Identification of antimony- and arsenic-oxidizing bacteria associated with antimony mine tailing

Distinct mechanisms of stibnite (Sb2S3) oxidative dissolution mediated by acid-generating and alkali-generating microorganisms within a wide pH range

Indigenous microorganisms in antimony mining areas facilitate stibnite dissolution over a wide pH range, yet their mechanisms remain poorly studied. Herein, the acid-generating Bosea sp. AS-1 and the alkali-generating Pseudomonas sp. PS-3 were selected to interact with stibnite (Sb2S3) under initial acidic (pH value = 5) and alkaline (pH value = 8) conditions, respectively. Results indicated that AS-1 and PS-3 promoted stibnite dissolution compared to the sterile control irrespective of initial pH conditions, but through distinct mechanisms. AS-1 oxidized sulfide to sulfate by regulating the expression of SoxB and SoxC genes, thereby driving the stibnite dissolution and oxidation. Up to 18.63 mg/L total antimony (Sb(tot)) was released and the dissolved Sb(III) was completely oxidized to Sb(V). Moreover, AS-1 prevented the passivation layer formation by inhibiting sulfur oxidation intermediates accumulation. Conversely, PS-3 could not oxidize sulfur, but produced more extracellular polymeric substances which bound microorganisms closely to stibnite. The stibnite dissolution was facilitated through pH elevation from 5.0 to above 9.0 mediated by PS-3, releasing up to 35.56 mg/L Sb(tot). However, the accumulated sulfur oxidation intermediates facilitated the passivation layer formation, inhibiting further dissolution of stibnite. Additionally, less than 44 % of the soluble Sb(III) was oxidized to Sb(V). These results contribute to understanding the microbial-mediated transformation, mobilization and oxidation of antimony.

Two complete genome sequences of antimonite-oxidizing bacteria, Mesorhizobium sp. strain ANAO-SY3R2 and Hydrogenophaga sp. strain ANAO-22, isolated from mine tailing soil

We report the complete genome sequences of two antimony-oxidizing bacteria, Mesorhizobium sp. strain ANAO-SY3R2, comprising one chromosome (4.3 Mbp) and four circular plasmids, and Hydrogenophaga sp. strain ANAO-22, comprising one chromosome (5.8 Mbp) and two circular plasmids. These genome information extend our understanding of physiological versatility of antimony-transforming microorganisms.

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.

Managing antimony pollution: Insights into Soil-Plant system dynamics and remediation Strategies

Researchers are increasingly concerned about antimony (Sb) in ecosystems and the environment. Sb primarily enters the environment through anthropogenic (urbanization, industries, coal mining, cars, and biosolid wastes) and geological (natural and chemical weathering of parent material, leaching, and wet deposition) processes. Sb is a hazardous metal that can potentially harm human health. However, no comprehensive information is available on its sources, how it behaves in soil, and its bioaccumulation. Thus, this study reviews more than 160 peer-reviewed studies examining Sb's origins, geochemical distribution and speciation in soil, biogeochemical mechanisms regulating Sb mobilization, bioavailability, and plant phytotoxicity. In addition, Sb exposure effects plant physio-morphological and biochemical attributes were investigated. The toxicity of Sb has a pronounced impact on various aspects of plant life, including a reduction in seed germination and impeding plant growth and development, resulting from restricted essential nutrient uptake, oxidative damages, disruption of photosynthetic system, and amino acid and protein synthesis. Various widely employed methods for Sb remediation, such as organic manure and compost, coal fly ash, biochar, phytoremediation, microbial-based bioremediation, micronutrients, clay minerals, and nanoremediation, are reviewed with a critical assessment of their effectiveness, cost-efficiency, and suitability for use in agricultural soils. This review shows how plants deal with Sb stress, providing insights into lowering Sb levels in the environment and lessening risks to ecosystems and human health along the food chain. Examining different methods like bioaccumulation, bio-sorption, electrostatic attraction, and complexation actively works to reduce toxicity in contaminated agricultural soil caused by Sb. In the end, the exploration of recent advancements in genetics and molecular biology techniques are highlighted, which offers valuable insights into combating Sb toxicity. In conclusion, the findings of this comprehensive review should help develop innovative and useful strategies for minimizing Sb absorption and contamination and thus successfully managing Sb-polluted soil and plants to reduce environmental and public health risks.

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.

Assessment of microbial communities from cold mine environments and subsequent enrichment, isolation and characterization of putative antimony- or copper-metabolizing microorganisms

Mining activities, even in arctic regions, create waste materials releasing metals and metalloids, which have an impact on the microorganisms inhabiting their surroundings. Some species can persist in these areas through tolerance to meta(loid)s via, e.g., metabolic transformations. Due to the interaction between microorganisms and meta(loid)s, interest in the investigation of microbial communities and their possible applications (like bioremediation or biomining) has increased. The main goal of the present study was to identify, isolate, and characterize microorganisms, from subarctic mine sites, tolerant to the metalloid antimony (Sb) and the metal copper (Cu). During both summer and winter, samples were collected from Finnish mine sites (site A and B, tailings, and site C, a water-treatment peatland) and environmental parameters were assessed. Microorganisms tolerant to Sb and Cu were successfully enriched under low temperatures (4°C), creating conditions that promoted the growth of aerobic and fermenting metal(loid) tolerating or anaerobic metal(loid) respiring organism. Microbial communities from the environment and Sb/Cu-enriched microorganisms were studied via 16S rRNA amplicon sequencing. Site C had the highest number of taxa and for all sites, an expected loss of biodiversity occurred when enriching the samples, with genera like Prauserella, Pseudomonas or Clostridium increasing their relative abundances and others like Corynebacterium or Kocuria reducing in relative abundance. From enrichments, 65 putative Sb- and Cu-metabolizing microorganisms were isolated, showing growth at 0.1 mM to 10 mM concentrations and 0°C to 40°C temperatures. 16S rRNA gene sequencing of the isolates indicated that most of the putative anaerobically Sb-respiring tolerators were related to the genus Clostridium. This study represents the first isolation, to our knowledge, of putative Sb-metabolizing cold-tolerant microorganisms and contributes to the understanding of metal (loid)-tolerant microbial communities in Arctic mine sites.

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.

The role of an Sb-oxidizing bacterium in modulating antimony speciation and iron plaque formation to reduce the accumulation and toxicity of Sb in rice (Oryza sativa L.)

