virulence factors. The current study provided direct evidence for MP mineralization by indigenous biodegraders and predicted their biodegradation pathway, which may be harnessed to improve bioremediation of MPs in urban rivers.

Immobile Iron-Rich Particles Promote Arsenic Retention and Regulate Arsenic Biotransformation in Treatment Wetlands

Remediation of arsenic (As)-contaminated wastewater by treatment wetlands (TWs) remains a technological challenge due to the low As adsorption capacity of wetland substrates and the release of adsorbed As to pore water. This study investigated the feasibility of using immobile iron-rich particles (IIRP) to promote As retention and to regulate As biotransformation in TWs. Iron-rich particles prepared were immobilized in the interspace of a gravel substrate. TWs with IIRP amendment (IIRP-TWs) achieved a stable As removal efficiency of 63 ± 4% over 300 days, while no As removal or release was observed in TWs without IIRP after 180 days of continuous operation. IIRP amendment provided additional adsorption sites and increased the stability of adsorbed As due to the strong binding affinity between As and Fe oxides. Microbially mediated As(III) oxidation was intensified by iron-rich particles in the anaerobic bottom layer of IIRP-TWs. Myxococcus and Fimbriimonadaceae were identified as As(III) oxidizers. Further, metagenomic binning suggested that these two bacterial taxa may have the capability for anaerobic As(III) oxidation. Overall, this study demonstrated that abiotic and biotic effects of IIRP contribute to As retention in TWs and provided insights into the role of IIRP for the remediation of As contamination.

Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis)

BACKGROUND

Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments.

RESULTS

Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using ¹⁵N₂ identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth.

CONCLUSIONS

This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.

Characterization of arsenic-metabolizing bacteria in an alkaline soil

Arsenite (As(III)) is more toxic, mobilizable and bioavailable than arsenate (As(V)). Hence, the transformations between As(III) and As(V) are crucial for the toxicity and mobility of arsenic (As). However, As transformation and microbial communities involved in alkaline soils are largely unknown. Here we investigate two major pathways of As transformation, i.e., As(III) oxidation and As(V) reduction, and identify the bacteria involved in the alkaline soil by combining stable isotope probing with shotgun metagenomic sequencing. As(III) oxidation and significant increase of the aioA genes copies were observed in the treatments amended with As(III) and NO₃^-, suggesting that As(III) oxidation can couple with nitrate reduction and was mainly catalyzed by the microorganisms containing aioA genes. As(V) reduction was detected in the treatments amended with As(V) and acetate where the abundance of arrA gene significantly increased, indicating that microorganisms with arrA genes were the key As(V) reducers. Acidovorax, Hydrogenophaga, and Ramlibacter were the putative nitrate-dependent As(III) oxidizers, and Deinococcus and Serratia were the putative respiratory As(V) reducers. These findings will improve our understanding of As metabolism and are meaningful for mapping out bioremediation strategies of As contamination in alkaline environment.

Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning

Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F₄₂₀H₂ dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.

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

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

Primary Succession Changes the Composition and Functioning of the Protist Community on Mine Tailings, Especially Phototrophic Protists

Primary succession in mine tailings is a prerequisite for tailing vegetation. Microorganisms, including bacteria, fungi, and protists, play an important role in this process in the driving force for improving the nutritional status. Compared to bacteria and fungi, protist populations have rarely been investigated regarding their role in mine tailings, especially for those inhabiting tailings associated with primary succession. Protists are the primary consumers of fungi and bacteria, and their predatory actions promote the release of nutrients immobilized in the microbial biomass, as well as the uptake and turnover of nutrients, affecting the functions of the wider ecosystems. In this study, three different types of mine tailings associated with three successional stages (original tailings, biological crusts, and Miscanthus sinensis grasslands) were selected to characterize the protistan community diversity, structure, and function during primary succession. Some members classified as consumers dominated the network of microbial communities in the tailings, especially in the original bare land tailings. The keystone phototrophs of Chlorophyceae and Trebouxiophyceae showed the highest relative abundance in the biological crusts and grassland rhizosphere, respectively. In addition, the co-occurrences between protist and bacterial taxa demonstrated that the proportion of protistan phototrophs gradually increased during primary succession. Further, the metagenomic analysis of protistan metabolic potential showed that abundances of many functional genes associated with photosynthesis increased during the primary succession of tailings. Overall, these results suggest that the primary succession of mine tailings drives the changes observed in the protistan community, and in turn, the protistan phototrophs facilitate the primary succession of tailings. This research offers an initial insight into the changes in biodiversity, structure, and function of the protistan community during ecological succession on tailings.

Keystone taxa and functional analysis in arsenic and antimony co-contaminated rice terraces

Both arsenic (As) and antimony (Sb) are primary environmental contaminants that often co-exist at contaminated sites. Though the microbial community compositions of As- and Sb-contaminated sites have been previously described, the changes in microbial community interactions and community functions remain elusive. In the current study, several key metabolic processes, such as As/Sb detoxification and carbon fixation, were enriched under heavily contaminated conditions. Furthermore, the identified keystone taxa, which are associated with the families Nitrosomonadaceae, Pedosphaeraceae, Halieaceae, and Latescibacterota, demonstrated positive correlations with As and Sb concentrations, indicating that they may be resistant to As and Sb toxicities. Accordingly, arsenic resistance-related functions, along with several functions such as carbon fixation, were found to be enriched in heavily contaminated sites. The current study elucidated the key microbial populations in As- and Sb-contaminated rice terraces and may provide useful information for remediation purposes.