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Feng GD, Wang YH, Zhang XJ, Chen WD, Zhang J, Xiong X, Zhu HH. Sphingomonas lenta sp. nov., a slowly growing bacterium isolated from an abandoned lead–zinc mine. Int J Syst Evol Microbiol 2019; 69:2214-2219. [DOI: 10.1099/ijsem.0.003427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guang-Da Feng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Yong-Hong Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Xian-Jiao Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Wen-Di Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Jun Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Xiong Xiong
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
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Fan QM, Zhang RG, Chen HY, Feng QQ, Lv J. Sphingomonas floccifaciens sp. nov., isolated from subterranean sediment. Int J Syst Evol Microbiol 2018; 69:1531-1536. [PMID: 30204585 DOI: 10.1099/ijsem.0.002983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, non-sporulating, rod-shaped, orange-pigmented bacterium, designated strain FQM01T, was isolated from a subterranean sediment sample in the Mohe permafrost area, China. Strain FQM01T grew optimally at 25 °C, pH 7.0 and NaCl concentration of 0 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FQM01T belonged to the genus Sphingomonas. The closest phylogenetic relative was Sphingomonas spermidinifaciens GDMCC 1.657T (97.6 %), followed by Sphingomonas mucosissima DSM 17494T (97.2 %). The DNA G+C content of the isolate was 66.9 mol%. Strain FQM01T contained Q-10 as the predominant ubiquinone, and C18 : 1ω6c and/or C18 : 1ω7c, C16 : 1ω6c and/or C16 : 1ω7c, C16 : 0, C14 : 0 2-OH and C18 : 1ω7c 11 methyl as the major fatty acids. Major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified glycolipid. Only sym-homospermidine was detected as the polyamine. On the basis of phylogenetic and phenotypic data, strain FQM01T is considered to represent a novel species of Sphingomonas for which the name Sphingomonasfloccifaciens sp. nov. is proposed. The type strain is FQM01T (=CGMCC 1.15797T=KCTC 52630T).
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Affiliation(s)
- Qiu-Ming Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Ren-Gang Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Han-Yi Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qing-Qing Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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Asaf S, Khan AL, Khan MA, Al-Harrasi A, Lee IJ. Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth. 3 Biotech 2018; 8:389. [PMID: 30175026 PMCID: PMC6111035 DOI: 10.1007/s13205-018-1403-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022] Open
Abstract
Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Muhammad Aaqil Khan
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566 Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566 Republic of Korea
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Tahon G, Willems A. Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains, East Antarctica. Syst Appl Microbiol 2017; 40:357-369. [DOI: 10.1016/j.syapm.2017.05.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 12/24/2022]
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Liu B, Liu GH, Sengonca C, Schumann P, Wang JP, Zhu YJ, Liu QY, Wang MK. Bacillus praedii sp. nov., isolated from purplish paddy soil. Int J Syst Evol Microbiol 2017; 67:2823-2828. [DOI: 10.1099/ijsem.0.002030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo Liu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A D-53115 Bonn, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße7B, 38124, Braunschweig, Germany
| | - Jie-Ping Wang
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Yu-Jing Zhu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Qin-Ying Liu
- Agricultural Bio-resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
- College of Life Science, Fujian Normal University, Fuzhou, Fujian 350117, PR China
| | - Ming-Kuang Wang
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan, ROC
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Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead–zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica. Int J Syst Evol Microbiol 2017; 67:2160-2165. [DOI: 10.1099/ijsem.0.001905] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Choi GM, Jo JH, Kang MS, Kim MS, Lee SY, Im WT. Sphingomonas aquatica sp. nov., isolated from tap water. Int J Syst Evol Microbiol 2017; 67:845-850. [DOI: 10.1099/ijsem.0.001682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Gyu-min Choi