Microbial antimony (Sb) oxidation in the root rhizosphere and the formation of iron plaque (IP) on the root surface are considered as two separate strategies to mitigate Sb(III) phytotoxicity. Here, the effect of an Sb-oxidizing bacterium Bacillus sp. S3 on IP characteristics of rice exposed to Sb(III) and its alleviating effects on plant growth were investigated. The results revealed that Fe(II) supply promoted IP formation under Sb(III) stress. However, the formed IP facilitated rather than hindered the uptake of Sb by rice roots. In contrast, the combined application of Fe(II) and Bacillus sp. S3 effectively alleviated Sb(III) toxicity in rice, resulting in improved rice growth and photosynthesis, reduced oxidative stress levels, enhanced antioxidant systems, and restricted Sb uptake and translocation. Despite the ability of Bacillus sp. S3 to oxidize Fe(II), bacterial inoculation inhibited the formation of IP, resulting in a reduction in Sb absorption on IP and uptake into the roots. Additionally, the bacterial inoculum enhanced the transformation of Sb(III) to less toxic Sb(V) in the culture solution, further influencing the adsorption of Sb onto IP. These findings highlight the potential of combining microbial Sb oxidation and IP as an effective strategy for minimizing Sb toxicity in sustainable rice production systems.

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.

Functional features of a novel Sb(III)- and As(III)-oxidizing bacterium: Implications for the interactions between bacterial Sb(III) and As(III) oxidation pathways

Antimony (Sb) and arsenic (As) share similar chemical characteristics and commonly coexist in contaminated environments. It has been reported that the biogeochemical cycles of antimony and arsenic affect each other. However, there is limited understanding regarding microbial coupling between the biogeochemical processes of antimony and arsenic. Here, we aimed to solve this issue. We successfully isolated a novel bacterium, Shinella sp. SbAsOP1, which possesses both Sb(III) and As(III) oxidase, and can effectively oxidize both Sb(III) and As(III) under aerobic and anaerobic conditions. SbAsOP1 exhibits greater aerobic oxidation activity for the oxidation of As(III) or Sb(III) compared to its anaerobic activity. SbAsOP1 also significantly catalyzes the oxidative mobilization of solid-phase Sb(III) under aerobic conditions. The activity of SbAsOP1 in oxidizing solid Sb(III) is 3 times lower than its activity in oxidizing soluble form. It is noteworthy that, in the presence of both Sb(III) and As(III) under aerobic conditions, either As(III) or Sb(III) significantly inhibits the oxidation of Sb(III) or As(III), respectively. In comparison, under anaerobic conditions and in the coexistence of Sb(III) and As(III), As(III) significantly inhibits Sb(III) oxidation, whereas Sb(III) almost completely inhibits As(III) oxidation. These findings suggest that under both aerobic and anaerobic conditions, SbAsOP1 demonstrates a partial preference for Sb(III) oxidation. Additionally, bacterial oxidations of Sb(III) and As(III) mutually inhibit each other to varying degrees. These observations gain a novel understanding of the interplay between the biogeochemical processes of antimony and arsenic.

Antimony oxidation and whole genome sequencing of Phytobacter sp. X4 isolated from contaminated soil near a flotation site

The conversion of the more toxic Sb(III) into less toxic Sb(V) is an effective strategy for the treatment of antimony-contaminated sites. In this study, a strain, Phytobacter sp. X4, which can tolerate high concentrations of antimony and can use nitrate as an electron acceptor for Sb(III) oxidation under anaerobic conditions, was isolated from the deep soil of an antimony mine flotation tailing. Unlike other antimony oxidizing bacteria, X4 oxidized better under high Sb(III) concentration, and the oxidation efficiency of 10 mM Sb(III) reached the maximum at 110 h with 61.8 %. Kinetic study showed X4 yielded a V_max of 1.093 μM∙min^-1 and a K_m of 718.2 μM. The genome of Phytobacter sp. X4 consists of a complete circular chromosome and two plasmids. In addition, X4 had more metal(loid)s resistance genes and highly expressed genes than other Phytobacter spp., reflecting its stronger adaptive advantage in harsh survival environments. We also analyzed the origin and evolution of arsB, arsC, and arsH, which may have been transferred horizontally from other species. iscR and arsH may have an important contribution to Sb(III) oxidation. Thus, Phytobacter sp. X4 has a good ability to remediate high antimony-contaminated sites and can be applied to an anaerobic environment.

Alleviation of metal stress in rape seedlings (Brassica napus L.) using the antimony-resistant plant growth-promoting rhizobacteria Cupriavidus sp. S-8-2

This study investigated an effective strategy for remediating antimony (Sb)-contaminated soil using the bacterial strain screened from Sb-contaminated fern rhizospheres due to its superior growth-promoting, heavy-metal(loid) resistant, and antibiotic-tolerant characteristics. The strain that belongs to Cupriavidus sp. was determined by 16S rRNA sequencing and showed no morphological changes when grown with high concentrations of Sb (608.8 mg/L). The strain showed prominent indole acetic acid (IAA), phosphate-solubilizing abilities, and ACC deaminase activity under Sb stress. Moreover, IAA and soluble phosphate levels increased in the presence of 608.8 mg/L Sb. Inoculation of rape seedlings with Cupriavidus sp. S-8-2 enhanced several morphological and biochemical growth features compared to untreated seedlings grown under Sb stress. Inoculation of Cupriavidus sp. S-8-2 increased root weight by more than four-fold for fresh weight and over two-fold for dry weight, despite high environmental Sb. The strain also reduced Sb-mediated oxidative stress and malondialdehyde contents by reducing Sb absorption, thus alleviating Sb-induced toxicity. Environmental Scanning Electron Microscope (ESEM) imaging and dilution plating technique revealed Cupriavidus sp. S-8-2 is localized on the surface of roots. Identifying the Sb-resistant plant growth-promoting bacterium suggested its usefulness in the remediation of contaminated agricultural soil and for the promotion of crop growth. We highly recommend the strain for further implementation in field experiments.

Synergistic Impacts of Arsenic and Antimony Co-contamination on Diazotrophic Communities

Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N₂ into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s.

Antimony redox processes in the environment: A critical review of associated oxidants and reductants

The environmental behavior of antimony (Sb) has recently received greater attention due to the increasing global use of Sb in a range of industrial applications. Although present at trace levels in most natural systems, elevated Sb concentrations in aquatic and terrestrial environments may result from anthropogenic activities. The mobility and toxicity of Sb largely depend on its speciation, which is dependent to a large extent on its oxidation state. To a certain extent, our understanding of the environmental behavior of Sb has been informed by studies of the environmental behavior of arsenic (As), as Sb and As have somewhat similar chemical properties. However, recently it has become evident that the speciation of Sb and As, especially in the context of redox reactions, may be fundamentally different. Therefore, it is crucial to study the biogeochemical processes impacting Sb redox transformations to understand the behavior of Sb in natural and engineered environments. Currently, there is a growing body of literature involving the speciation, mobility, toxicity, and remediation of Sb, and several reviews on these general topics are available; however, a comprehensive review focused on Sb environmental redox chemistry is lacking. This paper provides a review of research conducted within the past two decades examining the redox chemistry of Sb in aquatic and terrestrial environments and identifies knowledge gaps that need to be addressed to develop a better understanding of Sb biogeochemistry for improved management of Sb in natural and engineered systems.

