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Lopez Marin MA, Suman J, Jani K, Ulbrich P, Cajthaml T, Filipova A, Pajer P, Neumann-Schaal M, Strejcek M, Uhlik O. Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748542 DOI: 10.1099/ijsem.0.005678] [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: 01/26/2023] Open
Abstract
An actinobacterial strain, designated A5X3R13T, was isolated from a compost soil suspension supplemented with extracellular material from a Micrococcus luteus-culture supernatant. The strain was cultured on tenfold-diluted reasoner's 2A agar. The cells were ovoid-to-rod shaped, non-motile, Gram-stain-positive, oxidase-negative, catalase-positive and had a width of 0.5 µm and a length of 0.8-1.2 µm. The results of both 16S rRNA-based phylogenetic and whole-genome analyses indicate that A5X3R13T forms a distinct lineage within the family Nocardioidaceae (order Propionibacteriales). On the basis of the 16S rRNA gene sequence, A5X3R13T was closely related to Aeromicrobium terrae CC-CFT486T (96.2 %), Nocardioides iriomotensis IR27-S3T (96.2 %), Nocardioides guangzhouensis 130T (95.6 %), Marmoricola caldifontis YIM 730233T (95.5 %), Aeromicrobium alkaliterrae KSL-107T (95.4 %), Aeromicrobium choanae 9H-4T (95.4 %), Aeromicrobium panaciterrae Gsoil 161T (95.3 %), and Nocardioides jensenii NBRC 14755T (95.2 %). The genome had a length of 4 915 757 bp, and its DNA G+C content was 68.5 mol %. The main fatty acids were 10-methyl C17 : 0, C16 : 0, C15 : 0, C18 : 0, C17 : 0 and iso-C16 : 0. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. MK-9(H4) was the predominant respiratory quinone. The peptidoglycan type was A3γ (A41.1) and contained alanine, glycine, glutamic acid and ll-diaminopimelic acid in a molar ratio of 1.2 : 0.9 : 1.0 : 0.8. On the basis of the results of the phylogenetic and phenotypic analyses and comparisons with other members of the family Nocardioidaceae, strain A5X3R13T is proposed to represent a novel species within a novel genus, for which the name Solicola gregarius gen. nov., sp. nov. is proposed. The type strain is A5X3R13T (=DSM 112953T=NCCB 100840T).
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Affiliation(s)
- Marco A Lopez Marin
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Jachym Suman
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Kunal Jani
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Pavel Ulbrich
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Alena Filipova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02, Prague, Czech Republic
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7 B, 38124, Braunschweig, Germany
| | - Michal Strejcek
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
| | - Ondrej Uhlik
- University of Chemistry and Technology, Prague. Department of Biochemistry and Microbiology, Technicka 3, 16628 Prague, Czech Republic
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Kim DY, Jeong IC, Lee SY, Jeong YS, Han JE, Tak EJ, Lee JY, Kim PS, Hyun DW, Bae JW. Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748471 DOI: 10.1099/ijsem.0.005643] [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: 12/24/2022] Open
Abstract
Two novel Gram-stain-positive, non-motile and non-spore-forming bacterial strains, designated J2M5T and J1M15T, were isolated from the gastrointestinal tract of a lake prawn Palaemon paucidens. Strain J2M5T was an obligately aerobic bacterium that formed milky-coloured colonies and showed a rod-coccus cell cycle, while strain J1M15T was a facultatively aerobic bacterium that formed orangish-yellow-coloured colonies and showed rod-shaped cells. Strains J2M5T and J1M15T showed the highest 16S rRNA gene sequence similarity to Nocardioides ganghwensis JC2055T (98.63 %) and Tessaracoccus flavescens SST-39T (98.08 %), respectively. The whole-genome sequence of strain J2M5T was 4.52 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J2M5T was 72.5 mol%. The whole-genome sequence of strain J1M15T was 3.20 Mbp in size and the genomic G+C content directly calculated from the genome sequence of strain J1M15T was 69.6mol %. Strains J2M5T and J1M15T showed high OrthoANI similarity to N. ganghwensis JC2055T (83.6 %) and T. flavescens (77.2 %), respectively. We analysed the genome sequences of strains J2M5T and J1M15T in terms of carbohydrate-active enzymes, antibiotic resistance genes and virulence factor genes. Strains J2M5T and J1M15T contained MK-8 (H4) and MK-9 (H4) as the predominant respiratory quinones, respectively. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Additionally, strain J2M5T possessed phosphatidylcholine, phosphatidylserine and phosphatidylethanolamine. The cellular sugar components of strain J2M5T were ribose, mannose, glucose and galactose, and its cellular amino acid components were l-alanine and l-lysine. The cellular sugar components of strain J1M15T were rhamnose, ribose, mannose and glucose, and its cellular amino acid component was l-alanine. The major cellular fatty acids of strains J2M5T and J1M15T were iso-C16 : 0 and anteiso-C15 : 0, respectively. The multiple taxonomic analyses indicated that strains J2M5T and J1M15T represent novel species of the genus Nocardioides and Tessaracoccus, respectively. We propose the names Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov. for strain J2M5T (=KCTC 49461T=CCUG 74767T) and strain J1M15T (=KCTC 49462T=CCUG 74766T), respectively.
