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Zhang Z, Liu T, Li X, Ye Q, Bangash HI, Zheng J, Peng N. Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China. ENVIRONMENTAL RESEARCH 2023; 238:117144. [PMID: 37716381 DOI: 10.1016/j.envres.2023.117144] [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: 06/20/2023] [Revised: 08/31/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.
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Affiliation(s)
- Zhufeng Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tao Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.
| | - Xudong Li
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Qing Ye
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Hina Iqbal Bangash
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China.
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Omeroglu MA, Baltaci MO, Adiguzel A. Anoxybacillus: an overview of a versatile genus with recent biotechnological applications. World J Microbiol Biotechnol 2023; 39:139. [PMID: 36995480 DOI: 10.1007/s11274-023-03583-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
The Bacillaceae family members are considered to be a good source of microbial factories for biotechnological processes. In contrast to Bacillus and Geobacillus, Anoxybacillus, which would be thermophilic and spore-forming group of bacteria, is a relatively new genus firstly proposed in the year of 2000. The development of thermostable microbial enzymes, waste management and bioremediation processes would be a crucial parameter in the industrial sectors. There has been increasing interest in Anoxybacillus strains for biotechnological applications. Therefore, various Anoxybacillus strains isolated from different habitats have been explored and identified for biotechnological and industrial purposes such as enzyme production, bioremediation and biodegradation of toxic compounds. Certain strains have ability to produce exopolysaccharides possessing biological activities including antimicrobial, antioxidant and anticancer. This current review provides past and recent discoveries regarding Anoxybacillus strains and their potential biotechnological applications in enzyme industry, environmental processes and medicine.
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Affiliation(s)
- Mehmet Akif Omeroglu
- Faculty of Science, Department of Molecular Biology and Genetics, Ataturk University, Erzurum, 25400, Turkey
| | - Mustafa Ozkan Baltaci
- Faculty of Science, Department of Molecular Biology and Genetics, Ataturk University, Erzurum, 25400, Turkey.
| | - Ahmet Adiguzel
- Faculty of Science, Department of Molecular Biology and Genetics, Ataturk University, Erzurum, 25400, Turkey.
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Zhao J, Shakir Y, Deng Y, Zhang Y. Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring. BMC Microbiol 2023; 23:56. [PMID: 36869305 PMCID: PMC9983152 DOI: 10.1186/s12866-023-02803-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Thermostable microorganisms are extremophiles. They have a special genetic background and metabolic pathway and can produce a variety of enzymes and other active substances with special functions. Most thermo-tolerant microorganisms from environmental samples have resisted cultivation on artificial growth media. Therefore, it is of great significance to isolate more thermo-tolerant microorganisms and study their characteristics to explore the origin of life and exploit more thermo-tolerant enzymes. Tengchong hot spring in Yunnan contains a lot of thermo-tolerant microbial resources because of its perennial high temperature. The ichip method was developed by D. Nichols in 2010 and can be used to isolate so-called "uncultivable" microorganisms from different environments. Here, we describe the first application of modified ichip to isolate thermo-tolerant bacteria from hot springs. RESULTS In this study, 133 strains of bacteria belonging to 19 genera were obtained. 107 strains of bacteria in 17 genera were isolated by modified ichip, and 26 strains of bacteria in 6 genera were isolated by direct plating methods. 25 strains are previously uncultured, 20 of which can only be cultivated after being domesticated by ichip. Two strains of previously unculturable Lysobacter sp., which can withstand 85 °C, were isolated for the first time. Alkalihalobacillus, Lysobacter and Agromyces genera were first found to have 85 °C tolerance. CONCLUSION Our results indicate that the modified ichip approach can be successfully applied in a hot spring environment.
