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Arsenic (As) is a toxic metalloid that causes severe environmental contamination worldwide. Upon exposure to aqueous phases, the As-bearing minerals, such as orpiment (As 2 S 3 ) and realgar (As 4 S 4 ), 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 S 2- from minerals is abiotically impacted by SSA, while the microbial oxidation of As(III) and S 2- 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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

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 CO 2 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)., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

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.

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., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N 2 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., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriia-associated MAGs from five additional metal-contaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites., (© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.)

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., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Biological arsenite [As(III)] oxidation is an important process in the removal of toxic arsenic (As) from contaminated water. However, the diversity and metabolic potentials of As(III)-oxidizing bacteria (AOB) responsible for As(III) oxidation in wastewater treatment facilities are not well documented. In this study, two groups of bioreactors inoculated with activated sludge were operated under anoxic or oxic conditions to treat As-containing synthetic wastewater. Batch tests of inoculated sludges from the bioreactors further indicated that microorganisms could use nitrate or oxygen as electron acceptors to stimulate biological As(III) oxidation, suggesting the potentials of this process in wastewater treatment facilities. In addition, DNA-based stable isotope probing (DNA-SIP) was performed to identify the putative AOB in the activated sludge. Bacteria associated with Thiobacillus were identified as nitrate-dependent AOB, while bacteria associated with Hydrogenophaga were identified as aerobic AOB in activated sludge. Metagenomic binning reconstructed a number of high-quality metagenome-assembled genomes (MAGs) associated with the putative AOB. Functional genes encoding As resistance, As(III) oxidation, denitrification, and carbon fixation were identified in these MAGs, suggesting their potentials for chemoautotrophic As(III) oxidation. In addition, the presence of genes encoding secondary metabolite biosynthesis and extracellular polymeric substance metabolism in these MAGs may facilitate the proliferation of these AOB in activated sludge and enhance their capacity for As(III) oxidation. IMPORTANCE AOB play an important role in the removal of toxic arsenic from wastewater. Most of the AOB have been isolated from natural environments. However, knowledge regarding the structure and functional roles of As(III)-oxidizing communities in wastewater treatment facilities is not well documented. The combination of DNA-SIP and metagenomic binning provides an opportunity to elucidate the diversity of in situ AOB community inhabiting the activated sludges. In this study, the putative AOB responsible for As(III) oxidation in wastewater treatment facilities were identified, and their metabolic potentials, including As(III) oxidation, denitrification, carbon fixation, secondary metabolite biosynthesis, and extracellular polymeric substance metabolism, were investigated. This observation provides an understanding of anoxic and/or oxic AOB during the As(III) oxidation process in wastewater treatment facilities, which may contribute to the removal of As from contaminated water.

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., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

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., (© The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.)