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Yang R, Viswanatham T, Huang S, Li Y, Yu Y, Zhang J, Chen J, Herzberg M, Feng R, Rosen BP, Rensing C. A Sb(III)-specific efflux transporter from Ensifer adhaerens E-60. Microbiol Res 2024; 286:127830. [PMID: 39004025 DOI: 10.1016/j.micres.2024.127830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/16/2024]
Abstract
Antimony is pervasive environmental toxic substance, and numerous genes encoding mechanisms to resist, transform and extrude the toxic metalloid antimony have been discovered in various microorganisms. Here we identified a major facilitator superfamily (MFS) transporter, AntB, on the chromosome of the arsenite-oxidizing bacterium Ensifer adhaerens E-60 that confers resistance to Sb(III) and Sb(V). The antB gene is adjacent to gene encoding a LysR family transcriptional regulator termed LysRars, which is an As(III)/Sb(III)-responsive transcriptional repressor that is predicted to control expression of antB. Similar antB and lysRars genes are found in related arsenic-resistant bacteria, especially strains of Ensifer adhaerens, and the lysRars gene adjacent to antB encodes a member of a divergent subgroup of putative LysR-type regulators. Closely related AntB and LysRars orthologs contain three conserved cysteine residues, which are Cys17, Cys99, and Cys350 in AntB and Cys81, Cys289 and Cys294 in LysRars, respectively. Expression of antB is induced by As(III), Sb(III), Sb(V) and Rox(III) (4-hydroxy-3-nitrophenyl arsenite). Heterologous expression of antB in E. coli AW3110 (Δars) conferred resistance to Sb(III) and Sb(V) and reduced the intracellular concentration of Sb(III). The discovery of the Sb(III) efflux transporter AntB enriches our knowledge of the role of the efflux transporter in the antimony biogeochemical cycle.
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Affiliation(s)
- Ruixiang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Thiruselvam Viswanatham
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International Universitygrid.65456.34, Miami, FL, USA
| | - Shuangqin Huang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yanshuang Yu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jinlin Zhang
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Jian Chen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International Universitygrid.65456.34, Miami, FL, USA
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale) 06120, Germany
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International Universitygrid.65456.34, Miami, FL, USA
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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Kong T, Sun X, Gu Z, Yang N, Huang Y, Lan L, Gao P, Liu H, Wang Y, Jiang F, Li B, Sun W. Differential Mechanisms of Microbial As(III) and Sb(III) Oxidation and Their Contribution to Tailings Reclamation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11447-11458. [PMID: 38899977 DOI: 10.1021/acs.est.4c00863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
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.
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Affiliation(s)
- Tianle Kong
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Zhibin Gu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China
| | - Nie Yang
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yuqing Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Ling Lan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Pin Gao
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Huaqing Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yize Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Feng Jiang
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Chen X, Yu T, Xiao L, Zeng XC. Can Sb(III)-oxidizing prokaryote also oxidize As(III) under aerobic and anaerobic conditions, and vice versa? JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134135. [PMID: 38574656 DOI: 10.1016/j.jhazmat.2024.134135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/03/2024] [Accepted: 03/24/2024] [Indexed: 04/06/2024]
Abstract
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.
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Affiliation(s)
- Xiaoming Chen
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Tingting Yu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Linhai Xiao
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China.
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Li M, Wang W, Wu M, Lei J, Lu X, Wang H. Stibnite dissolution and Sb oxidation by Paraccocus versutus XT0.6 via direct and indirect contact. JOURNAL OF HAZARDOUS MATERIALS 2024; 467:133731. [PMID: 38340562 DOI: 10.1016/j.jhazmat.2024.133731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/10/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
In this study Paraccocus versutus XT0.6 was employed to address the mechanism of microbial dissolution and oxidation of stibnite. Results showed that with the growth of XT0.6, pH increased to 9.0 in both microbe-mineral contact (MM) and microbe-mineral non-contact groups (M[M]). Dissolved Sb(III) was released from stibnite, which was subsequently quickly oxidized to Sb(V) completely in MM and partially in M[M] groups. On the contrast, the final pH decreased to 6.5 and 4.9, respectviely, in system amended with extracellular secretion (EM) of XT0.6 and abiotic groups. Dissolution of stibnite and oxidation of Sb(III) were also observed in EM group, suggesting a potential contribution of extracellular enzyme in Sb(III) oxidation. The dissolution and oxidation rates were the highest in MM group, followed by those in M[M], EM and abiotic groups. To be noted, Sb(V) concentration decreased in MM group on the fifth day, which might indicate the formation of Sb(V)-bearing secondary mineral. Genome of XT0.6 consisted of two chromosomes and one plasmid, and most genes responsible for antimony oxidation and antimony resistance were located on the chromosomes. Proteomics analysis of the extracellular secretions indicated the up-regulated proteins were mainly related to electron-transfer, suggesting their potential role in Sb(III) oxidation.