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Affiliation(s)
- Juntian Zhao
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yasmeen Shakir
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ying Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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Cai X, Zhang Z, Yin N, Lu W, Du H, Yang M, Cui L, Chen S, Cui Y. Controlling microbial arsenite oxidation and mobilization in arsenite-adsorbed iron minerals: The Influence of pH conditions and mineralogical composition. JOURNAL OF HAZARDOUS MATERIALS 2022; 433:128778. [PMID: 35358812 DOI: 10.1016/j.jhazmat.2022.128778] [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: 02/02/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
The oxidation of aqueous arsenite (As(III)) by As(III)-oxidizing bacteria is known to attenuate the mobilization and toxicity of arsenic, and is regarded as potential method for As(III)-pollution remediation. However, during the interactions between As(III)-oxidizing bacteria and different As(III)-adsorbed soil Fe-minerals, the oxidation and partitioning of solid-phase As(III), as well as the controlling mechanisms, remain unclear. In this study, we therefore incubated three As(III)-adsorbed Fe-minerals with a typical As(III)-oxidizing bacteria (Pseudomonas sp. HN-1) at different pH conditions. After microbial oxidation, the percentage of arsenate (As(V)) was significantly higher at pH 7 (15-94%) and 9 (12-89%) than at pH 4 (6-50%) in all Fe-minerals. Incubation of As(III)-oxidizing bacteria promoted As-immobilization under acidic-conditions but As-mobilization under alkaline-conditions. Arsenic-X-ray adsorption spectroscopy results showed that solid-phase As(V) fraction in goethite, hematite and magnetite was 27-64%, 5-12% and 50-91%, respectively. Compared with the corner-sharing As(III)-adsorption complexes formed on magnetite, the edge-sharing complexes on hematite were significantly more stable towards microbial-oxidation. Additionally, the strong adhesion between strain HN-1 and hematite probably limit bacterial-activity and mobility, thereby inhibiting microbial As(III)-oxidation. Our findings elucidate the controlling mechanisms of microbial As(III)-oxidation in different As(III)-adsorbed Fe-minerals and demonstrate strain HN-1 is an excellent candidate for As(III)-remediation in soils containing goethite and magnetite.
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Affiliation(s)
- Xiaolin Cai
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Zhennan Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Naiyi Yin
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Wenyi Lu
- Binzhou Institute of Technology, Binzhou, Shandong Province 256606, People's Republic of China
| | - Huili Du
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Mei Yang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Liwei Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China
| | - Shibao Chen
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China.
| | - Yanshan Cui
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, People's Republic of China; Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.
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Current knowledge on molecular mechanisms of microorganism-mediated bioremediation for arsenic contamination: A review. Microbiol Res 2022; 258:126990. [DOI: 10.1016/j.micres.2022.126990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
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Yuan C, Li P, Qing C, Kou Z, Wang H. Different Regulatory Strategies of Arsenite Oxidation by Two Isolated Thermus tengchongensis Strains From Hot Springs. Front Microbiol 2022; 13:817891. [PMID: 35359718 PMCID: PMC8963470 DOI: 10.3389/fmicb.2022.817891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Arsenic is a ubiquitous constituent in geothermal fluids. Thermophiles represented by Thermus play vital roles in its transformation in geothermal fluids. In this study, two Thermus tengchongensis strains, named as 15Y and 15W, were isolated from arsenic-rich geothermal springs and found different arsenite oxidation behaviors with different oxidation strategies. Arsenite oxidation of both strains occurred at different growth stages, and two enzyme-catalyzed reaction kinetic models were observed. The arsenite oxidase of Thermus strain 15W performed better oxidation activity, exhibiting typical Michaelis–Menten kinetics. The kinetic parameter of arsenite oxidation in whole cell showed a Vmax of 18.48 μM min–1 and KM of 343 μM. Both of them possessed the arsenite oxidase-coding genes aioB and aioA. However, the expression of gene aioBA was constitutive in strain 15W, whereas it was induced by arsenite in strain 15Y. Furthermore, strain 15Y harbored an intact aio operon including the regulatory gene of the ArsR family, whereas a genetic inversion of an around 128-kbp fragment produced the inactivation of this regulator in strain 15W, leading to the constitutive expression of aioBA genes. This study provides a valuable insight into the adaption of thermophiles to extreme environments.