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Affiliation(s)
- Do-Yeon Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - In-Chul Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - So-Yeon Lee
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yun-Seok Jeong
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jeong Eun Han
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Euon Jung Tak
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - June-Young Lee
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Dong-Wook Hyun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea.,Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
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Chhetri G, Kim I, Kang M, Kim J, So Y, Seo T. Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542392 DOI: 10.1099/ijsem.0.005012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10T was affiliated to the genus Nocardioides and the closest species were Nocardioides glacieisoli HLT3-15T (98.8 %), Nocardioides zhouii HLT2-9T (98.8 %), Nocardioides ganghwensis JC2055T (98.7 %), Nocardioides cavernae YIM A1136T (98.6 %), Nocardioides flavus Y4T (98.5 %), Nocardioides oleivorans DSM 16090T (98.3 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides exalbidus DSM 22017T (98.1 %) and Nocardioides hwasunensis KCTC 19197T (98.1 %). Strain G10T formed a monophyletic cluster with N. glacieisoli HLT3-15T, N. zhouii HLT2-9T and N. hwasunensis KCTC 19197T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C16 : 0 and C17 : 1 ω8c. MK-8(H4) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA-DNA hybridization values were 78.6-88.7 % and 21.5-36.2 %, respectively, with the type strains of related species of the genus Nocardioides, suggesting that strain G10T represents a novel species. The genome of strain G10T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10T represent a novel species within the genus Nocardioides, for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10T (=KCTC 49626T=NBRC 114801T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Minchung Kang
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
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Suzuki M, Tachibana Y, Takizawa R, Morikawa T, Takeno H, Kasuya KI. A novel poly(3-hydroxybutyrate)-degrading actinobacterium that was isolated from plastisphere formed on marine plastic debris. Polym Degrad Stab 2021. [DOI: 10.1016/j.polymdegradstab.2020.109461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Roh SG, Lee C, Kim MK, Kang HJ, Kim YS, Kim MJ, Malik A, Kim SB. Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2020; 70:2682-2689. [PMID: 32141810 DOI: 10.1099/ijsem.0.004095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three aerobic, rod-shaped actinobacterial strains, designated MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T, were isolated from soil and their taxonomic positions were analysed using a polyphasic approach. The isolates showed best growth at 30 °C, pH 7 and 0-1 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolates were affiliated to the genus Nocardioides, and the closest species to MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T were Nocardioides aestuarii JC2056T (97.76%), Nocardioides currus IB-3T (97.41%) and Nocardioides exalbidus RC825T (98.71%), respectively. Each isolate formed a distinct cluster within the Nocardioides clade in the phylogenetic tree. The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 74.4-85.7 % and 16.6-39.2 %, respectively, with the type strains of related species. The major polar lipids in all three strains were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids were iso-C16 : 0 and C17 : 1 ω8c. MK-8(H4) was the major isoprenoid quinone and ll-DAP was the major diamino acid. Galactose, glucose and rhamnose were present in the whole-cell hydrolysate, and MMS17-SY213T also contained mannose and ribose. The DNA G+C contents of MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T were 72.2, 70.4 and 71.5 mol%, respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of each strain as representing a new species of Nocardioides, for which the names Nocardioides euryhalodurans sp. nov. (MMS17-SY117T=KCTC 49175T=JCM 32831T), Nocardioides seonyuensis sp. nov. (MMS17-SY207-3T=KCTC 49176T=JCM 32832T) and Nocardioides eburneiflavus sp. nov. (MMS17-SY213T=KCTC 49177T=JCM 32833T) are proposed accordingly.
