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Xia ZJ, Wu HZ, Cui CX, Chen Q, Zhao GY, Wang HX, Dai MX. Larsenimonas suaedae sp. nov., a moderately halophilic, endophytic bacterium isolated from the halophyte Suaeda salsa. Int J Syst Evol Microbiol 2016; 66:2952-2958. [PMID: 27129697 DOI: 10.1099/ijsem.0.001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A moderately halophilic, Gram-stain-negative, non-endospore-forming endophytic bacterium designated strain ST307T was isolated from the euhalophyte Suaeda salsa in Dongying, China. Strain ST307T was aerobic, rod-shaped, motile and orange-yellow-pigmented. The organism grew at NaCl concentrations of 0.6-20 % (w/v) (optimum 5-6 %, w/v), at temperatures of 5-45 °C (optimum 35 °C) and at pH 5-9 (optimum pH 7-8). It accumulated poly-β-hydroxybutyric acid and produced exopolysaccharides. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The predominant lipoquinone was ubiquinone Q-9. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a glycoaminolipid and a phosphoglycoaminolipid. The DNA G+C content was 60.5 mol%. Phylogenetic analyses of 16S rRNA gene sequences and concatenated atpA, rpoD and secA gene sequences revealed that the strain represents a member of the genus Larsenimonas. The closest related type strain was Larsenimonas salina M1-18T. Mean DNA-DNA relatedness values between strain ST307T and the related species L. salina M1-18T, Chromohalobacter beijerinckii DSM 7218T, C. canadensis DSM 6769T, C. israelensis DSM 6768T, C. marismortui CGMCC 1.2321T, C. nigrandesensis DSM 14323T, C. salexigens DSM 3043T and C. sarecensis DSM 15547T were 15±2-45±1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain ST307T clearly represents a novel species of the genus Larsenimonas. The name Larsenimonassuaedae sp. nov. is proposed, with ST307T (=CGMCC 1.8902T=DSM 22428T) as the type strain.
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Affiliation(s)
- Zhi-Jie Xia
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Hong-Zhen Wu
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Chun-Xiao Cui
- Medical College, Shandong Xiehe University, Jinan 250107, PR China
| | - Qi Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Guo-Yan Zhao
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Hai-Xia Wang
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
| | - Mei-Xue Dai
- College of Life Science, Shandong Normal University, Jinan 250014, PR China
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Lee HW, Kim DW, Lee MH, Kim BY, Cho YJ, Yim KJ, Song HS, Rhee JK, Seo MJ, Choi HJ, Choi JS, Lee DG, Yoon C, Nam YD, Roh SW. Draft genome sequence of the extremely halophilic archaeon Haladaptatus cibarius type strain D43(T) isolated from fermented seafood. Stand Genomic Sci 2015; 10:53. [PMID: 26380039 PMCID: PMC4571117 DOI: 10.1186/s40793-015-0051-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 07/27/2015] [Indexed: 11/21/2022] Open
Abstract
An extremely halophilic archaeon, Haladaptatus cibarius D43T, was isolated from traditional Korean salt-rich fermented seafood. Strain D43T shows the highest 16S rRNA gene sequence similarity (98.7 %) with Haladaptatus litoreus RO1-28T, is Gram-negative staining, motile, and extremely halophilic. Despite potential industrial applications of extremely halophilic archaea, their genome characteristics remain obscure. Here, we describe the whole genome sequence and annotated features of strain D43T. The 3,926,724 bp genome includes 4,092 protein-coding and 57 RNA genes (including 6 rRNA and 49 tRNA genes) with an average G + C content of 57.76 %.
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Affiliation(s)
- Hae-Won Lee
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea.,World Institute of Kimchi, Gwangju, 503-360 Republic of Korea
| | - Dae-Won Kim
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongju, 361-951 Republic of Korea
| | - Mi-Hwa Lee
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam, 463-746 Republic of Korea
| | - Byung-Yong Kim
- ChunLab Inc., Seoul National University, Seoul, 151-742 Republic of Korea
| | - Yong-Joon Cho
- ChunLab Inc., Seoul National University, Seoul, 151-742 Republic of Korea
| | - Kyung June Yim
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Hye Seon Song
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering, Ewha Womans University, Seoul, 120-750 Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon, 406-772 Republic of Korea
| | - Hak-Jong Choi
- World Institute of Kimchi, Gwangju, 503-360 Republic of Korea
| | - Jong-Soon Choi
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Dong-Gi Lee
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Changmann Yoon
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
| | - Young-Do Nam
- Research Group of Gut Microbiome, Korea Food Research Institute, Sungnam, 463-746 Republic of Korea
| | - Seong Woon Roh
- Biological Disaster Analysis Group, Korea Basic Science Institute, Daejeon, 305-806 Republic of Korea
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Papke RT, Corral P, Ram-Mohan N, de la Haba RR, Sánchez-Porro C, Makkay A, Ventosa A. Horizontal gene transfer, dispersal and haloarchaeal speciation. Life (Basel) 2015; 5:1405-26. [PMID: 25997110 PMCID: PMC4500145 DOI: 10.3390/life5021405] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 11/28/2022] Open
Abstract
The Halobacteria are a well-studied archaeal class and numerous investigations are showing how their diversity is distributed amongst genomes and geographic locations. Evidence indicates that recombination between species continuously facilitates the arrival of new genes, and within species, it is frequent enough to spread acquired genes amongst all individuals in the population. To create permanent independent diversity and generate new species, barriers to recombination are probably required. The data support an interpretation that rates of evolution (e.g., horizontal gene transfer and mutation) are faster at creating geographically localized variation than dispersal and invasion are at homogenizing genetic differences between locations. Therefore, we suggest that recurrent episodes of dispersal followed by variable periods of endemism break the homogenizing forces of intrapopulation recombination and that this process might be the principal stimulus leading to divergence and speciation in Halobacteria.
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Affiliation(s)
- R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
- Author to whom correspondence should be addressed; E-Mail:
| | - Paulina Corral
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Nikhil Ram-Mohan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
| | - Andrea Makkay
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; E-Mails: (N.R.-M.); (A.M.)
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, University of Seville, 41004 Seville, Spain; E-Mails: (P.C.); (R.R.H.); (C.S.-P.); (A.V.)
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