Identification of Antimonate Reducing Bacteria and Their Potential Metabolic Traits by the Combination of Stable Isotope Probing and Metagenomic-Pangenomic Analysis

Sun, Weimin; Sun, Xiaoxu; Häggblom, Max M.; Lan, Ling; Li, Baoqin; Dong, Yiran; Xu, Rui; Li, Fangbai

doi:10.1021/acs.est.1c03967

Cited by 34 publications

(10 citation statements)

References 73 publications

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“…According to the extraction results, the concentration of water-soluble Sb decreased by 66.40%, 51.17%, and 65.17% of Sb (III)1600, Sb (III)3200, and Sb (III)4800 in the 60 d aging treatment compared with the 10 d aging treatment ( Figure 4 ). This is consistent with prior research, which found that Sb has a strong attraction for crystalline and non-crystalline Fe oxides, as well as hydroxide minerals [ 55 ]. Mn minerals coupled with Fe oxides demonstrated considerable promise for immobilizing Sb via oxidation of Sb (III) and sorption of Sb (V) [ 20 ].…”

Section: Discussionsupporting

confidence: 93%

Ecotoxicological Differences of Antimony (III) and Antimony (V) on Earthworms Eisenia fetida (Savingy)

Bai

Chen

et al. 2023

Toxics

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In this study, we assessed the acute and chronic toxic effects of Sb (III) and Sb (V) on Eisenia fetida (Savingy) (E. fetida) by applying the filter paper contact method, aged soil treatment, and avoidance test experiment. In the acute filter paper contact test, the LC50 values for Sb (III) were 2581 mg/L (24 h), 1427 mg/L (48 h), and 666 mg/L (72 h), which were lower than Sb (V). In the chronic aged soil exposure experiment, when the Sb (III)-contaminated soil was aged 10 d, 30 d, and 60 d after exposure for 7 d, the LC50 value of E. fetida was 370, 613, and >4800 mg/kg, respectively. Compared to Sb (V) spiked soils aged only for 10 d, the concentrations causing 50% mortality significantly increased by 7.17-fold after 14 days of exposure in soil aged for 60 d. The results show that Sb (III) and Sb (V) could cause death and directly affect the avoidance behavior of E. fetida; yet, the toxicity of Sb (III) was higher than that of Sb (V). Consistent with the decrease in water-soluble Sb, the toxicity of Sb to E. fetida was greatly reduced with time. Therefore, in order to avoid overestimating the ecological risk of Sb with varying oxidative states, it is important to consider the forms and bioavailability of Sb. This study accumulated and supplemented the toxicity data, and provided a more comprehensive basis for the ecological risk assessment of Sb.

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Section: Discussionsupporting

confidence: 93%

Ecotoxicological Differences of Antimony (III) and Antimony (V) on Earthworms Eisenia fetida (Savingy)

Bai

Chen

et al. 2023

Toxics

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“…Many studies have confirmed that microorganisms can metabolize As and Sb through through the same biological processes ( 71–73 ). For example, Sb(III) is transported by the As(III) transporter Acr3 or ArsB ( 71 , 72 ), and Sb(V) can be reduced through an arsenate respiratory reductase encoded by arrAB ( 73 ). Therefore, AsgeneDB, with its comprehensive and complete information on microbial As metabolism, can contribute a lot of novel information useful to the microbial community.…”

Section: Discussionmentioning

confidence: 99%

AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation

Stirling

Zhao

et al. 2022

NAR Genomics and Bioinformatics

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Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe-mediated As metabolism plays an important role in global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 400 242 representative sequences from 59 As metabolism gene families, which are affiliated with 1653 microbial genera from 46 phyla. AsgeneDB achieved 100% annotation sensitivity and 99.96% annotation accuracy for an artificial gene dataset. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment and soil). The results showed that AsgeneDB substantially improved the mapping ratio of short reads in metagenomes from various environments. Compared with other databases, AsgeneDB provides more accurate, more comprehensive and faster analysis of As metabolic genes. In addition, we developed an R package, Asgene, to facilitate the analysis of metagenome sequencing data. Therefore, AsgeneDB and the associated Asgene package will greatly promote the study of As metabolism in microbial communities in various environments.

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“…Microbes are the key drivers for Sb redox transformations, catalyzing both Sb(III) oxidation and Sb(V) reduction. − Many bacteria mediate Sb(III) oxidation, either for detoxification or for energy generation. − Generation of energy from Sb(III) oxidation may be coupled to nitrogen fixation . Sb(III) oxidation has been proposed to be a microbial detoxification process that has the potential for Sb remediation .…”

Section: Introductionmentioning

confidence: 99%

Widespread Distribution of the arsO Gene Confers Bacterial Resistance to Environmental Antimony

Tang,

Song,

Chen

et al. 2023

Environ. Sci. Technol.

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Microbial oxidation of environmental antimonite (Sb(III)) to antimonate (Sb(V)) is an antimony (Sb) detoxification mechanism. Ensifer adhaerens ST2, a bacterial isolate from a Sb-contaminated paddy soil, oxidizes Sb(III) to Sb(V) under oxic conditions by an unknown mechanism. Genomic analysis of ST2 reveals a gene of unknown function in an arsenic resistance (ars) operon that we term arsO. The transcription level of arsO was significantly upregulated by the addition of Sb(III). ArsO is predicted to be a flavoprotein monooxygenase but shows low sequence similarity to other flavoprotein monooxygenases. Expression of arsO in the arsenic-hypersensitive Escherichia coli strain AW3110Δars conferred increased resistance to Sb(III) but not arsenite (As(III)) or methylarsenite (MAs(III)). Purified ArsO catalyzes Sb(III) oxidation to Sb(V) with NADPH or NADH as the electron donor but does not oxidize As(III) or MAs(III). The purified enzyme contains flavin adenine dinucleotide (FAD) at a ratio of 0.62 mol of FAD/mol protein, and enzymatic activity was increased by addition of FAD. Bioinformatic analyses show that arsO genes are widely distributed in metagenomes from different environments and are particularly abundant in environments affected by human activities. This study demonstrates that ArsO is an environmental Sb(III) oxidase that plays a significant role in the detoxification of Sb(III).

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Identification of Antimonate Reducing Bacteria and Their Potential Metabolic Traits by the Combination of Stable Isotope Probing and Metagenomic-Pangenomic Analysis

Cited by 34 publications

References 73 publications

Ecotoxicological Differences of Antimony (III) and Antimony (V) on Earthworms Eisenia fetida (Savingy)

Ecotoxicological Differences of Antimony (III) and Antimony (V) on Earthworms Eisenia fetida (Savingy)

AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation

Widespread Distribution of the arsO Gene Confers Bacterial Resistance to Environmental Antimony

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