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Affiliation(s)
- Su Gwon Roh
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea.,Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chan Lee
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Min-Kyeong Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea.,Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Hye-Jeong Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea.,Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Yeong Seok Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Min Ji Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Adeel Malik
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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Nocardioides jejuensis sp. nov., isolated from soil. Antonie van Leeuwenhoek 2019; 113:339-347. [PMID: 31637662 DOI: 10.1007/s10482-019-01343-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/02/2019] [Indexed: 10/25/2022]
Abstract
A Gram-stain positive, asporogenous, aerobic, white -coloured bacterium, designated 18JY15-6T, was isolated from soil from Jeju Island, Korea. Pairwise analysis of the 16S rRNA gene sequence of strain 18JY15-6T indicated high similarity to Nocardioides phosphati DSM 104026T (97.4%), Marmoricola terrae KACC 17308T (96.7%) and Nocardioides jensenii KCTC 0074BPT (96.6%). Phylogenetic analysis revealed that strain 18JY15-6T formed a distinct lineage within the family Nocardioidaceae and is closely related to members of the genus Nocardioides. Genome sequencing of strain 18JY15-6T revealed 3221 total genes, including 3162 protein coding genes, 59 RNA and 31 pseudogenes. Growth was observed at 18-37 °C (optimal 30 °C) in R2A medium at pH 7.0. The major cellular fatty acids of strain 18JY15-6T were identified as C16:0, C18:1ω9c, C18:0 10-methyl, tuberculostearic and C17:0. The fatty acid profile of strain 18JY15-6T was more dissimilar when compared with M. terrae. The only respiratory quinone present was found to be MK-8(H4). The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The results of phylogenetic, biochemical and chemotaxonomic characterisation allow the differentiation of strain 18JY15-6T from N. phosphati WYH11-7T, M. terrae JOS5-1T and N. jensenii NBRC 14755T which supports the conclusion that this strain represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides jejuensis sp. nov. The type strain of Nocardioides jejuensis is 18JY15-6T (= KCTC 49105T = JCM 33182T).
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Zhang GQ, Liu Q, Liu HC, Zhou YG, Xin YH. Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China. Int J Syst Evol Microbiol 2019; 69:2329-2334. [PMID: 31135330 DOI: 10.1099/ijsem.0.003471] [Citation(s) in RCA: 4] [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 novel Gram-stain-positive, non-motile, rod-shaped, non-spore-forming bacterium, designated HLT2-9T, was isolated from the ice tongue surface of Hailuogou Glacier in Sichuan Province, PR China. Colonies of cells were cream yellow, convex and round. Growth occurred at 0-27 °C (optimum, 20 °C), pH 7.0-10.0 (pH 7.0) and in the presence of 0-2.0 % (w/v) NaCl (0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HLT2-9T belonged to the genus Nocardioides. The highest level of sequence similarities were found to Nocardioides glacieisoli CGMCC1.11097T (99.24 %), Nocardioides oleivorans CGMCC 4.6882T (98.54 %) and Nocardioides ganghwensis CGMCC 4.6875T (98.54 %). However, the low average nucleotide identity (85.6-87.9 %) and digital DNA-DNA hybridization values (26.4-30.2 %) of strain HLT2-9T to its three closest relatives demonstrated that it represents a novel species of the genus Nocardioides. The major cellular fatty acids of strain HLT2-9T were C17 : 1ω8c and iso-C16 : 0. Strain HLT2-9T contained ll-2,6-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinone is MK-8(H4). The G+C content of the genomic DNA was 70.65 mol%. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Nocardioideszhouii sp. nov. is proposed, with HLT2-9T (=CGMCC 1.11084T=NBRC 109783T) as the type strain.
