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Li X, Mu L, Zhang Y, Zhu Z, Xiao Y, Fang Z. Sphingomicrobium clamense sp. nov., Isolated from Sediment of Clam Island Beach in China. Curr Microbiol 2024; 81:104. [PMID: 38393394 DOI: 10.1007/s00284-024-03639-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 02/13/2024] [Indexed: 02/25/2024]
Abstract
A Gram-stain-negative, non-flagellated, aerobic, ovoid or rod-shaped bacterium with motility, designated B8T, was isolated from the sediment of Clam Island beach, Liaoning province, China. The optimum growth of strain B8T occurred at 35 oC, pH 7.0, and in the presence of 4.0-5.0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B8T formed a distinct lineage within the genus Sphingomicrobium and was closely related to Sphingomicrobium nitratireducens O-35T (98.3% sequence similarity), Sphingomicrobium aestuariivivum KCTC 42286T (96.9%), and Sphingomicrobium astaxanthinifaciens JCM 18551T (96.5%). The digital DNA-DNA hybridization and average nucleotide identity values between strain B8T and closely related strains were lower than 21.0% and 78.0%, much lower than the cutoff values of 70.0% and 95.0%, respectively, for bacterial species delineation. The dominant respiratory quinone of strain B8T was ubiquinone-10. The major fatty acids were Sum In Feature 8 (C18:1ω7c and/or C18:1ω6c), Sum In Feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17:1ω6c, C18:1 2-OH, and C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, glycolipids, and four unknown polar lipids. The DNA G + C content of strain B8T was 63.9%. Based on the phenotypic, phylogenetic, and chemotaxonomic analyses, strain B8T is considered a new species of Sphingomicrobium, for which the name Sphingomicrobium clamense sp. nov. is proposed. The type strain is B8T (= CGMCC 1.19486T = KCTC 92052T).
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Affiliation(s)
- Xing Li
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Lulu Mu
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Yanfeng Zhang
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Zimu Zhu
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Yazhong Xiao
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China
| | - Zemin Fang
- School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China.
- Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui, 230601, China.
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, 230601, China.
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You H, Xu L, Kong YH, Sun C, Zhou P, Xu XW. Sphingomicrobium nitratireducens sp. nov., isolated from a tidal flat in Guangxi. Arch Microbiol 2022; 204:671. [PMID: 36242647 DOI: 10.1007/s00203-022-03273-2] [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] [Received: 08/22/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022]
Abstract
An aerobic, yellow-pigmented and Gram-stain-negative strain, designated as O-35 T, was isolated from a tidal flat sediment collected in Dangjiang Town, the southern China. Colonies of strain O-35 T were circular with 0.5-1.0 mm in diameter, convex and smooth. Cells of strain O-35 T were coccoid-shaped, non-spore forming, non-motile and the strain could reduce nitrate. Growth of strain O-35 T was observed at 15-40 °C (optimum 30 °C), at pH 6.0-9.5 (optimum 7.5-8.0) and in 0.5-5.0% NaCl (optimum 2%, w/v). Strain O-35 T showed 16S rRNA gene sequence identities of 97.3-97.5% with Sphingomicrobium lutaoense CC-TBT-3 T and Sphingomicrobium aestuariivivum AH-M8T, higher than the rest of Sphingomicrobium type strains. Phylogenetic trees based on the 16S rRNA gene and the core-genome sequences demonstrated that strain O-35 T was affiliated within the genus Sphingomicrobium. Overall genome relatedness index calculations revealed that strain O-35 T had < 75.8% of average nucleotide identity and < 19.2% of digital DNA-DNA hybridization values with Sphingomicrobium type strains. The sole isoprenoid quinone was ubiquinone-10. The major fatty acids (> 10%) were summed feature 8, summed feature 3, C16:0 and C18:1 2-OH. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, sphingoglycolipid, two unidentified glycolipids, one unidentified lipid and one unidentified phospholipid. On the basis of the phenotypic, chemotaxonomic and genomic properties, strain O-35 T represents a novel species in the genus Sphingomicrobium, for which the name Sphingomicrobium nitratireducens sp. nov. is proposed. The type strain is O-35 T (= KCTC 92308 T = MCCC 1K07589T).
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Affiliation(s)
- Hao You
- Ocean College, Zhejiang University, Zhoushan, 316021, People's Republic of China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Yan-Hui Kong
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.