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Affiliation(s)
- Changguo Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
- *Correspondence: Ping Li,
| | - Chun Qing
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Zhu Kou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
| | - Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan, China
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Huang C, Wang H, Shi X, Wang Y, Li P, Yin H, Shao Y. Two new selenite reducing bacterial isolates from paddy soil and the potential Se biofortification of paddy rice. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1465-1475. [PMID: 32880083 DOI: 10.1007/s10646-020-02273-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Selenium (Se) is an essential element for human health. Se-enriched agricultural products can promote people's intake of Se. Microorganisms play an important role in Se cycling. In this study, two new bacterial strains were isolated from paddy soil and were identified as Chitinophaga sp. and Comamonas testosteroni, respectively. More than 44% and 39% of 1.0 mM selenite were reduced in 84 h by them using yeast extract as carbon source, respectively. Scanning electron microscope (SEM) and Energy dispersive X-ray spectrometry (EDS) results indicated that the reduction product of selenite was nanometer Se. These strains could promote the available Se in soil and the content of Se in rice plants in pot experiments. Organic combined Se in soils was increased up to 35%, accompanied by the 92% and 130% increase of Se in rice plants. To our best knowledge, this is the first report of Se reduction by Chitinophaga. This work might provide a prospective strategy for microbial fortification of Se in corps.
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Affiliation(s)
- Chunlei Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
- Zhejiang Institute of Geological Survey, Hangzhou, 311203, PR China
| | - Helin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Xinyan Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China.
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China.
| | - Hanqin Yin
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, PR China
- Zhejiang Institute of Geological Survey, Hangzhou, 311203, PR China
| | - Yixian Shao
- Zhejiang Institute of Geological Survey, Hangzhou, 311203, PR China
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Pal S, Sengupta K. In silico analysis of phylogeny, structure, and function of arsenite oxidase from unculturable microbiome of arsenic contaminated soil. J Genet Eng Biotechnol 2021; 19:47. [PMID: 33779860 PMCID: PMC8006529 DOI: 10.1186/s43141-021-00146-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/12/2021] [Indexed: 11/10/2022]
Abstract
Background Arsenite oxidase (EC 1.20.2.1) is a metalloenzyme that catalyzes the oxidation of arsenite into lesser toxic arsenate. In this study, 78 amino acid sequences of arsenite oxidase from unculturable bacteria available in metagenomic data of arsenic-contaminated soil have been characterized by using standard bioinformatics tools to investigate its phylogenetic relationships, three-dimensional structure and functional parameters. Results The phylogenetic relationship of all arsenite oxidase from unculturable microorganisms was revealed their closeness to bacterial order Rhizobiales. The higher aliphatic content showed that these enzymes are thermostable and could be used for in situ bioremediation. A representative protein from each phylogenetic cluster was analysed for secondary structure arrangements which indicated the presence of α-helices (~63%), β-sheets (57–60%) and turns (13–15%). The validated 3D models suggested that these proteins are hetero-dimeric with two chains whereas alpha chain is the main catalytic subunit which binds with arsenic oxides. Three representative protein models were deposited in Protein Model Database. The query enzymes were predicted with two conserved motifs, one is Rieske 3Fe-4S and the other is molybdopterin protein. Conclusions Computational analysis of protein interactome revealed the protein partners might be involved in the whole process of arsenic detoxification by Rhizobiales. The overall report is unique to the best of our knowledge, and the importance of this study is to understand the theoretical aspects of the structure and functions of arsenite oxidase in unculturable bacteria residing in arsenic-contaminated sites. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00146-x.
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Affiliation(s)
- Siddhartha Pal
- National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Kriti Sengupta
- Bioenergy Group, Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, India.
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Bagade A, Nandre V, Paul D, Patil Y, Sharma N, Giri A, Kodam K. Characterisation of hyper tolerant Bacillus firmus L-148 for arsenic oxidation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114124. [PMID: 32078878 DOI: 10.1016/j.envpol.2020.114124] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/01/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Groundwater arsenic pollution causes millions of deaths worldwide. Long term natural and anthropogenic activities have increased arsenic levels in groundwater causing higher threats of arsenic exposure. Arsenic hyper-tolerant Firmicute Bacillus firmus L-148 was isolated from arsenic limiting Lonar lake soil, which tolerated more than 3 M arsenic and could oxidize 75 mM arsenite [As(III)] in 14 days. It oxidized As(III) in presence of heavy metals and had unusual pH optima at 9.2. B. firmus L-148 was studied at the biochemical, protein, genomic and transcript level for understanding its arsenic oxidizing machinery. The proteomic and transcript analysis exhibited the presence of ars and aio operon and supported the inducible nature of ars operon. Robust, hyper-tolerant, fast As(III) oxidizing, least nutrient requiring and multi-metal resistance qualities of the strain were used in microcosm studies for bioremediation. Artificial groundwater mimicking microcosm with 75 mM As(III) was developed. Modulation of carbon source, iron and multi metals affected growth and As(III) oxidation rate. The As(III) oxidation was recorded to be 77% in 15 days in presence of sodium acetate and Fe ions. This microcosm study can be explored for bioremediation of arsenic contaminated water and followed by precipitation using other methods.