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Affiliation(s)
- Min Li
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Weiqi Wang
- State key Laboratory of Biogeology and Environmental Geology, China
| | - Mengxiaojun Wu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jingwen Lei
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaolu Lu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; State key Laboratory of Biogeology and Environmental Geology, China.
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5
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Yu T, Chen X, Zeng XC, Wang Y. 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. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:169893. [PMID: 38185173 DOI: 10.1016/j.scitotenv.2024.169893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
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.
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Affiliation(s)
- Tingting Yu
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Xiaoming Chen
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China.
| | - Yanxin Wang
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China
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Zhang D, Li X, Wu Y, Xu X, Liu Y, Shi B, Peng Y, Dai D, Sha Z, Zheng J. Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields. MICROBIOME 2023; 11:160. [PMID: 37491386 PMCID: PMC10367259 DOI: 10.1186/s40168-023-01601-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/17/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats. RESULTS Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments. CONCLUSIONS This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.
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Affiliation(s)
- Dechao Zhang
- Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Geology, Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xudong Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, 310012, Hangzhou, China
| | - Xuewei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, 310012, Hangzhou, China
| | - Yanxia Liu
- Laboratory for Marine Geology, Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Benze Shi
- Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Geology, Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Peng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dadong Dai
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongli Sha
- Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Geology, Laoshan Laboratory, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jinshui Zheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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Zhou J, Wu C, Pang S, Yang L, Yao M, Li X, Xia S, Rittmann BE. Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14808-14816. [PMID: 36201672 DOI: 10.1021/acs.est.2c04939] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A hydrogen-based membrane biofilm reactor (H2-MBfR) was operated to investigate the bioreduction of antimonate [Sb(V)] in terms of Sb(V) removal, the fate of Sb, and the pathways of reduction metabolism. The MBfR achieved up to 80% Sb(V) removal and an Sb(V) removal flux of 0.55 g/m2·day. Sb(V) was reduced to Sb(III), which mainly formed Sb2O3 precipitates in the biofilm matrix, although some Sb(III) was retained intracellularly. High Sb(V) loading caused stress that deteriorated performance that was not recovered when the high Sb(V) loading was removed. The biofilm community consisted of DSbRB (dissimilatory Sb-reduction bacteria), SbRB (Sb-resistant bacteria), and DIRB (dissimilatory iron-reducing bacteria). Dissimilatory antimonate reduction, mediated by the respiratory arsenate reductase ArrAB, was the main reduction route, but respiratory reduction coexisted with cytoplasmic Sb(V)-reduction mediated by arsenate reductase ArsC. Increasing Sb(V) loading caused stress that led to increases in the expression of arsC gene and intracellular accumulation of Sb(III). By illuminating the roles of the dissimilatory and cytoplasmic Sb(V) reduction mechanism in the biofilms of the H2-MBfR, this study reveals that the Sb(V) loading should be controlled to avoid stress that deteriorates Sb(V) reduction.