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Jung Hun Jo
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Myung-Suk Kang
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Minseok S. Kim
- Department of Biomedical Engineering, Konyang University, 121 Daehak-ro, Nonsan, Chungnam, Republic of Korea
| | - Soon-Youl Lee
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
- Center for Genetic Information, Graduate School of Bio and Information Technology, Hankyong National University, 327 Chungang-no Anseong-si, Kyonggi-do 17579, Republic of Korea
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Sukweenadhi J, Kim YJ, Kang CH, Farh MEA, Nguyen NL, Hoang VA, Choi ES, Yang DC. Sphingomonas panaciterrae sp. nov., a plant growth-promoting bacterium isolated from soil of a ginseng field. Arch Microbiol 2015; 197:973-81. [PMID: 26163005 DOI: 10.1007/s00203-015-1134-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/09/2015] [Accepted: 06/28/2015] [Indexed: 11/25/2022]
Abstract
Strain DCY91(T), a Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, was isolated from soil of ginseng field in Gyeonggi province, South Korea. Strain DCY91(T) shared the highest 16S rRNA gene sequence similarity with Sphingomonas mucosissima DSM 17494(T) (98.55%), Sphingomonas dokdonensis KACC 17420(T) (98.11%) and Sphingomonas xinjiangensis DSM 26736(T) (96.68%). The strain DCY91(T) was found to able to grow best in trypticase soy agar at 28 °C, at pH 7 and at 0.5 % NaCl. Ubiquinone 10 was identified as the isoprenoid quinone. The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The major fatty acids of strain DCY91(T) were identified as unsaturated C18:1 ω7c and saturated C16:0. The major polyamine content was sym-homospermidine. The DNA G + C content was determined to be 65.8 mol% (HPLC). After 6 days of incubation, strain DCY91(T) produced 9.64 ± 1.73 and 33.73 ± 4.66 µg/ml indole-3-acetic acid, using media without L-tryptophan and supplemented with L-tryptophan, respectively. Strain DCY91(T) was also weakly solubilized phosphate and produced siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY91(T) is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas panaciterrae sp. nov. is proposed. The type strain is DCY91(T) (=KCTC 42346(T) =JCM 30807(T)).
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Affiliation(s)
- Johan Sukweenadhi
- Graduate School of Biotechnology and Ginseng Bank, College of Life Science, Kyung Hee University, Yongin, 446-701, Korea
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Liu Y, Yao S, Lee YJ, Cao Y, Zhai L, Zhang X, Su J, Ge Y, Kim SG, Cheng C. Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch. Int J Syst Evol Microbiol 2015; 65:2817-2823. [PMID: 25985831 DOI: 10.1099/ijs.0.000340] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow bacterial strains, designated NBD5(T) and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strains were members of a novel species of the genus Sphingomonas, the seven closest neighbours being Sphingomonas oligoaromativorans SY-6(T) (96.9% similarity), Sphingomonas polyaromaticivorans B2-7(T) (95.8%), Sphingomonas yantingensis 1007(T) (94.9%), Sphingomonas sanguinis IFO 13937(T) (94.7%), Sphingomonas ginsenosidimutans Gsoil 1429(T) (94.6%), Sphingomonas wittichii RW1(T) (94.6%) and Sphingomonas formosensis CC-Nfb-2(T) (94.5%). Strains NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. Strains NBD5(T) and NBD8 were clearly distinguished from reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data analysis, and comparison of a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains NBD5(T) and NBD8 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas morindae sp. nov. is proposed. The type strain is NBD5(T) ( = DSM 29151(T) = KCTC 42183(T) = CICC 10879(T)).
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Affiliation(s)
- Yang Liu
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Su Yao
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Yong-Jae Lee
- Microbial Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Yanhua Cao
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Lei Zhai
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Xin Zhang
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Jiaojiao Su
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Yuanyuan Ge
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
| | - Song-Gun Kim
- Microbial Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea.,University of Science and Technology, Yuseong-gu, Daejeon 305-850, Republic of Korea
| | - Chi Cheng
- China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing 100015, PR China
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