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Affiliation(s)
- Guo-Qing Zhang
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Lee DW, Lee AH, Lee H, Kim JJ, Khim JS, Yim UH, Kim BS. Nocardioides litoris sp. nov., isolated from the Taean seashore. Int J Syst Evol Microbiol 2017; 67:2332-2336. [DOI: 10.1099/ijsem.0.001954] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dong Wan Lee
- BK21 Plus Eco-Leader Education Center, Korea University, Seoul 02841, Republic of Korea
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Aslan Hwanhwi Lee
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science and Ecological Engineering, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Science and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | - Beom Seok Kim
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJ. Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave. Int J Syst Evol Microbiol 2017; 67:633-639. [PMID: 27902315 DOI: 10.1099/ijsem.0.001676] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterial strain, designated YIM A1136T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-staining-positive and rod-shaped. Colonies of the strain were circular, convex, opaque and yellowish-white in colour. On the basis of 16S rRNA gene sequence analysis, strain YIM A1136T was most closely related to the type strains Nocardioides ganghwensis JC2055T (98.3 % sequence similarity), Nocardioides exalbidus RC825T (98.2 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides hwasunensis HFW-21T (98.0 %), Nocardioides oleivorans DSM 16090T (97.9 %) and Nocardioides furvisabuli SBS-26T (97.8 %) and is therefore considered to represent a member of the genus Nocardioides. DNA-DNA hybridization values between strain YIM A1136T and related type strains of the genus Nocardioides were less than 70 %. ll-Diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose, rhamnose and ribose. The major isoprenoid quinone was MK-8(H4), while the major fatty acids (>10 %) were C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The genomic DNA G+C content was 71.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain YIM A1136T merits representation of a novel species of the genus Nocardioides, for which the name Nocardioides cavernae sp. nov. is proposed. The type strain is YIM A1136T (=KCTC 39551T=DSM 29950T).
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Affiliation(s)
- Ming-Xian Han
- Medical Faculty of Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming 650500, PR China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ye Tian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wan-Qin Zhang
- College of Biology and Chemistry, Xingyi Normal University for Nationalities, Xingyi 562400, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zi-Tong Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Da-Qiao Wei
- Medical Faculty of Kunming University of Science and Technology, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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Wang S, Zhou Y, Zhang G. Nocardioides flavus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:5275-5280. [PMID: 27654931 DOI: 10.1099/ijsem.0.001507] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short rod-shaped actinomycete strain, Y4T, was isolated from a sediment sample collected from the Western Pacific. This isolate grew in the presence of 0-10 % (w/v) NaCl and at pH 6.0-9.0 and 4-40 °C; optimum growth was observed with 1 % (w/v) NaCl and at pH 7.0 and 35-37 °C. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain Y4T belonged to the genus Nocardioides and was most closely related to the type strains Nocardioides ganghwensis JC2055T (98.0 %) and Nocardioides exalbidus RC825T (98.0 %), followed by Nocardioides alpinus Cr7-14T (97.9 %), Nocardioides oleivorans DSM 16090T (97.9 %), Nocardioides furvisabuli SBS-26T (97.4 %) and Nocardioides hwasunensis HFW-21T (97.4 %). Sequence similarities between strain Y4T and the other related species of the genus Nocardioides were less than 96.3 %. Strain Y4T had MK-8(H4) and MK-7(H4) as the predominant respiratory quinones and C17 : 1ω8c, iso-C16 : 0 and C17 : 0 as major fatty acids. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phospholipid, two unknown glycolipids and one unknown lipid. The DNA G+C content was 70.4 mol%. The diagnostic diamino acid in the cell-wall peptidoglycan was ll-diaminopimelic acid. Strain Y4T could be differentiated from recognized Nocardioides species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. Thus, strain Y4T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides flavus sp. nov. is proposed. The type strain is Y4T (=MCCC 1A09944T=LMG 28100T=JCM 19770T=CGMCC 1.12791T).