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Affiliation(s)
- Jingzhou Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Chengyang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Si Pang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Lin Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Mengying Yao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Xiaodi Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85287-5701, United States
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8
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Li J, Zhang Y, Wang X, Walk ST, Wang G. Integrated Metabolomics and Targeted Gene Transcription Analysis Reveal Global Bacterial Antimonite Resistance Mechanisms. Front Microbiol 2021; 12:617050. [PMID: 33584619 PMCID: PMC7876068 DOI: 10.3389/fmicb.2021.617050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/12/2021] [Indexed: 11/17/2022] Open
Abstract
Antimony (Sb)-resistant bacteria have potential applications in the remediation of Sb-contaminated sites. However, the effect of Sb(III) exposure on whole-cell metabolic change has not been studied. Herein, we combined untargeted metabolomics with a previous proteomics dataset and confirmatory gene transcription analysis to identify metabolic responses to Sb(III) exposure in Agrobacterium tumefaciens GW4. Dynamic changes in metabolism between control and Sb(III)-exposed groups were clearly shown. KEGG pathway analysis suggested that with Sb(III) exposure: (1) the branching pathway of gluconeogenesis is down-regulated, resulting in the up-regulation of pentose phosphate pathway to provide precursors of anabolism and NADPH; (2) glycerophospholipid and arachidonic acid metabolisms are down-regulated, resulting in more acetyl-CoA entry into the TCA cycle and increased capacity to produce energy and macromolecular synthesis; (3) nucleotide and fatty acid synthesis pathways are all increased perhaps to protect cells from DNA and lipid peroxidation; (4) nicotinate metabolism increases which likely leads to increased production of co-enzymes (e.g., NAD+ and NADP+) for the maintenance of cellular redox and Sb(III) oxidation. Expectedly, the total NADP+/NADPH content, total glutathione, and reduced glutathione contents were all increased after Sb(III) exposure in strain GW4, which contribute to maintaining the reduced state of the cytoplasm. Our results provide novel information regarding global bacterial responses to Sb(III) exposure from a single gene level to the entire metabolome and provide specific hypotheses regarding the metabolic change to be addressed in future research.
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Affiliation(s)
- Jingxin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuxiao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xing Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Li J, Gu T, Li L, Wu X, Shen L, Yu R, Liu Y, Qiu G, Zeng W. Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium. BMC Microbiol 2020; 20:106. [PMID: 32354325 PMCID: PMC7193398 DOI: 10.1186/s12866-020-01737-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/25/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce. RESULTS Here, we identified a 5,436,472 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As (III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Furthermore, a wide variety of genes associated with Sb(III) and other heavy metal (loid) s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), Bacillus sp. S3 was proved to a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed the evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal (loid) s resistance genes emphasized its indispensable role in the harsh eco-environment of Bacillus genus. Real-time quantitative PCR (RT-qPCR) analysis indicated that Sb(III)-related genes were all induced under the Sb(III) stress, while arsC gene was down-regulated. CONCLUSIONS The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationships between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.
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Affiliation(s)
- Jiaokun Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Tianyuan Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Xueling Wu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Runlan Yu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Yuandong Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China.
- Key Laboratory of Biometallurgy, Ministry of Education, Central South University, Changsha, 410083, China.
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Regulation of antimonite oxidation and resistance by the phosphate regulator PhoB in Agrobacterium tumefaciens GW4. Microbiol Res 2019; 226:10-18. [PMID: 31284939 DOI: 10.1016/j.micres.2019.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/13/2019] [Accepted: 04/24/2019] [Indexed: 11/21/2022]
Abstract
Microbial oxidation of antimonite [Sb(III)] to antimonate [Sb(V)] is a detoxification process which contributes to Sb(III) resistance. Antimonite oxidase AnoA is essential for Sb(III) oxidation, however, the regulation mechanism is still unknown. Recently, we found that the expressions of phosphate transporters were induced by Sb(III) using proteomics analysis in Agrobacterium tumefaciens GW4, thus, we predicted that the phosphate regulator PhoB may regulate bacterial Sb(III) oxidation and resistance. In this study, comprehensive analyses were performed and the results showed that (1) Genomic analysis revealed two phoB (named as phoB1 and phoB2) and one phoR gene in strain GW4; (2) Reporter gene assay showed that both phoB1 and phoB2 were induced in low phosphate condition (50 μM), but only phoB2 was induced by Sb(III); (3) Genes knock-out/complementation, Sb(III) oxidation and Sb(III) resistance tests showed that deletion of phoB2 significantly inhibited the expression of anoA and decreased bacterial Sb(III) oxidation efficiency and Sb(III) resistant. In contrast, deletion of phoB1 did not obviously affect anoA's expression level and Sb(III) oxidation/resistance; (4) A putative Pho motif was predicted in several A. tumefaciens strains and electrophoretic mobility shift assay (EMSA) showed that PhoB2 could bind with the promoter sequence of anoA; (5) Site-directed mutagenesis and short fragment EMSA revealed the exact DNA binding sequence for the protein-DNA interaction. These results showed that PhoB2 positively regulates Sb(III) oxidation and PhoB2 is also associated with Sb(III) resistance. Such regulation mechanism may provide a great contribution for bacterial survival in the environment with Sb and for bioremediation application.