Relevance of the microbial community to Sb and As biogeochemical cycling in natural wetlands

Mining activities lead to elevated levels of antimony (Sb) and arsenic (As) in river systems, having adverse effects on the aquatic environment and human health. Microbes inhabiting river sediment can mediate the transformation of Sb and As, thus changing the toxicity and mobility of Sb and As. Compared to river sediments, natural wetlands could introduce distinct geochemical conditions, leading to the formation of different sedimentary microbial compositions between river sediments and wetland sediments. However, whether such changes in microbial composition could influence the microbially mediated geochemical behavior of Sb or As remains poorly understood. In this study, we collected samples from a river contaminated by Sb tailings and a downstream natural wetland to study the influence of microorganisms on the geochemical behavior of Sb and As after the Sb/As-contaminated river entered the natural wetland. We found that the microbial compositions in the natural wetland soil differed from those in the river sediment. The Sb/As contaminant components (Sb(III), As(III), As(V), As_exe) and nutrients (TC) were important determinants of the difference in the compositions of the microbial communities in the two environments. Taxonomic groups were differentially enriched between the river sediment and wetland soil. For example, the taxonomic groups Xanthomonadales, Clostridiales and Desulfuromonadales were important in the wetland and were likely to involve in Sb/As reduction, sulfate reduction and Fe(III) reduction, whereas Burkholderiales, Desulfobacterales, Hydrogenophilales and Rhodocyclales were important taxonomic groups in the river sediments and were reported to involve in Sb/As oxidation and sulfide oxidation. Our results suggest that microorganisms in both river sediments and natural wetlands can affect the geochemical behavior of Sb/As, but the mechanisms of action are different.

Kinetics of antimony biogeochemical processes under pre-definite anaerobic and aerobic conditions in a paddy soil

While the transformation of antimony (Sb) in paddy soil has been previously investigated, the biogeochemical processes of highly chemical active Sb in the soil remain poorly understood. In addition, there is a lack of quantitative understanding of Sb transformation in soil. Therefore, in this study, the kinetics of exogenous Sb in paddy soils were investigated under anaerobic and aerobic incubation conditions. The dissolved Sb(V) and the Sb(V) extracted by diffusive gradient technique decreased under anaerobic conditions and then increased under aerobic conditions. The redox reaction of Sb occurred, and Sb bioavailability significantly decreased after 55 days of incubation. The kinetics of Fe and the scanning transmission electron microscopy analysis revealed that the Fe oxides were reduced and became dispersed under anaerobic conditions, whereas they were oxidized and re-aggregated during the aerobic stage. In addition, the redox processes of sulfur and nitrogen were detected under both anaerobic and aerobic conditions. Based on these observations, a simplified kinetic model was established to distinguish the relative contributions of the transformation processes. The bioavailability of Sb was controlled by immobilization as a result of S reduction and by mobilization as a result of Fe reductive dissolution and S oxidation, rather than the pH. These processes coupled with the redox reaction of Sb jointly resulted in the complex behavior of Sb transformation under anaerobic and aerobic conditions. The model-based method and findings of this study provide a comprehensive understanding of the Sb transformation in a complex soil biogeochemical system under changing redox conditions.

Antimony transformation and mobilization from stibnite by an antimonite oxidizing bacterium Bosea sp. AS-1

Soils and waters are heavily contaminated by antimony in Xikuangshan (XKS) mine area. It is widely accepted that oxidative dissolution of sulfide minerals and aqueous dissolution are the most prevalent geochemical mechanisms for the release of Sb to the environment. Bosea sp. AS-1 is an antimonite-oxidizer isolated from the mine slag in Xikuangshan Sb mine. Whole genome sequencing revealed the presence of multiple sulfur-oxidizing genes, antimony (Sb) metabolism genes and carbon fixation genes in AS-1's genome. We therefore hypothesized that under oxic conditions, AS-1 could mediate the oxidation of sulfide and Sb(III) in stibnite (Sb₂S₃) and lead to the release of Sb. Indeed, strain AS-1 was discovered as an autotrophic Sb(III)-oxidizer. Antimony mobilization studies conducted with strain AS-1 showed significantly enhanced mobilization of Sb, and complete oxidation of released Sb and sulfur to Sb(V) and sulfate. In addition, AS-1 induced a faster release of Sb under heterotrophic condition, and new acicular minerals might form. These findings support the hypothesis that microorganisms play an important role in the mobilization and transformation of Sb in XKS mine area and may contribute to our further understanding of the Sb biogeochemical redox cycle in natural environment.

Variation in the diazotrophic community in a vertical soil profile contaminated with antimony and arsenic

A nitrogen (N) deficiency will usually hinder bioremediation efforts in mining-derived habitats such as occurring in mining regions. Diazotrophs can provide N to support the growth of plants and microorganisms in these environments. However, diazotrophic communities in mining areas have been not studied frequently and are more poorly understood than those in other environments, such as in agricultural soils or in the presence of legumes. The current study compares the differences in depth-resolved diazotrophic community compositions and interactions in two contrasting sites (to depths of 2 m), including a highly contaminated and a moderately contaminated site. Antimony (Sb) and arsenic (As) co-contamination induced a loosely connected biotic interaction, and a selection of deep soils by diazotrophic communities. Multiple lines of evidence, including the enrichment of diazotrophic taxa in the highly contaminated sites, microbe-microbe interactions, environment-microbe interactions, and a machine learning approach (random forests regression), demonstrated that Rhizobium was the keystone taxon within the vertical profile of contaminated soil and was resistant to the Sb and As contaminant fractions. All of these observations suggest that one diazotroph, Rhizobium, may play an important role in N fixation in the examined contaminated sites.

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

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

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

Microorganisms can mediate arsenic (As) and antimony (Sb) transformation and thus change the As and Sb toxicity and mobility. The influence of As and Sb on the innate microbiome has been extensively characterized. However, how microbial metabolic potentials are influenced by the As and Sb co-contamination is still ambiguous. In this study, we selected two contrasting sites located in the Shimen realgar mine, the largest realgar mine in Asia, to explore the adaptability and response of the soil microbiome to As and Sb co-contamination and the impact of co-contamination on microbial metabolic potentials. It is observed that the geochemical parameters, including the As and Sb fractions, were the driving forces that reshaped the community composition and metabolic potentials. Bacteria associated with Bradyrhizobium, Nocardioides, Sphingomonas, Burkholderia, and Streptomyces were predicted to be tolerant to high concentrations of As and Sb. Co-occurrence network analysis revealed that the genes related to C fixation, nitrate/nitrite reduction, N fixation, and sulfate reduction were positively correlated with the As and Sb fractions, suggesting that As and Sb biogeochemical cycling may interact with and benefit from C, N, and S cycling. The results suggest that As and Sb co-contamination not only influences As-related genes, but also influences other genes correlated with microbial C, N, and S cycling.