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Affiliation(s)
- Shuang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Yuan Zhou
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
| | - Gaiyun Zhang
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, PR China
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11
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Singh H, Yin CS. Nocardioides flava sp. nov., isolated from rhizosphere of poppy plant, Republic of Korea. Arch Microbiol 2016; 198:279-85. [DOI: 10.1007/s00203-015-1178-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/01/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
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12
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Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi TH. Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. Int J Syst Evol Microbiol 2016; 66:371-378. [DOI: 10.1099/ijsem.0.000730] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hina Singh
- Department of Oriental Medicine Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Juan Du
- Department of Oriental Medicine Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Huan Trinh
- Department of Oriental Medicine Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - KyungHwa Won
- Department of Oriental Medicine Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - Jung-Eun Yang
- Department of Oriental Medicine Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - ChangShik Yin
- Acupunture Merdian Science Research Center, College of Korean Medicine, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
| | - MooChang Kook
- Department of Marine Biotechnology, Anyang University, Incheon 417-833, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicine Biotechnology, College of Life science, Kyung Hee University Global Campus, 1732 Deokyoungdaero, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea
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13
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Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Nocardioides glacieisoli sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2015; 65:4845-4849. [DOI: 10.1099/ijsem.0.000658] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, non-spore-forming bacterium (strain HLT3-15T) was isolated from the ice tongue surface of the Hailuogou glacier in Szechwan Province, PR China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain HLT3-15T belonged to the genus Nocardioides. The highest levels of sequence similarities were found with Nocardioides hwasunensis CGMCC 4.6881T and Nocardioides ganghwensis CGMCC 4.6875T (98.5 % and 98.3 %, respectively). However, DNA–DNA relatedness demonstrated that strain HLT3-15T was distinct from its closest phylogenetic neighbours. The major cellular fatty acids of strain HLT3-15T were C17 : 1ω8c and iso-C16 : 0. Strain HLT3-15T contained ll-2,6-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan and MK-8(H4) as the predominant menaquinone. On the basis of a polyphasic approach, a novel species, Nocardioides glacieisoli sp. nov., is proposed with HLT3-15T ( = CGMCC 1.11097T = NBRC 109781T) as the type strain.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jian-Li Zhang
- School of Life Science and Technology, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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14
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Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH, Shen FT, Lai WA, Young CC. Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla). Int J Syst Evol Microbiol 2015; 65:1953-1958. [DOI: 10.1099/ijs.0.000206] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, non-motile, rod-shaped, yellow-pigment-producing bacterium, (designated strain CC-CZW004T), was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW004T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW004T with respect to other members of the genus Nocardioides. The novel strain shared highest 16S rRNA gene sequence similarities to Nocardioides daejeonensis JCM 16922T (96.4 %), Nocardioides pacificus JCM 19260T (96.3 %), and Marmoricola scoriae JCM 17444T (96.2 %). The major fatty acids of strain CC-CZW004T consisted of C17:0, C16:1ω5c, C17:1ω8c`, iso-C16:0 and C19:1ω11c/C19:1ω9c (summed feature 6). The diagnostic diamino acid in the cell wall was ll-2,6-diaminopimelic acid. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and aminophospholipid. The DNA G+C content was 73.3 mol%. The predominant quinone system was menaquinone (MK-8). On the basis of polyphasic taxonomic evidences presented here, strain CC-CZW004T represents a novel species of the genus Nocardioides, for which the name Nocardioides echinoideorum sp. nov. is proposed. The type strain is CC-CZW004T ( = BCRC 16974T = JCM 30276T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Cheng-Zhe Wen
- Bachelor Program of Bio-Industry Management, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Fo-Ting Shen
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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15
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Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2015; 65:1604-1610. [DOI: 10.1099/ijs.0.000147] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24T, was isolated from a soil sample collected from the rhizosphere of Alhagi sparsifolia on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24T grew optimally without NaCl at 28–30 °C and pH 7.0–8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24T belonged to the genus
Nocardioides
and shared the highest 16S rRNA gene sequence similarity with
Nocardioides salarius
CL-Z59T (96.51 %),
N. pyridinolyticus
OS4T (96.43 %) and
N. ginsengagri
BX5-10T (96.37 %). The DNA G+C content of strain SC8A-24T was 71 mol%. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid, and MK-8(H4) was the predominant menaquinone. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The major fatty acids were C17 : 1ω8c, 10-methyl C17 : 0 and C18 : 1ω9c. On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain SC8A-24T represents a novel species of the genus
Nocardioides
, for which the name Nocardioides deserti sp. nov. is proposed. The type strain is SC8A-24T ( = DSM 26045T = CGMCC 4.7183T).