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Li J, Zhang Y, Zheng S, Liu F, Wang G. Anaerobic Bacterial Immobilization and Removal of Toxic Sb(III) Coupled With Fe(II)/Sb(III) Oxidation and Denitrification. Front Microbiol 2019; 10:360. [PMID: 30873144 PMCID: PMC6400856 DOI: 10.3389/fmicb.2019.00360] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 02/12/2019] [Indexed: 11/17/2022] Open
Abstract
Antimony (Sb) pollution is a worldwide problem. In some anoxic sites, such as Sb mine drainage and groundwater sediment, the Sb concentration is extremely elevated. Therefore, effective Sb remediation strategies are urgently needed. In contrast to microbial aerobic antimonite [Sb(III)] oxidation, the mechanism of microbial anaerobic Sb(III) oxidation and the effects of nitrate and Fe(II) on the fate of Sb remain unknown. In this study, we discovered the mechanism of anaerobic Sb(III) oxidation coupled with Fe(II) oxidation and denitrification in the facultative anaerobic Sb(III) oxidizer Sinorhizobium sp. GW3. We observed the following: (1) under anoxic conditions with nitrate as the electron acceptor, strain GW3 was able to oxidize both Fe(II) and Sb(III) during cultivation; (2) in the presence of Fe(II), nitrate and Sb(III), the anaerobic Sb(III) oxidation rate was remarkably enhanced, and Fe(III)-containing minerals were produced during Fe(II) and Sb(III) oxidation; (3) qRT-PCR, gene knock-out and complementation analyses indicated that the arsenite oxidase gene product AioA plays an important role in anaerobic Sb(III) oxidation, in contrast to aerobic Sb(III) oxidation; and (4) energy-dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and powder X-ray diffraction (XRD) analyses revealed that the microbially produced Fe(III) minerals were an effective chemical oxidant responsible for abiotic anaerobic Sb(III) oxidation, and the generated Sb(V) was adsorbed or coprecipitated on the Fe(III) minerals. This process included biotic and abiotic factors, which efficiently immobilize and remove soluble Sb(III) under anoxic conditions. The findings revealed a significantly novel development for understanding the biogeochemical Sb cycle. Microbial Sb(III) and Fe(II) oxidation coupled with denitrification has great potential for bioremediation in anoxic Sb-contaminated environments.
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Affiliation(s)
- Jingxin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuxiao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shiling Zheng
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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He M, Wang N, Long X, Zhang C, Ma C, Zhong Q, Wang A, Wang Y, Pervaiz A, Shan J. Antimony speciation in the environment: Recent advances in understanding the biogeochemical processes and ecological effects. J Environ Sci (China) 2019; 75:14-39. [PMID: 30473279 DOI: 10.1016/j.jes.2018.05.023] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/24/2018] [Accepted: 05/28/2018] [Indexed: 05/14/2023]
Abstract
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.
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Affiliation(s)
- Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Ningning Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xiaojing Long
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Chengjun Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Congli Ma
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qianyun Zhong
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Aihua Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Ying Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Aneesa Pervaiz
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Jun Shan
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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Li J, Guo W, Shi M, Cao Y, Wang G. High-quality-draft genomic sequence of Paenibacillus ferrarius CY1 T with the potential to bioremediate Cd, Cr and Se contamination. Stand Genomic Sci 2017; 12:60. [PMID: 29046739 PMCID: PMC5634878 DOI: 10.1186/s40793-017-0273-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/21/2017] [Indexed: 11/23/2022] Open
Abstract
Paenibacillus ferrarius CY1T (= KCTC 33419T = CCTCC AB2013369T) is a Gram-positive, aerobic, endospore-forming, motile and rod-shaped bacterium isolated from iron mineral soil. This bacterium reduces sulfate (SO42-) to S2-, which reacts with Cd(II) to generate precipitated CdS. It also reduces the toxic chromate [Cr(VI)] and selenite [Se(VI)] to the less bioavailable chromite [Cr(III)] and selenium (Se0), respectively. Thus, strain CY1T has the potential to bioremediate Cd, Cr and Se contamination, which is the main reason for the interest in sequencing its genome. Here we describe the features of strain CY1T, together with the draft genome sequence and its annotation. The 9,184,169 bp long genome exhibits a G + C content of 45.6%, 7909 protein-coding genes and 81 RNA genes. Nine putative Se(IV)-reducing genes, five putative Cr(VI) reductase and nine putative sulfate-reducing genes were identified in the genome.
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Affiliation(s)
- Jingxin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Wei Guo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Manman Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Yajing Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 People’s Republic of China
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