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Affiliation(s)
- Aditi Bagade
- Biochemistry Division, Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, India
| | - Vinod Nandre
- Biochemistry Division, Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, India
| | - Dhiraj Paul
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, 411021, India
| | - Yugendra Patil
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Nisha Sharma
- Biochemistry Division, Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, India
| | - Ashok Giri
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Kisan Kodam
- Biochemistry Division, Department of Chemistry, Savitribai Phule Pune University, Pune, 411007, India.
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Han YH, Yin DX, Jia MR, Wang SS, Chen Y, Rathinasabapathi B, Chen DL, Ma LQ. Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:1178-1189. [PMID: 31470481 DOI: 10.1016/j.scitotenv.2019.07.098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/06/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
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.
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Affiliation(s)
- Yong-He Han
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, China
| | - Dai-Xia Yin
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Meng-Ru Jia
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Shan-Shan Wang
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China
| | - Yanshan Chen
- School of the Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Bala Rathinasabapathi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Deng-Long Chen
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; Innovative Center for Eco-Friendly Polymeric Materials, Quanzhou, Fujian 362801, China.
| | - Lena Q Ma
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States.
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11
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Leon CG, Moraga R, Valenzuela C, Gugliandolo C, Lo Giudice A, Papale M, Vilo C, Dong Q, Smith CT, Rossello-Mora R, Yañez J, Campos VL. Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile). PLoS One 2018; 13:e0195080. [PMID: 29715297 PMCID: PMC5929503 DOI: 10.1371/journal.pone.0195080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 03/17/2018] [Indexed: 12/20/2022] Open
Abstract
Arsenic (As), a highly toxic metalloid, naturally present in Camarones River (Atacama Desert, Chile) is a great health concern for the local population and authorities. In this study, the taxonomic and functional characterization of bacterial communities associated to metal-rich sediments from three sites of the river (sites M1, M2 and M3), showing different arsenic concentrations, were evaluated using a combination of approaches. Diversity of bacterial communities was evaluated by Illumina sequencing. Strains resistant to arsenic concentrations varying from 0.5 to 100 mM arsenite or arsenate were isolated and the presence of genes coding for enzymes involved in arsenic oxidation (aio) or reduction (arsC) investigated. Bacterial communities showed a moderate diversity which increased as arsenic concentrations decreased along the river. Sequences of the dominant taxonomic groups (abundances ≥1%) present in all three sites were affiliated to Proteobacteria (range 40.3–47.2%), Firmicutes (8.4–24.8%), Acidobacteria (10.4–17.1%), Actinobacteria (5.4–8.1%), Chloroflexi (3.9–7.5%), Planctomycetes (1.2–5.3%), Gemmatimonadetes (1.2–1.5%), and Nitrospirae (1.1–1.2%). Bacterial communities from sites M2 and M3 showed no significant differences in diversity between each other (p = 0.9753) but they were significantly more diverse than M1 (p<0.001 and p<0.001, respectively). Sequences affiliated with Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi and Actinobacteria at M1 accounted for more than 89% of the total classified bacterial sequences present but these phyla were present in lesser proportions in M2 and M3 sites. Strains isolated from the sediment of sample M1, having the greatest arsenic concentration (498 mg kg-1), showed the largest percentages of arsenic oxidation and reduction. Genes aio were more frequently detected in isolates from M1 (54%), whereas arsC genes were present in almost all isolates from all three sediments, suggesting that bacterial communities play an important role in the arsenic biogeochemical cycle and detoxification of arsenical compounds. Overall, results provide further knowledge on the microbial diversity of arsenic contaminated fresh-water sediments.