Production of two morphologically different antimony trioxides by a novel antimonate-reducing bacterium, Geobacter sp. SVR

A novel dissimilatory antimonate [Sb(V)]-reducing bacterium, strain SVR, was isolated from soil of a former antimony (Sb) mine. Strain SVR coupled Sb(V) reduction to acetate oxidation with an apparent reduction rate of 2.4 mM d^-1. The reduction of Sb(V) was followed by the precipitation and accumulation of white microcrystals in the liquid medium. The precipitates were initially small and amorphous, but they eventually developed to the crystal phase with a length > 50 µm. Strain SVR removed 96% of dissolved Sb as the precipitates. An X-ray diffraction analysis indicated that the microcrystals were the orthorhombic Sb trioxide (Sb₂O₃), i.e., valentinite. Phylogenetic and physiological analyses revealed that strain SVR is a member of the genus Geobacter. The cell suspension of strain SVR incubated with acetate and Sb(V) at pH 7.0 was able to form valentinite. Interestingly, at pH 8.0, the cell suspension formed another crystalline Sb₂O₃ with a cubic structure, i.e., senarmontite. Our findings provide direct evidence that Geobacter spp. are involved in Sb(V) reduction in nature. Considering its superior capacity for Sb removal, strain SVR could be used for the recovery of Sb and the individual productions of valentinite and senarmontite from Sb-contaminated wastewater.

Investigation of the antimony fractions and indigenous microbiota in aerobic and anaerobic rice paddies

The accumulation of antimony (Sb) by rice is a severe threat to exposed populations. Previous studies demonstrated that, compared to flooded (anaerobic) water management, dry cultivation management (aerobic) could substantially decrease As, an analog of Sb, uptake by rice. However, the effects of different water management strategies on the accumulation of Sb by rice are less understood. It is proposed that microorganisms play an important role in regulating Sb mobility in rice paddies. Hence, the current study compared the microbial communities in rice paddies receiving different water management, i.e., flooded (anaerobic) and dry (aerobic)) rice cultivation. Significant decrease in Sb uptake by rice, in both the roots and grains, was observed under the aerobic compared to the anaerobic conditions. This could partially be attributed to the differences in the microbial communities as shaped by the redox environment. In aerobic soils, the gene responsible for Sb oxidation (i.e., aioA) was significantly, while in anaerobic soils the gene responsible for Sb reduction (i.e., arrA) was enriched, suggesting that variation in redox conditions may trigger different microbial responses. Accordingly, geochemical analysis indicated that accumulation of Sb(III) was only observed under anaerobic conditions, but not under aerobic conditions. The environment-microbe interactions were distinct between the two treatments with a greater number of interactions between Sb fractions and the microbial assemblage under anaerobic conditions, while Eh was the most influential geochemical parameter under aerobic conditions. Finally, the presence of a core microbiome under the two conditions suggested the possibility of microorganisms that support rice growth, nutrition, and health. The reduction of Sb in rice grain significantly decreases Sb exposure to the residents in Sb contaminated regions, and should be considered for future rice cultivation practices.

Bacteria responsible for antimonite oxidation in antimony-contaminated soil revealed by DNA-SIP coupled to metagenomics

Antimony (Sb), the analog of arsenic (As), is a toxic metalloid that poses risks to the environment and human health. Antimonite (Sb(III)) oxidation can decrease Sb toxicity, which contributes to the bioremediation of Sb contamination. Bacteria can oxidize Sb(III), but the current knowledge regarding Sb(III)-oxidizing bacteria (SbOB) is limited to pure culture studies, thus underestimating the diversity of SbOB. In this study, Sb(III)-oxidizing microcosms were set up using Sb-contaminated rice paddies as inocula. Sb(III) oxidation driven by microorganisms was observed in the microcosms. The increasing copies and transcription of the arsenate-oxidizing gene, aioA, in the microcosms during biotic Sb(III) oxidation indicated that microorganisms mediated Sb(III) oxidation via the aioA genes. Furthermore, a novel combination of DNA-SIP and shotgun metagenomic was applied to identify the SbOB and predict their metabolic potential. Several putative SbOB were identified, including Paracoccus, Rhizobium, Achromobacter and Hydrogenophaga. Furthermore, the metagenomic analysis indicated that all of these putative SbOB contained aioA genes, confirming their roles in Sb(III) oxidation. These results suggested the concept of proof of combining DNA-SIP and shotgun metagenomics directly. In addition, the identification of the novel putative SbOB expands the current knowledge regarding the diversity of SbOB.

Microbiome-environment interactions in antimony-contaminated rice paddies and the correlation of core microbiome with arsenic and antimony contamination

Mining activities of antimony (Sb) and arsenic (As) typically result in severe environmental contamination. These contaminants accumulate in rice and thus threaten the health of local residents, who consume Sb- and As-enriched rice grains. Microorganisms play a critical role in the transformation and transportation of Sb and As in paddy soil. Thus, an understanding of the microbiology of contaminated sites would promote the production of safe agricultural products. In this study, six Sb- and As-contaminated rice fields near an active Sb-mining area were investigated. The Sb and As concentrations of all samples were elevated compared to the background level in China. Nitrate, total As, total Sb, and Fe(III) were the major determinants of the microbial community structure. Seven bacterial taxa (i.e. Bradyrhizobium, Bryobacter, Candidatus Solibacter, Geobacter, Gemmatimonas, Halingium, and Sphingomonas) were identified as the core microbiome. These taxa were strongly correlated with the As and Sb contaminant fractions and likely to metabolize As and Sb. Results imply that many soil microbes can survival in the Sb/As contaminated sites.

Draft Genome Sequence of Stenotrophomonas sp. Strain SbOxS2, an Antimony-Oxidizing Bacterium Isolated from Stibnite Mine Tailing Soil

The antimony-oxidizing Stenotrophomonas sp. strain SbOxS2 was isolated from stibnite mine tailing soil. The draft genome sequence of strain SbOxS2 comprises 4.76 Mbp with 4,211 predicted protein-coding sequences. This genome will provide useful information for characterizing the molecular mechanisms associated with heavy metal resistance within the genus Stenotrophomonas.

The antimony-oxidizing Stenotrophomonas sp. strain SbOxS2 was isolated from stibnite mine tailing soil. The draft genome sequence of strain SbOxS2 comprises 4.76 Mbp with 4,211 predicted protein-coding sequences. This genome will provide useful information for characterizing the molecular mechanisms associated with heavy metal resistance within the genus Stenotrophomonas.

Draft Genome Sequence of the Antimony-Oxidizing Pseudomonas sp. Strain SbOxS1, Isolated from Stibnite Mine Tailing Soil

Pseudomonas sp. strain SbOxS1 was isolated from stibnite mine tailing soil for its ability to oxidize antimonite. We present a draft genome sequence of strain SbOxS1, which contains 6,484 predicted protein-coding sequences. This genome information extends our understanding of the physiological versatility of antimony-transforming microorganisms.