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Zhang Q, Kanjanasuntree R, Kim JH, Yoon JH, Sukhoom A, Kantachote D, Kim W. Sphingomicrobium arenosum sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2018; 68:2551-2556. [PMID: 29927368 DOI: 10.1099/ijsem.0.002875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, motile by one single flagellum, dark-orange pigmented and rod-shaped bacterial strain, designated CAU 1457T, was isolated from marine sediment in the Republic of Korea and its taxonomic position was investigated by using a polyphasic approach. The isolate grew optimally at 30 °C, at pH 6.0 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequences similarity, strain CAU 1457T belonged to the genus Sphingomicrobium and was related most closely to Sphingomicrobium astaxanthinifaciens JCM 18551T (98.2 % similarity). Strain CAU 1457T contained ubiquinone-10 as the predominant isoprenoid quinone and 11-methyl C18 : 1ω7c and summed feature 8 (C18 : 1ω7c/ω6c) as the major cellular fatty acids. Triamine sym-homospermidine was detected as the major compound in the polyamine pattern. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, four unidentified glycolipids, one unidentified aminophospholipid, two unidentified phospholipids, one unidentified aminolipid and one unidentified lipid. DNA-DNA relatedness between strain CAU 1457T and the closely related strains, Sphingomicrobium astaxanthinifaciens JCM 18551T and Sphingomicrobium aestuariivivum KCTC 42286T were 32.7 and 28.4 %, respectively. The DNA G+C content of strain was 68.8 mol%. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain CAU 1457T represents a novel species of the genus Sphingomicrobium, for which the name Sphingomicrobium arenosum sp. nov. is proposed. The type strain is CAU 1457T (=KCTC 62233T=NBRC 113094T).
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Affiliation(s)
- Qi Zhang
- 1Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Rungravee Kanjanasuntree
- 1Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hwa Kim
- 1Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Hoon Yoon
- 2Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ampaitip Sukhoom
- 3Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Duangporn Kantachote
- 3Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Wonyong Kim
- 1Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
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Binariimonas pacifica gen. nov., sp. nov., a Novel Marine Bacterium of Family Sphingomonadaceae Isolated from East Pacific Ocean Surface Seawater. Curr Microbiol 2015; 72:276-81. [PMID: 26613616 DOI: 10.1007/s00284-015-0948-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
A novel rod-shaped binary fission, and yellow-pigmented bacterial strain, JLT 2480(T), was isolated from surface seawater in the East Pacific Ocean. The strain is Gram negative and oxidase negative. Phylogenetic analyses based on 16S rRNA gene sequence indicate that strain JLT 2480(T) falls in the family Sphingomonadaceae, sharing highest similarity (95.6 %) with the species Blastomonas ursincola. The DNA G+C content of JLT 2480(T) is 65.5 mol%, and the sole respiratory quinone is coenzyme Q10. The predominant polar lipids are sphingoglycolipids (SGL1 and SGL2), phosphatidylglycerols, phosphatidylethanolamines, phospholipids, glycolipids, and phosphatidylcholines. The predominant cellular fatty acids are C16:0, C18:0, C18:1ω7c, C12:0, and C16:1ω7c. Strain JLT 2480(T) is distinct from the B. ursincola type strain DSM 9006(T) as reflected by major chemotaxonomic distinctions between the two. Furthermore, two notable characteristics of the genus Blastomonas, that is, the presence of bacteriochlorophyll a and the puf genes, are not detected in JLT 2480(T). On the basis of present evidence, we consider JLT 2480(T) to be a novel species in a new genus of the family Sphingomonadaceae, and propose the name Binariimonas pacifica gen. nov., sp. nov., with strain JLT 2480(T) (=CGMCC 1.12850(T) = DSM 28646(T)) to be the type strain for genus Binariimonas.
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Park S, Park JM, Sun Joo E, Won SM, Kyum Kim M, Yoon JH. Sphingomicrobium aestuariivivum sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015; 65:2678-2683. [PMID: 25964515 DOI: 10.1099/ijs.0.000320] [Citation(s) in RCA: 8] [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 Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, designated AH-M8T, was isolated from a tidal flat sediment collected from Aphae Island in the south-western sea, South Korea. Strain AH-M8T grew optimally at 35 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0% (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain AH-M8T belonged to the genus Sphingomicrobium, clustering with the type strain of Sphingomicrobium astaxanthinifaciens, with which it shared 99.0% 16S rRNA gene sequence similarity. Sequence similarities to the type strains of other species of the genus Sphingomicrobium were 95.4-96.0%. Strain AH-M8T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain AH-M8T were phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and one unidentified glycolipid. The major polyamine is triamine sym-homospermidine. The DNA G+C content of strain AH-M8T was 66.7 mol% and its mean DNA-DNA relatedness value with S. astaxanthinifaciens JCM 18551T was 21%. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain AH-M8T is separated from other species of the genus Sphingomicrobium. On the basis of the data presented, strain AH-M8T is considered to represent a novel species of the genus Sphingomicrobium, for which the name Sphingomicrobium aestuariivivum sp. nov. is proposed. The type strain is AH-M8T ( = KCTC 42286T = NBRC 110678T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Eun Sun Joo
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, South Korea
| | - Sung-Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
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