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Affiliation(s)
- Carla G. Leon
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Ruben Moraga
- Microbiology Laboratory, Faculty of Renewable Natural Resources, Arturo Prat University, Iquique, Chile
| | - Cristian Valenzuela
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Concetta Gugliandolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Angelina Lo Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Claudia Vilo
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Qunfeng Dong
- Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Carlos T. Smith
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Institut Mediterrani d’Estudis Avancats (CSIC-UIB), Esporles, Spain
| | - Jorge Yañez
- Department of Analytical and Inorganic Chemistry, Faculty of Chemical Sciences, University of Concepcion, Concepcion, Chile
| | - Victor L. Campos
- Environmental Microbiology Laboratory, Department of Microbiology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
- * E-mail:
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12
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Crognale S, Zecchin S, Amalfitano S, Fazi S, Casentini B, Corsini A, Cavalca L, Rossetti S. Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin. Front Microbiol 2017; 8:2468. [PMID: 29312179 PMCID: PMC5732945 DOI: 10.3389/fmicb.2017.02468] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/28/2017] [Indexed: 11/16/2022] Open
Abstract
Arsenic (As) is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria, affiliated to Alpha- and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulfate reduction and heterotrophic As(III)-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III)-oxidizers, autotrophic and heterotrophic As(V)-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V) detoxifying reduction, were found in all samples whereas aioA [As(III) oxidase] and arrA genes [As(V) respiratory reductase] were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As.
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Affiliation(s)
- Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Sarah Zecchin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Stefano Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Stefano Fazi
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Barbara Casentini
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Anna Corsini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
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13
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Wang J, Wan J, Wu Z, Li H, Li H, Dagot C, Wang Y. Flexible biological arsenite oxidation utilizing NO x and O 2 as alternative electron acceptors. CHEMOSPHERE 2017; 178:136-142. [PMID: 28324835 DOI: 10.1016/j.chemosphere.2017.03.044] [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: 10/31/2016] [Revised: 03/01/2017] [Accepted: 03/10/2017] [Indexed: 06/06/2023]
Abstract
The feasibility of flexible microbial arsenite (AsIII) oxidation coupled with the reduction of different electron acceptors was investigated. The results indicated the acclimated microorganisms could oxidize AsIII with oxygen, nitrate and nitrite as the alternative electron acceptors. A series of batch tests were conducted to measure the kinetic parameters of AsIII oxidation and to evaluate the effects of environmental conditions including pH and temperature on the activity of biological AsIII oxidation dependent on different electron acceptors. Kinetic results showed that oxygen-dependent AsIII oxidation had the highest oxidation rate (0.59 mg As g-1 VSS min-1), followed by nitrate- (0.40 mg As g-1 VSS min-1) and nitrite-dependent AsIII oxidation (0.32 mg As g-1 VSS min-1). The kinetic data of aerobic AsIII oxidation were fitted well with the Monod kinetic model, while the Haldane substrate inhibition model was better applicable to describe the inhibition of anoxic AsIII oxidation. Both aerobic and anoxic AsIII oxidation performed the optimal activity at the near neutral pH. Besides, the optimal temperature for oxygen-, nitrate- and nitrite-dependent AsIII oxidation was 30 ± 1 °C, 40 ± 1 °C and 20 ± 1 °C, respectively.
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Affiliation(s)
- Jie Wang
- School of Chemical Engineering and Energy, Zhengzhou University, 100 Science Avenue, 450001, PR China
| | - Junfeng Wan
- School of Chemical Engineering and Energy, Zhengzhou University, 100 Science Avenue, 450001, PR China.