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16
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Hamedi J, Mohammadipanah F, Panahi HKS. Biotechnological Exploitation of Actinobacterial Members. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2015. [DOI: 10.1007/978-3-319-14595-2_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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17
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Glaeser SP, McInroy JA, Busse HJ, Kämpfer P. Nocardioides zeae sp. nov., isolated from the stem of Zea mays. Int J Syst Evol Microbiol 2014; 64:2491-2496. [PMID: 24801154 DOI: 10.1099/ijs.0.061481-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive aerobic organism, isolated from the healthy stem of a Zea mays plant was studied for its taxonomic position. Based on 16S rRNA gene sequence analysis strain JM-1068(T) was most closely related to Nocardioides alkalitolerans (97.2%). The 16S rRNA gene sequence similarity to all other species of the genus Nocardioides was ≤ 96.1%. The quinone system of strain JM-1068(T) contained the major menaquinone MK-8(H4). The diagnostic diamino acid of the peptidoglycan was LL-diaminopimelic acid. In the polar lipid profile, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids were predominant. The polyamine pattern contained predominantly spermidine and spermine. The fatty acid profile was composed of iso-C16 : 0 and C18 : 1ω9c in addition to C16 : 0, C17 : 0 and C17 : 1ω8c and low amounts of C16 : 0 2-OH and C17 : 0 2-OH. This supported the allocation of the strain to the genus Nocardioides. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain JM-1068(T) from N. alkalitolerans. It is concluded that JM-1068(T) represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides zeae sp. nov., with JM-1068(T) ( = CIP 110696(T) = LMG 28079(T)) as the type strain.
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Affiliation(s)
- Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Auburn University, Department of Entomology and Plant Pathology, Auburn, Alabama 36849, USA
| | - Hans-Jürgen Busse
- Abteilung für Klinische Mikrobiologie und Infektionsbiologie, Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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18
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Fan X, Qiao Y, Gao X, Zhang XH. Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment. Int J Syst Evol Microbiol 2014; 64:2217-2222. [PMID: 24699067 DOI: 10.1099/ijs.0.059873-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, strictly aerobic, rod-shaped, non-motile bacterium, designated strain XH274(T), was isolated from a deep sub-seafloor sediment sample collected from the South Pacific Gyre (41° 58' S 163° 11' W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH274(T) belonged to the genus Nocardioides and shared the highest 16S rRNA gene sequence similarity with Nocardioides kribbensis KSL-2(T) (96.81%), Nocardioides daedukensis MDN22(T) (96.74%) and Nocardioides psychrotolerans RHLT2-1(T) (96.61%). The DNA G+C content of strain XH274(T) was 74.6 mol%. The cell wall of strain XH274(T) contained ll-2,6-diaminopimelic acid as the diagnostic diamino acid, and ribose, glucose, galactose and mannose as the major whole-cell sugars. The major fatty acids were iso-C16 : 0, C18 : 1ω9c and C17 : 1ω8c. The major respiratory quinone was menaquinone-8(H4). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. On the basis of data from the polyphasic analysis, strain XH274(T) is considered to represent a novel species in the genus Nocardioides, for which the name Nocardioides pacificus sp. nov. is proposed. The type strain is XH274(T) ( = DSM 27278(T) = JCM 19260(T)).
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Affiliation(s)
- Xiaoyang Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Xin Gao
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
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Bacterial structure and spatiotemporal distribution in a horizontal subsurface flow constructed wetland. Appl Microbiol Biotechnol 2013; 98:3191-203. [DOI: 10.1007/s00253-013-5341-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 10/14/2013] [Accepted: 10/17/2013] [Indexed: 10/26/2022]
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Cho Y, Jang GI, Cho BC. Nocardioides
marinquilinus sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2013; 63:2594-2599. [DOI: 10.1099/ijs.0.047902-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, non-motile, strictly aerobic, non-spore-forming and short rod-shaped bacterial strain, CL-GY44T, was isolated from coastal seawater, Korea. Analysis of the 16S rRNA gene sequence of strain CL-GY44T revealed a clear affiliation with the genus
Nocardioides
. Based on phylogenetic analysis, strain CL-GY44T showed the closest phylogenetic relationship with
Nocardioides ginsengagri
BX5-10T and
Nocardioides plantarum
NCIMB 12834T. Strain CL-GY44T was not able to grow in the presence of NaCl but grew with 0–5.5 % sea salts. The optimum temperature and pH for growth were 30 °C and pH 7.0. The major cellular fatty acids of strain CL-GY44T were C17 : 1ω6c, iso-C16 : 0, C16 : 0 and iso-C15 : 0 and the major menaquinone was MK-8(H4). The cell-wall analysis showed that strain CL-GY44T contained ll-diaminopimelic acid. The genomic DNA G+C content was 71.6 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain CL-GY44T could be clearly distinguished from members of the genus
Nocardioides
. Thus, strain CL-GY44T should be classified as representing a novel species in the genus
Nocardioides
, for which the name Nocardioides marinquilinus sp. nov. is proposed. The type strain is CL-GY44T ( = KCCM 90109T = JCM 18459T).