Genomic and physiological characterization of an antimony and arsenite-oxidizing bacterium Roseomonas rhizosphaerae

Antimony (Sb) and arsenic (As) are two toxic metalloids, which are listed as priority environmental pollutants by the European Union and the U.S. Environmental Protection Agency (EPA). Antimony taken up by plants enters the food chain and poses a threat to human health. Microbial oxidation of antimonite (Sb(III)) and arsenite (As(III)) to the less toxic antimonate (Sb(V)) and arsenate (As(V)), has great potential for the immobilization of Sb and As in the environment. A heterotrophic aerobic bacterium, Roseomonas rhizosphaerae YW11, oxidized both Sb(III) and As(III) in the modified R2A medium. In the same medium, strain YW11 preferred to oxidize Sb(III), whereas the As(III) oxidation rate was only 50%. Genomic analysis of YW11 confirmed the presence of several As-resistance gene islands. The aioAB genes encoding As(III) oxidase were also induced by Sb(III). The role of aioA in Sb(III) oxidation and resistance was confirmed by disrupting this gene in strain YW11, resulting in the loss of Sb(III) oxidation abilities. This study documents an enzymatic basis for microbial Sb(III) oxidation in strain YW11, which is a novel bacterial strain showing simultaneous oxidation of Sb(III) and As(III), and may be a potential candidate for bioremediation of heavy metal-contaminated environments.

Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings

Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.

Impacts of antimony and arsenic co-contamination on the river sedimentary microbial community in an antimony-contaminated river

Antimony (Sb) and arsenic (As) are toxic elements that occur widely in trace soil concentrations. Expansion of mining activities has increased Sb and As pollution, thus posing a severe threat to human welfare and ecological systems worldwide. Knowledge regarding the composition and adaptation of the microbial communities in these metal(loid) contaminated sites is still limited. In the current study, samples along a river flowing through the world's largest Sb mining area (Xikuangshan) were selected to investigate the microbial response to different Sb or As species. A comprehensive analysis of geochemical parameters, high-throughput sequencing, and statistical methods were applied to reveal the different effects of Sb and As on sedimentary microorganisms. Results suggested that the majority of the Sb and As fractions were not bioavailable. The Sb extractable fraction had a stronger effect on the microbial community compared with its As counterpart. Random forest analyses indicated that the easily exchangeable Sb fraction and specifically sorbed surface-bound fraction were the two most selective variables shaping microbial community diversity. A total of 11 potential keystone phyla, such as bacteria associated with the Bacteroidetes, Proteobacteria, and Firmicutes, were identified according to a molecular ecological network analysis. Strong correlations (|R| > 0.7, P < 0.05) were identified among the indigenous microbial community and pH (negative), sulfate (negative), and exchangeable Sb fraction (positive). Bacteria associated with the genera Geobacter, Phormidium, Ignavibacterium, Desulfobulbus, Ferruginibacter, Fluviicola, Methylotenera, and Scytonema, were predicted to tolerate or metabolize the Sb extractable fraction.

Copper stress in flooded soil: Impact on enzyme activities, microbial community composition and diversity in the rhizosphere of Salix integra

Climate change has increased flooding frequency, making the heavy metal polluted areas more vulnerable, and led to increased global land degradation. Information about the alteration of soil microbiota under heavy metal pollution and flooding is still rather limited. Fast-growing trees are candidates for phytoremediation of heavy metal polluted soils. Therefore, the impact of Cu pollution on microbiota in soil used for cultivating Salix integra Thunb. was investigated with and without flooding for 60 d. Bacterial and fungal communities were accessed via partial 16S rRNA (V₃-V₄) and internal transcribed spacer (ITS) genes. The activity of invertase, urease and cellulase were markedly decreased by 28.5-59%, 55.0-76.7% and 17.3-34.1%, respectively, with increasing Cu levels. Flooding significantly increased the activity of polyphenol oxidase and peroxidase by 56.3% and 41.4% at the highest Cu level compared to its respective non-flooded condition. High Cu concentration significantly decreased the richness and diversity of the bacterial community, and fungi were more sensitive than bacteria under flooding conditions. Redundancy analysis suggests that Cu, Fe and soil organic matter are the key determinants affecting the composition of microbial communities. Our findings provide new insight into the responses of soil microbes to Cu-contamination and contribute to our understanding of metal toxicity in soil-woody plant systems under flooded conditions.

Abundant and diverse arsenic-metabolizing microorganisms in peatlands treating arsenic-contaminated mining wastewaters

Mining operations produce large quantities of wastewater. At a mine site in Northern Finland, two natural peatlands are used for the treatment of mining‐influenced waters with high concentrations of sulphate and potentially toxic arsenic (As). In the present study, As removal and the involved microbial processes in those treatment peatlands (TPs) were assessed. Arsenic‐metabolizing microorganisms were abundant in peat soil from both TPs (up to 10⁸ cells g_dw⁻¹), with arsenate respirers being about 100 times more abundant than arsenite oxidizers. In uninhibited microcosm incubations, supplemented arsenite was oxidized under oxic conditions and supplemented arsenate was reduced under anoxic conditions, while little to no oxidation/reduction was observed in NaN₃‐inhibited microcosms, indicating high As‐turnover potential of peat microbes. Formation of thioarsenates was observed in anoxic microcosms. Sequencing of the functional genemarkers aioA (arsenite oxidizers), arrA (arsenate respirers) and arsC (detoxifying arsenate reducers) demonstrated high diversity of the As‐metabolizing microbial community. The microbial community composition differed between the two TPs, which may have affected As removal efficiencies. In the present situation, arsenate reduction is likely the dominant net process and contributes substantially to As removal. Changes in TP usage (e.g. mine closure) with lowered water tables and heightened oxygen availability in peat might lead to re‐oxidation and re‐mobilization of bound arsenite.

Microbial diversity response in thallium polluted riverbank soils of the Lanmuchang

Thallium (Tl) is a toxic element, but little is known about microbial communities' response to TI mobilization and sequestration. Here, we characterize the microbial communities and their feedbacks to Tl-pollution in riverbank soils to understand the distribution of microbial metal tolerance. These soils have been affected by pollution sourced from a Tl-rich mineralized area in Lanmuchang, Guizhou, China. In all studied soil samples, Proteobacteria, Acidobacteria, and Actinobacteria were revealed relatively in higher abundance at the phylum level. The results indicated that a number of microbial communities including Gemmatimonadetes, and Actinobacteria were correlated with total Tl, suggesting potential roles of these microbes to Tl tolerance. The patterns of phylogenetic beta-diversity in studied samples showed a high diversity of the microbial community in soils with high Tl concentrations. Sequence analysis of microbial community indicated that most of the environmental parameters in soils were associated with the major phylogenetic groups such as Gemmobacteria, Bryobacteria, Proteobacteria, Actinobacteria, Firmicutes, and Rhodobacteria. Some species of microbes, Nocardioides (genus), Actinomycetales (Order), Ralstonia (phyla) and Sphingomonas (genus) might are tolerant of Tl. These results provide direction to the microbial communities in the presence of elevated Tl concentration in Lanmuchang and shed light on bioremediation of Tl polluted locations.