| | - Zihao Wu
- School of Chemical Engineering and Energy, Zhengzhou University, 100 Science Avenue, 450001, PR China
| | - Hongli Li
- School of Chemical Engineering and Energy, Zhengzhou University, 100 Science Avenue, 450001, PR China
| | - Haisong Li
- School of Chemical Engineering and Energy, Zhengzhou University, 100 Science Avenue, 450001, PR China
| | - Christophe Dagot
- GRESE EA 4330, Université de Limoges, 123 Avenue Albert Thomas, F-87060, Limoges Cedex, France; INSERM, U1092, Limoges, France
| | - Yan Wang
- School of Chemical Engineering and Energy, Zhengzhou University, 100 Science Avenue, 450001, PR China
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14
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Khalil A, Sivakumar N, Arslan M, Qarawi S. Novel Anoxybacillus flavithermus AK1: A Thermophile Isolated from a Hot Spring in Saudi Arabia. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2017. [DOI: 10.1007/s13369-017-2622-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Yang Y, Mu Y, Zeng XC, Wu W, Yuan J, Liu Y, Guoji E, Luo F, Chen X, Li H, Wang J. Functional genes and thermophilic microorganisms responsible for arsenite oxidation from the shallow sediment of an untraversed hot spring outlet. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:490-501. [PMID: 28251437 DOI: 10.1007/s10646-017-1779-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
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.
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Affiliation(s)
- Ye Yang
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Yao Mu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China.
| | - Weiwei Wu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Jie Yuan
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Yichen Liu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - E Guoji
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Feng Luo
- School of Medicine, Jianghan University, Wuhan, 430056, People's Republic of China.
| | - Xiaoming Chen
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Hao Li
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
| | - Jianing Wang
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, People's Republic of China
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16
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Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring. Sci Rep 2016; 6:25262. [PMID: 27126380 PMCID: PMC4850476 DOI: 10.1038/srep25262] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
Alkaline sulfide-rich hot springs provide a unique environment for microbial community and arsenic (As) biogeochemistry. In this study, a representative alkaline sulfide-rich hot spring, Zimeiquan in the Tengchong geothermal area, was chosen to study arsenic geochemistry and microbial community using Illumina MiSeq sequencing. Over 0.26 million 16S rRNA sequence reads were obtained from 5-paired parallel water and sediment samples along the hot spring’s outflow channel. High ratios of As(V)/AsSum (total combined arsenate and arsenite concentrations) (0.59–0.78), coupled with high sulfide (up to 5.87 mg/L), were present in the hot spring’s pools, which suggested As(III) oxidation occurred. Along the outflow channel, AsSum increased from 5.45 to 13.86 μmol/L, and the combined sulfide and sulfate concentrations increased from 292.02 to 364.28 μmol/L. These increases were primarily attributed to thioarsenic transformation. Temperature, sulfide, As and dissolved oxygen significantly shaped the microbial communities between not only the pools and downstream samples, but also water and sediment samples. Results implied that the upstream Thermocrinis was responsible for the transformation of thioarsenic to As(III) and the downstream Thermus contributed to derived As(III) oxidation. This study improves our understanding of microbially-mediated As transformation in alkaline sulfide-rich hot springs.
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17
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Belduz AO, Canakci S, Chan KG, Kahar UM, Chan CS, Yaakop AS, Goh KM. Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey. Stand Genomic Sci 2015; 10:70. [PMID: 26413199 PMCID: PMC4584021 DOI: 10.1186/s40793-015-0065-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 09/04/2015] [Indexed: 11/20/2022] Open
Abstract
Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many biotechnological applications. Anoxybacillus ayderensis AB04T (= NCIMB 13972T = NCCB 100050T) was isolated from the Ayder hot spring in Rize, Turkey, and is one of the earliest described Anoxybacillus type strains. The present work reports the cellular features of A. ayderensis AB04T, together with a high-quality draft genome sequence and its annotation. The genome is 2,832,347 bp long (74 contigs) and contains 2,895 protein-coding sequences and 103 RNA genes including 14 rRNAs, 88 tRNAs, and 1 tmRNA. Based on the genome annotation of strain AB04T, we identified genes encoding various glycoside hydrolases that are important for carbohydrate-related industries, which we compared with those of other, sequenced Anoxybacillus spp. Insights into under-explored industrially applicable enzymes and the possible applications of strain AB04T were also described.
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Affiliation(s)
- Ali Osman Belduz
- Faculty of Sciences, Department of Biology, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Sabriye Canakci
- Faculty of Sciences, Department of Biology, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ummirul Mukminin Kahar
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Amira Suriaty Yaakop
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
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