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Yoon J. Thetidibacter halocola gen. nov., sp. nov., a novel member within the family Roseobacteraceae isolated from seawater. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01832-1. [PMID: 37133556 DOI: 10.1007/s10482-023-01832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
A Gram-staining-negative, strictly aerobic, dark beige-colored, rod-shaped, chemoorganoheterotrophic, and catalase- and oxidase-positive bacterium, designated as KMU-90T, was isolated from coastal seawater in the Republic of Korea, and subjected to a polyphasic study. The novel isolate was able to grow at 0-6.0% NaCl concentrations (w/v), pH 6.5-9.5, and 4-45 °C. The 16S rRNA gene sequences-based phylogeny revealed that the novel marine isolate belongs to the family Roseobacteraceae of class Alphaproteobacteria and that it shared the greatest sequence similarity (97.3%) with Aestuariicoccus marinus NAP41T. The novel strain could be distinguished phenotypically from related representatives of the family Roseobacteraceae. The major (> 10%) fatty acids of strain KMU-90T were C18:1 ω7c and C18:1 ω7c 11-methyl and the only respiratory quinone was ubiquinone-10 (Q-10). Strain KMU-90T contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, two unidentified aminolipids, an unidentified phospholipid, and three unidentified glycolipids as polar lipids. The assembled draft genome size of strain KMU-90T was 4.84 Mbp with a DNA G + C content of 66.5%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between the genomes of strain KMU-90T and its closely related representatives were 77.0-79.0%, 14.6-20.0%, and 60.0-69.9%, respectively. From the polyphasic taxonomic results obtained, the strain is considered to represent a novel genus and a new species of the family Roseobacteraceae, for which the name Thetidibacter halocola gen. nov., sp. nov. is proposed. The type species is T. halocola, with the type strain KMU-90T (= KCCM 90287T = NBRC 113375T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-gu, Daegu, 42601, Republic of Korea.
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Huang Y, Liu L, Li J, Pan J, Li M. Limibaculum sediminis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2022; 72. [PMID: 36269565 DOI: 10.1099/ijsem.0.005580] [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] [Indexed: 06/16/2023] Open
Abstract
A Gram-stain-negative, cream-coloured, aerobic, motile and ovoid- to rod-shaped bacterium, designated as FT325T, was isolated from mangrove sediment collected in Shenzhen, PR China. The taxonomic position of strain FT325T was established by phylogenetic, physiological, biochemical and chemotaxonomic analyses. Strain FT325T grew optimally at 37-40 °C and pH 6.0 in the presence of 0 % (w/v) NaCl. Results of 16S rRNA gene sequence analysis showed that strain FT325T was most similarly related to Limibaculum halophilum CAU 1123T (96.2 %), Phaeovulum vinaykumarii DSM 18714T (93.9%) and Amaricoccus solimangrovi HB 172011T (93.7 %). The major fatty acids (>10 %) were C18 : 1 ω7c (60.0 %) and 11-methyl C18 : 1 ω7c (16.7 %). The sole respiratory quinone was Q-10. The polar lipids were phosphatidylglycerol, one unidentified glycolipid, three unidentified aminolipids and three unidentified phospholipids. Its estimated genome size was 4 318 768 bp and the genomic DNA G+C content was 69.6 mol%. Based on its distinct phenotypic, chemotaxonomic and phylogenetic characteristics, strain FT325T represents a novel species of the genus Limibaculum, for which the name Limibaculum sediminis sp. nov. is proposed (=MCCC 1K07397T=KCTC 92313T).
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Affiliation(s)
- Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Jiayi Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Xbiome Biotech Co. Ltd, Shenzhen, Guangdong 518058, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
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Wang Z, Du RB, Sun QL, Sun YY, Zhang J, Tang YZ. Pontivivens ytuae sp. nov., isolated from deep sea sediment of the Mariana Trench. Int J Syst Evol Microbiol 2021; 71. [PMID: 34520339 DOI: 10.1099/ijsem.0.004967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A Gram-stain-negative, light pink-coloured, rod-shaped, flagellated and facultative anaerobic bacterial strain, designated MT2928T, was isolated from deep-sea sediment collected from the Mariana Trench. Growth of strain MT2928T occurred optimally at 28 °C, pH 8.0-9.0 and in the presence of 1.0-2.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MT2928T belongs to the genus Pontivivens and has the highest sequence similarity to Pontivivens insulae GYSW-23T (96.6 %). Genomic analysis indicated that strain MT2928T contains a circular chromosome of 4 199 362 bp with G+C content of 67.2 mol%. The strain did not produce bacteriochlorophyll a, but produced carotenoid. The predominant respiratory quinone of MT2928T was ubiquinone-10. The polar lipids of MT2928T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified lipids and two unidentified phospholipids. The major fatty acids of strain MT2928T contained summed feature 8 (C18 : 1 ω7c or/and C18 : 1 ω6c), C18 : 0 and summed feature 2 (iso-C16 : 1 I and/or C14 : 0 3-OH). On the basis of phylogenetic, physiological, biochemical and other phenotypic properties, strain MT2928T represents a novel species of the genus Pontivivens, and the name Pontivivens ytuae sp. nov. is proposed with the type species MT2928T (=MCCC 1K05575T=JCM 34320T).