Sb(III)-resistance mechanisms of a novel bacterium from non-ferrous metal tailings

Understanding the mechanism(s) of microbial resistance to antimony (Sb) is critical in the bioremediation of Sb polluted environments. Here a novel bacterium (Acinetobacter sp. JH7) isolated from mine tailings decreased the Microtox toxicity of a Sb(III)-containing medium. DNA sequencing and physiological testing were employed for the identification and characterization of strain JH7. Following a batch experiment, Fourier transform infrared spectroscopy (FTIR) and antimony speciation analyses determined the adsorption and oxidation of antimony. Analyses of Sb(III) distribution revealed that extracellular polymeric substances and cell walls inhibited Sb(III) entry into JH7 cells. FTIR studies indicated that key functional groups including -OH, C-N, and C-O likely participated in Sb(III) biosorption. Isothermal and kinetic studies revealed that Sb(III) sorption to viable JH7 cells fitted the Langmuir model (R² = 0.99) and could be described by pseudo-second order kinetics (R² = 0.99). Furthermore, the increase of anti-oxidative enzymatic activity of JH7 enhanced the intracellular detoxification of Sb(III), which would indirectly contribute to the Sb(III) resistance ability of strain JH7. Our results indicate that biosorption and ROS oxidation of Sb(III) were likely responsible for the decreased toxicity of Sb. The greater understanding how Acinetobacter sp. JH7 lowers the environmental Sb(III) toxicity could provide a basis for future research and subsequent development of technologies for the remediation of Sb contaminated sites.

Characteristics of Bacterial Community and Function in Paddy Soil Profile around Antimony Mine and Its Response to Antimony and Arsenic Contamination

Research of bacterial communities and metabolism potential of paddy soils contaminated by antimony (Sb) and arsenic (As) are vital to acquire understanding for their bioremediation. Here, the relative abundance of Sb and As metabolism genes, the diversity and composition of the bacterial community, and the influences of geochemical properties and the bacterial community and metabolism potential have been researched by Tax4Fun2 prediction and high-throughput sequencing. LEfSe (linear discriminant analysis effect size) analysis shown different taxa were enriched in dissimilar soil layers. RDA (Redundancy analysis) and relative importance analysis indicated the main properties including total sulfur (TS), total organic carbon (TOC), pH, and the bioavailable fractions of Sb and As affects the bacterial community, which Sbrec, Astot, and Asrec had greater impact on the bacterial taxonomic community. For example, Asrec, Astot, and Sbrec had a positive correlation with Chloroflexi and Rokubacteria, but negatively correlated with Proteobacteria and Actinobacteria. Obtaining metabolic function genes by using the tax prediction method. RDA, relative importance analysis, and co-occurrence network analysis showed the geochemical properties and bacterial community affected Sb and As related bacterial functions. The partial least squares path model (PLS-PM) analysis indicated Sb and As contamination fractions had negative effects on ecological function, bacterial community structure had positive influences on ecological function, and the direct effects of geochemical properties on ecological function was greater than community structure. The direct impact of As contamination fractions on bacterial community structure was greater than Sb, while the direct impact of Sb contamination fractions on bacterial function was more remarkable than As. Obviously, this study provides a scientific basis for the potential of biochemical remediation of Sb and As contamination in paddy soils profile.

Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses

Microbial arsenic transformation is important in As biogeochemical cycles in the environment. In this study, a new As-resistant bacterial strain Leclercia adecarboxylata As3-1 was isolated and its associated mechanisms in As resistance and detoxification were evaluated based on genome sequencing and gene annotations. After subjecting strain As3-1 to medium containing arsenate (AsV), AsV reduction occurred and an AsV-enhanced bacterial growth was observed. Strain As3-1 lacked arsenite (AsIII) oxidation ability and displayed lower AsIII resistance than AsV, probably due to its higher AsIII accumulation. Polymerase chain reaction and phylogenetic analysis showed that strain As3-1 harbored a typical AsV reductase gene (arsC) on the plasmids. Genome sequencing and gene annotations identified four operons phoUpstBACS, arsHRBC, arsCRDABC and ttrRSBCA, with 8 additional genes outside the operons that might have involved in As resistance and detoxification in strain As3-1. These included 5 arsC genes explaining why strain As3-1 tolerated high AsV concentrations. Besides ArsC, TtrB, TtrC and TtrA proteins could also be involved in AsV reduction and consequent energy acquisition for bacterial growth. Our data provided a new example of diverse As-regulating systems and AsV-enhanced growth without ArrA in bacteria. The information helps to understand the role of As in selecting microbial systems that can transform and utilize As.

Role of extracellular polymeric substance (EPS) in toxicity response of soil bacteria Bacillus sp. S3 to multiple heavy metals

Heavy metal resistant bacteria are of great interest because of their potential use in bioremediation. Understanding the survival and adaptive strategies of these bacteria under heavy metal stress is important for better utilization of these bacteria in remediation. The objective of this study was to investigate the role of bacterial extracellular polymeric substance (EPS) in detoxifying against different heavy metals in Bacillus sp. S3, a new hyper antimony-oxidizing bacterium previously isolated from contaminated mine soils. The results showed that Bacillus sp. S3 is a multi-metal resistant bacterial strain, especially to Sb(III), Cu(II) and Cr(VI). Toxic Cd(II), Cr(VI) and Cu(II) could stimulate the secretion of EPS in Bacillus sp. S3, significantly enhancing the adsorption and detoxification capacity of heavy metals. Both Fourier transform infrared spectroscopy (FTIR) and three-dimensional excitation-emission matrix (3D-EEM) analysis further confirmed that proteins were the main compounds of EPS for metal binding. In contrast, the EPS production was not induced under Sb(III) stress. Furthermore, the TEM-EDX micrograph showed that Bacillus sp. S3 strain preferentially transported the Sb(III) to the inside of the cell rather than adsorbed it on the extracellular surface, indicating intracellular detoxification rather than extracellular EPS precipitation played an important role in microbial resistance towards Sb(III). Together, our study suggests that the toxicity response of EPS to heavy metals is associated with difference in EPS properties, metal types and corresponding environmental conditions, which is likely to contribute to microbial-mediated remediation.

