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Zhang Z, Huang C, Du B, Xie C, Jiang L, Tang S, Xu X. Draft genome sequence of a new carotenoid-producing strain Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China. 3 Biotech 2022; 12:298. [PMID: 36276479 PMCID: PMC9522940 DOI: 10.1007/s13205-022-03366-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 09/17/2022] [Indexed: 11/01/2022] Open
Abstract
Some species of the genus Brevibacterium are orange bacteria involved in cheese ripening, synthesis of odoriferous compounds, and carotenoids with aromatic end groups. Here, we report the genome sequence of Brevibacterium sp. XU54, isolated from radioactive soil in Xinjiang, China. The genome of XU54 consists of 4,899,099 base pairs with a GC content of 62.2%. The genome sequence was annotated with 4453 genes, encoding 4260 proteins, 13 rRNAs, and 49 tRNAs. 16S rRNA BLAST and comparative genomic analysis both indicated that XU54 may be a new species of Brevibacterium. In addition, compared to the type strains, some enzymes related to sulfur metabolism showed a low similarity of 66.85, 79.53 and 14.61%, respectively. The carotenoids biosynthesis gene cluster was identified and analyzed according to the genomic data, which revealed relatively low identity (5-85%) with existing strains. The optimum conditions for its growth and carotenoid production were then discussed. The whole-genome sequence of Brevibacterium sp. XU54 will be beneficial for utilizing these newly identified genes in carotenoid biosynthesis and regulation of sulfur metabolism pathway to promote the production of novel carotenoids and other structurally diverse compounds through combinatorial biosynthesis, which facilitates cheese ripening and coloration. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03366-1.
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Affiliation(s)
- Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Chunyan Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Bangmian Du
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
| | - Chengjia Xie
- School of Chemical Engineering, Yangzhou Polytechnic Institute, Yangzhou, 225127 Jiangsu China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Susu Tang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046 Jiangsu China
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Kavehei A, Gore DB, Chariton AA, Hose GC. Characterizing the spatial distributions of soil biota at a legacy base metal mine using environmental DNA. CHEMOSPHERE 2022; 286:131899. [PMID: 34426292 DOI: 10.1016/j.chemosphere.2021.131899] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 05/20/2023]
Abstract
Characterizing the distribution of biota in response to contaminants is a critical element of site risk assessments. In this study we investigated the spatial distributions of biota and soil chemistry data in surface soil from Sunny Corner, a legacy base metal sulfide mine, Australia. Our results showed that copper (Cu), zinc (Zn), arsenic (As) and lead (Pb) in the surface soil exceeded Australian national soil quality guidelines and posed risks to the environment. Environmental (e)DNA metabarcoding of prokaryote and eukaryote composition confirmed the suggestion of environmental risk posed by these elements collectively explaining 72.9 % and 60.5 % of the total variation in the composition of soil prokaryotes and eukaryotes, respectively. Prokaryotic taxa from the phyla Gemmatimonadetes, Verrucomicrobia and Deinococcus-Thermus showed similar spatial patterns to As and Pb, and were positively correlated. Eukaryotic taxa from the phylum Chlorophyta had similar positive correlations with As and Pb in the soil. In contrast, Amoebozoa and Cercozoa, were sensitive to metals and metalloids, having higher relative abundances in soils with lower concentrations of contaminants. Our study shows that metabarcoding is a promising ecological approach for rapid, large scale assessment of contaminated and potentially impacted sites.
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Affiliation(s)
- Armin Kavehei
- Department of Earth and Environmental Sciences, Macquarie University, Sydney, 2109, Australia.
| | - Damian B Gore
- Department of Earth and Environmental Sciences, Macquarie University, Sydney, 2109, Australia
| | - Anthony A Chariton
- Department of Biological Sciences, Macquarie University, Sydney, 2109, Australia
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney, 2109, Australia
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Chu X, Liu J, Gu W, Tian L, Tang S, Zhang Z, Jiang L, Xu X. Study of the properties of carotenoids and key carotenoid biosynthesis genes from Deinococcus xibeiensis R13. Biotechnol Appl Biochem 2021; 69:1459-1473. [PMID: 34159631 DOI: 10.1002/bab.2217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 06/14/2021] [Indexed: 02/01/2023]
Abstract
To investigate the properties of carotenoids from the extremophile Deinococcus xibeiensis R13, the factors affecting the stability of carotenoids extracted from D. xibeiensis R13, including temperature, illumination, pH, redox chemicals, metal ions, and food additives, were investigated. The results showed that low temperature, neutral pH, reducing agents, Mn2+ , and food additives (xylose and glucose) can effectively improve the stability of Deinococcus carotenoids. The carotenoids of D. xibeiensis R13 exhibited strong antioxidant activity, with the scavenging rate of hydroxyl radicals reaching 71.64%, which was higher than the scavenging efficiency for 1,1-diphenyl-2-picrylhydrazyl free radicals and 2,2'-azino-bis (3-ethyl-benzothiazoline-6-sulfonic acid) free radicals (44.55 and 27.65%, respectively). In addition, the total antioxidant capacity reached 0.60 U/ml, which was 2.61-fold that of carotenoids from the model strain Deinococcus radiodurans R1. Finally, we predicted the gene clusters encoding carotenoid biosynthesis pathways in the genome of R13 and identified putative homologous genes. The key enzyme genes (crtE, crtB, crtI, crtLm, cruF, crtD, and crtO) in carotenoid synthesis of D. xibeiensis R13 were cloned to construct the multigene coexpression plasmids pET-EBI and pRSF-LmFDO. The carotenoid biosynthesis pathway was heterologously introduced into engineered Escherichia coli EBILmFDO, which exhibited a higher yield (7.14 mg/L) than the original strain. These analysis results can help us to better understand the metabolic synthesis of carotenoids in extremophiles.
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Affiliation(s)
- Xiaoting Chu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu Province, China
| | - Jie Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Wanyi Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Liqing Tian
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu Province, China
| | - Susu Tang
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, Jiangsu Province, China
| | - Zhidong Zhang
- Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Uyghur Autonomous Region, Urumqi, People's Republic of China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, Jiangsu Province, China
| | - Xian Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, Jiangsu Province, China
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