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Affiliation(s)
- Zhen Wang
- School of Ocean, Yantai University, Yantai, PR China
| | - Rong-Bin Du
- School of Ocean, Yantai University, Yantai, PR China
| | - Qing-Lei Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, PR China
| | - Yuan-Yuan Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, PR China
| | - Jian Zhang
- School of Ocean, Yantai University, Yantai, PR China
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Zongyanglinia huanghaiensis gen. nov., sp. nov., a novel denitrifying bacterium isolated from the yellow sea, and transfer of Pelagicola marinus to Zongyanglinia gen. nov. as Zongyanglinia marinus comb. nov. Antonie van Leeuwenhoek 2021; 114:137-149. [DOI: 10.1007/s10482-020-01507-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/27/2020] [Indexed: 11/26/2022]
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Lee SD, Choe H, Kim JS, Kim IS. Kangsaoukella pontilimi gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from a tidal mudflat. Int J Syst Evol Microbiol 2020; 70:5235-5242. [PMID: 32853133 DOI: 10.1099/ijsem.0.004401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, Gram-stain-negative, non-motile, ovoid- and rod-shaped bacterium, designated strain GH1-50T, was isolated from a tidal mudflat sample collected from Dongmak seashore on Gangwha Island, Republic of Korea. The organism showed growth at 20-40 °C (optimum, 30 °C), pH 7-8 (optimum, pH 7) and 2-6 % (w/v) NaCl (optimum, 5 %). The pufLM genes were present but bacteriochlorophyll a was not detected. The major isoprenoid quinone was Q-10. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminolipid and five unidentified lipids. The predominant cellular fatty acids were C18 : 1 ω7c, C18 : 1 ω7c 11-methyl and C18 : 0. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that the isolate belonged to the family Rhodobacteraceae and was loosely associated with members of the recognized genera. The closest relative was the type strain of Pseudoruegeria marinistellae (96.8 % similarity) followed by Boseongicola aestuarii (96.4 %). Other members of the family shared 16S rRNA gene similarity values below 96.0 % to the novel isolate. The DNA G+C content calculated from the draft genome sequence was 64.0 %. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values between genome sequences of strain GH1-50T and all the type strains of the recognized taxa compared were <70.0, <84.1 and <20.5 %, respectively. Based on data obtained by a polyphasic approach, strain GH1-50T (=KCTC 72224T=NBRC 113929T) represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Kangsaoukella pontilimi gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju 63243, Republic of Korea
| | - Hanna Choe
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea
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Ren H, Ma H, Li H, Huang L, Luo Y. Acidimangrovimonas sediminis gen. nov., sp. nov., isolated from mangrove sediment and reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov. Int J Syst Evol Microbiol 2019; 69:2445-2451. [PMID: 31169491 DOI: 10.1099/ijsem.0.003513] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, short-rod bacterium, strain MS2-2T, was isolated from mangrove sediment sampled at Jiulong River Estuary, Fujian province, PR China. 16S rRNA gene sequence similarity analysis showed that strain MS2-2T was most closely related to Defluviimonas indica 20V17T (97.41 %) and Defluviimonas pyrenivorans PrR001T (96.18 %). Phylogenetic trees based on 16S rRNA genes and genome sequences both revealed that strain MS2-2T formed a distinct cluster with D. indica 20V17T and D. pyrenivorans PrR001T within family Rhodobacteracea, quite separate from other type species in the genus Defluviimonas. The average nucleotide identity value between strain MS2-2T and D. indica 20V17T was 78.35 %. Growth of strain MS2-2T was observed at 16-41 ° C (optimum, 34 ° C), pH 3.6-7.5 (pH 6.0) and 0.5-10.0 % (w/v) NaCl (4.0 %). The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C18 : 0. Ubiquinone 10 was the sole quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 67.9 mol%. The combined genotypic and phenotypic data show that strain MS2-2T represents a novel species of a novel genus in the family Rhodobacteraceae, for which the name Acidimangrovimonassediminis gen. nov., sp. nov. is proposed, with the type strain MS2-2T (=MCCC 1K02682T=NBRC 112978T). We also propose the reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov.
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Affiliation(s)
- Hao Ren
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.,Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.,Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Hao Li
- School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Lingfeng Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China.,Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Yuanrong Luo
- Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen 361102, PR China
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Chang YQ, Meng X, Du ZZ, Du ZJ. Oceanibium sediminis gen. nov., sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2019; 69:249-254. [DOI: 10.1099/ijsem.0.003139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ya-Qi Chang
- 1College of Marine Science, Shandong University, Weihai, 264209, PR China
| | - Xue Meng
- 1College of Marine Science, Shandong University, Weihai, 264209, PR China
| | - Zhao-Zhong Du
- 1College of Marine Science, Shandong University, Weihai, 264209, PR China
| | - Zong-Jun Du
- 2State key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- 1College of Marine Science, Shandong University, Weihai, 264209, PR China
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