Vegetation type impacts microbial interaction with antimony contaminants in a mining-contaminated soil environment

Antimony (Sb) contamination is a growing environmental concern due to the increasing use of this metalloid in mining and industrial activities. The remediation of Sb-contaminated soil is a lengthy and costly process. Phytoremediation has been suggested as a cost-effective method for the long-term management of Sb-contaminated sites. Various plant types have been found to thrive in contaminated sites and have the potential to remediate Sb contamination; however, their impacts on Sb speciation and the indigenous microbial community remain unclear. In the current study, soils from three types of vegetation environment (i.e., grass, forest, and agricultural) were collected from two Sb mining areas in Guizhou, China. Comparisons of geochemical and microbiological properties among the three vegetation types revealed that vegetation was a major driver of soil biogeochemical characteristics. Contaminant fractions (i.e., extractable fractions of Sb and As) had a greater influence on microbial communities in grass and forest soil, whereas pH had a greater impact in agricultural soil. This difference may indicate distinct microbe-environment interactions in agricultural soil affected by anthropogenic activity. The dominant taxa, including Flavobacterium, Geobacter, Janthinobacterium, Clostridium, and Mycobacterium responded positively to various contaminant fractions, indicating that the community had adapted to the chronically contaminated environment. However, the regulation of these dominant genera by geochemical properties appears to be taxon-specific. Our results demonstrate that vegetation type has a substantial impact on Sb and As biogeochemical cycles, and should be considered in future remediation efforts.

Bacterial response to antimony and arsenic contamination in rice paddies during different flooding conditions

Rice is more vulnerable to arsenic (As) and antimony (Sb) contamination than other cereals due to the special cultivation methods, during which irrigation conditions are adjusted depending upon the growth stages. The changes in irrigation conditions may alter the oxidation states of Sb and As, which influences their mobility and bioavailability and hence uptake by rice. In this study, bacterial responses to As and Sb contamination in rice fields were investigated during two different stages of rice growth: the vegetative stage (flooded conditions), and the ripening stage (drained conditions). The substantial changes in the irrigation conditions caused a variation in geochemical parameters including the As- and Sb-extractable fractions. As and Sb were more mobile and bioaccessible during the flooded than under drained conditions. The microbial communities varied during two irrigation conditions, suggesting that the geochemical conditions may have different effects on the innate paddy microbiota. Therefore, various statistical tools including co-occurrence network and random forest (RF) were performed to reveal the environment-microbe interactions in two different irrigation conditions. One of the notable findings is that Sb- and As-related parameters exerted more influences during the flooded than under drained conditions. Furthermore, a detailed RF analysis indicated that the individual bacterial taxa may also respond differently to contaminant fractions during the two irrigation conditions. Notably, RF indicated that individual taxa such as Clostridiaceae and Geobacter may be responsible for biotransformation of As and Sb (e.g., As and Sb reduction). The results provided knowledge for As and Sb transformation during contrasting irrigation conditions and the potential mitigation strategy for contaminant removal.

Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation

Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria valorizable into (1) removal of radioactive elements and toxic heavy metals, (2) promotion of plant growth, (3) oxidation and (4) reduction of sulfate. These bacteria can be explored further for applications in the bioremediation of by-products, like PG, by different processes.

Arsenic-tolerant microbial consortia from sediments of Copahue geothermal system with potential applications in bioremediation

Although arsenic (As) is recognized as a toxic element for living species, some microorganisms have the ability to tolerate and transform it; recent studies have proposed to take advantage of such capacity to develop sustainable bioremediation strategies. In this study, we evaluated the adaptation to increasing concentrations of As(III) and As(V) of three metabolically different microbial cultures (heterotrophic, autotrophic-acidophilic, and anaerobic) obtained from a sample with low-soluble As content from the Copahue geothermal system. At the end of the adaptation process, the heterotrophic culture was able to grow at 20 mM and 450 mM of As(III) and As(V), respectively; the autotrophic-acidophilic culture showed tolerance to 15 mM of As(III) and 150 mM of As(V), whereas the anaerobic culture only developed in As(V) at concentrations up to 50 mM. The most tolerant consortia were characterized by their growth performance, complexity, and the presence of genes related to As metabolism and resistance. Regarding the consortia complexity, the predominant genera identified were: Paenibacillus in both heterotrophic consortia, Acidithiobacillus in the autotrophic-acidophilic consortium tolerant to As(III), Acidiphilium in the autotrophic-acidophilic consortium tolerant to As(V), and Thiomonas and Clostridium in the anaerobic consortium. This study is the first report of As tolerance microorganisms obtained from Copahue and reasserts the versatility and flexibility of the community of this natural extreme environment; also, it opens the door to the study of possible uses of these consortia in the design of biotechnological processes where the As concentration may fluctuate.

Changes in rhizosphere bacterial communities during remediation of heavy metal-accumulating plants around the Xikuangshan mine in southern China

Mining and smelting activities are the major sources of antimony (Sb) contamination. The soil around Xikuangshan (XKS), one of the largest Sb mines in the world, has been contaminated with high concentrations of Sb and other associated metals, and has attracted extensive scholarly attention. Phytoremediation is considered a promising method for removing heavy metals, and the diversity and structure of rhizosphere microorganisms may change during the phytoremediation process. The rhizosphere microbiome is involved in soil energy transfer, nutrient cycling, and resistance and detoxification of metal elements. Thus, changes in this microbiome are worthy of investigation using high-throughput sequencing techniques. Our study in Changlongjie and Lianmeng around XKS revealed that microbial diversity indices in the rhizospheres of Broussonetia papyrifera and Ligustrum lucidum were significantly higher than in bulk soil, indicating that plants affect microbial communities. Additionally, most of the bacteria that were enriched in the rhizosphere belonged to the Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes. In Changlongjie and Lianmeng, the diversity and abundance of the microbial community in the B. papyrifera rhizosphere were higher than in L. lucidum. In parallel, the soil pH of the B. papyrifera rhizosphere increased significantly in acidic soil and decreased significantly in near-neutral soil. Redundancy analyses indicated that pH was likely the main factor affecting the overall bacterial community compositions, followed by moisture content, Sb, arsenic (As), and chromium (Cr).

Antimony speciation in the environment: Recent advances in understanding the biogeochemical processes and ecological effects

Antimony (Sb) is a toxic metalloid, and its pollution has become a global environmental problem as a result of its extensive use and corresponding Sb-mining activities. The toxicity and mobility of Sb strongly depend on its chemical speciation. In this review, we summarize the current knowledge on the biogeochemical processes (including emission, distribution, speciation, redox, metabolism and toxicity) that trigger the mobilization and transformation of Sb from pollution sources to the surrounding environment. Natural phenomena such as weathering, biological activity and volcanic activity, together with anthropogenic inputs, are responsible for the emission of Sb into the environment. Sb emitted in the environment can adsorb and undergo redox reactions on organic or inorganic environmental media, thus changing its existing form and exerting toxic effects on the ecosystem. This review is based on a careful and systematic collection of the latest papers during 2010-2017 and our research results, and it illustrates the fate and ecological effects of Sb in the environment.

Extreme Geochemical Conditions and Dispersal Limitation Retard Primary Succession of Microbial Communities in Gold Tailings

Microbial community succession in tailings materials is poorly understood at present, and likely to be substantially different from similar processes in natural primary successional environments due to the unusual geochemical properties of tailings and the isolated design of tailings storage facilities. This is the first study to evaluate processes of primary succession in microbial communities colonizing unamended tailings, and compare the relative importance of stochastic (predominantly dust-borne dispersal) and deterministic (strong selection pressures from extreme geochemical properties) processes in governing community assembly rates and trajectories to those observed in natural environments. Dispersal-based recruitment required > 6 months to shift microbial community composition in unamended, field-weathered gold tailings; and in the absence of targeted inoculants, recruitment was dominated by salt- and alkali-tolerant species. In addition, cell numbers were less than 10⁶ cells/g tailings until > 6 months after deposition. Laboratory experiments simulating microbial cell addition via dust revealed that high (>6 months' equivalent) dust addition rates were required to effect stabilization of microbial cell counts in tailings. In field-weathered tailings, topsoil addition during rehabilitation works exerted a double effect, acting as a microbial inoculant and correcting geochemical properties of tailings. However, microbial communities in rehabilitated tailings remained compositionally distinct from those of reference soils in surrounding environments. pH, water extractable Mg, and water extractable Fe emerged as major controls on microbial community composition in the field-weathered gold tailings. Overall, this study highlights the need for application of targeted microbial inoculants to accelerate rates of microbial community succession in tailings, which are limited primarily by slow dispersal due to physical and spatial isolation of tailings facilities from inoculant sources; and for geochemical properties of tailings to be amended to moderate values to encourage microbial community diversification and succession.

Characterization of the antimonite- and arsenite-oxidizing bacterium Bosea sp. AS-1 and its potential application in arsenic removal

Arsenic (As) and antinomy (Sb) usually coexist in natural environments where both of them pollute soils and water. Microorganisms that oxidize arsenite [As(III)] and tolerate Sb have great potential in As and Sb bioremediation, In this study, a Gram-negative bacterial strain, Bosea sp. AS-1, was isolated from a mine slag sample collected in Xikuangshan Sb mine in China. AS-1 could tolerate 120 mM of As(III) and 50 mM of antimonite [Sb(III)]. It could also oxidize 2 mM of As(III) or Sb(III) completely under heterotrophic and aerobic conditions. Interestingly, strain AS-1 preferred to oxidize As(III) with yeast extract as the carbon source, whereas Sb(III) oxidation was favored with lactate in the medium. Genomic analysis of AS-1 confirmed the presence of several gene islands for As resistance and oxidation. Notably, a system of AS-1 and goethite was found to be able to remove 99% of the As with the initial concentration of 500 μg/L As(III) and 500 μg/L Sb(III), which suggests the potential of this approach for As removal in environments especially with the presence of high Sb.

Influence of the Chemical Form of Antimony on Soil Microbial Community Structure and Arsenite Oxidation Activity

In the present study, the influence of the co-contamination with various chemical forms of antimony (Sb) with arsenite (As[III]) on soil microbial communities was investigated. The oxidation of As(III) to As(V) was monitored in soil columns amended with As(III) and three different chemical forms of Sb: antimony potassium tartrate (Sb[III]-tar), antimony(III) oxide (Sb₂O₃), and potassium antimonate (Sb[V]). Soil microbial communities were examined qualitatively and quantitatively using 16S rDNA- and arsenite oxidase gene (aioA)-targeted analyses. Microbial As(III) oxidation was detected in all soil columns and 90–100% of added As(III) (200 μmol L⁻¹) was oxidized to As(V) in 9 d, except in the Sb(III)-tar co-amendments that only oxidized 30%. 16S rDNA- and aioA-targeted analyses showed that the presence of different Sb chemical forms significantly affected the selection of distinct As(III)-oxidizing bacterial populations. Most of the 16S rRNA genes detected in soil columns belonged to Betaproteobacteria and Gammaproteobacteria, and some sequences were closely related to those of known As(III) oxidizers. Co-amendments with Sb(III)-tar and high concentrations of Sb₂O₃ significantly increased the ratios of aioA-possessing bacterial populations, indicating the enrichment of As(III) oxidizers resistant to As and Sb toxicity. Under Sb co-amendment conditions, there was no correlation between aioA gene abundance and the rates of As(III) oxidation. Collectively, these results demonstrated that the presence of different Sb chemical forms imposed a strong selective pressure on the soil bacterial community and, thus, the co-existing metalloid is an important factor affecting the redox transformation of arsenic in natural environments.

Bacterial community profile of contaminated soils in a typical antimony mining site

The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb_DGT, As_DGT, potential ecological risk index (RI), TC, TN), among which pH, Sb_DGT, and As_DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh

Long-term exposure to trace levels of arsenic (As) in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V)] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III)] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V) reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III) and As(V) reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V) and Fe(III) in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.IMPORTANCE The consumption of arsenic in waters collected from tube wells threatens the lives of millions worldwide and is particularly acute in the floodplains and deltas of southern Asia. The cause of arsenic mobilization from natural sediments within these aquifers to groundwater is complex, with recent studies suggesting that sediment-dwelling microorganisms may be the cause. In the absence of oxygen at depth, specialist bacteria are thought able to use metals within the sediments to support their metabolism. Via these processes, arsenic-contaminated iron minerals are transformed, resulting in the release of arsenic into the aquifer waters. Focusing on a field site in Bangladesh, a comprehensive, multidisciplinary study using state-of-the-art geological and microbiological techniques has helped better understand the microbes that are present naturally in a high-arsenic aquifer and how they may transform the chemistry of the sediment to potentially lethal effect.

Functional genes and thermophilic microorganisms responsible for arsenite oxidation from the shallow sediment of an untraversed hot spring outlet

Hot Springs have unique geochemical features. Microorganisms-mediated arsenite oxidation is one of the major biogeochemical processes occurred in some hot springs. This study aimed to understand the diversities of genes and microorganisms involved in arsenite oxidation from the outlet of an untraversed hot spring located at an altitude of 4226 m. Microcosm assay indicated that the microbial community from the hot spring was able to efficiently oxidize As(III) using glucose, lactic acid, yeast extract or sodium bicarbonate as the sole carbon source. The microbial community contained 7 phyla of microorganisms, of which Proteobacteria and Firmicutes are largely dominant; this composition is unique and differs significantly from those of other described hot springs. Twenty one novel arsenite oxidase genes were identified from the samples, which are affiliated with the arsenite oxidase families of α-Proteobacteria, β-Proteobacteria or Archaea; this highlights the high diversity of the arsenite-oxidizing microorganisms from the hot spring. A cultivable arsenite-oxidizer Chelatococcu sp. GHS311 was also isolated from the sample using enrichment technique. It can completely convert 75.0 mg/L As(III) into As(V) in 18 days at 45 °C. The arsenite oxidase of GHS311 shares the maximal sequence identity (84.7%) to that of Hydrogenophaga sp. CL3, a non-thermotolerant bacterium. At the temperature lower than 30 °C or higher than 65 °C, the growth of this strain was completely inhibited. These data help us to better understand the diversity and functional features of the thermophilic arsenite-oxidizing microorganisms from hot springs.