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Affiliation(s)
- Yirang Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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Cho Y, Jang GI, Hwang CY, Kim EH, Cho BC. Nocardioides salsibiostraticola sp. nov., isolated from biofilm formed in coastal seawater. Int J Syst Evol Microbiol 2013; 63:3800-3806. [PMID: 23667145 DOI: 10.1099/ijs.0.051037-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, non-motile, aerobic, non-spore-forming and short rod-shaped bacterial strain, PAMC 26527(T), was isolated from biofilm formed in coastal seawater of the Norwegian Sea. Analysis of the 16S rRNA gene sequence of strain PAMC 26527(T) revealed a clear affiliation with the genus Nocardioides. Based on phylogenetic analysis, strain PAMC 26527(T) showed the closest phylogenetic relationship with Nocardioides caricicola YC6903(T) with 16S rRNA gene sequence similarity of 96.3 %. Strain PAMC 26527(T) grew in the presence of 0-5.0 % sea salts. The optimum temperature and pH for growth were 20 °C and pH 7.5. The major cellular fatty acids of strain PAMC 26527(T) were iso-C16 : 0, C17 : 1ω8c and C18 : 1ω9c and the major isoprenoid quinone was MK-8(H4). Cell-wall analysis showed that strain PAMC 26527(T) contained LL-diaminopimelic acid. The genomic DNA G+C content was 69.3 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain PAMC 26527(T) could be clearly distinguished from recognized members of the genus Nocardioides. Thus, strain PAMC 26527(T) should be classified as representing a novel species in the genus Nocardioides, for which the name Nocardioides salsibiostraticola sp. nov. is proposed. The type strain is PAMC 26527(T) ( = KCTC 29158(T) = JCM 18743(T)).
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Affiliation(s)
- Yirang Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Gwang Il Jang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Chung Yeon Hwang
- Division of Polar Life Sciences, Korea Polar Research Institute, Songdo Techno Park, Songdo-dong 7-50, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Eun-Hye Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Songdo Techno Park, Songdo-dong 7-50, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea
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22
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Du HJ, Wei YZ, Su J, Liu HY, Ma BP, Guo BL, Zhang YQ, Yu LY. Nocardioides perillae sp. nov., isolated from surface-sterilized roots of Perilla frutescens. Int J Syst Evol Microbiol 2012; 63:1068-1072. [PMID: 22707530 DOI: 10.1099/ijs.0.044982-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped actinobacterium, designated strain I10A-01402(T), was isolated from surface-sterilized roots of a medicinal plant, Perilla frutescens, collected in a suburb of Beijing, China. Chemotaxonomically, the strain contained ll-diaminopimelic acid as the diagnostic diamino acid and MK-8(H4) as the predominant menaquinone. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The major fatty acids were C17 : 1ω9c, C18 : 1ω9c, C17 : 0, C16 : 0 and iso-C16 : 0. The genomic DNA G+C content was 70.4 mol%. 16S rRNA gene sequence analysis indicated that strain I10A-01402(T) belonged to the genus Nocardioides. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate formed a robust cluster with Nocardioides ginsengisegetis Gsoil 485(T), N. koreensis MSL-09(T) and N. alkalitolerans KSL-1(T). On the basis of the evidence from our polyphasic taxonomic study, a novel species, Nocardioides perillae sp. nov., is proposed. The type strain is I10A-01402(T) ( = CPCC 203382(T) = DSM 24552(T) = KCTC 29022(T)).
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Affiliation(s)
- Hui-Jing Du
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Zhen Wei
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Yu Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Bai-Ping Ma
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Bao-Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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23
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Zhang DC, Schumann P, Redzic M, Zhou YG, Liu HC, Schinner F, Margesin R. Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:445-450. [DOI: 10.1099/ijs.0.031047-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, non-motile, rod-shaped, psychrophilic actinomycete, designated strain Cr7-14T, was isolated from alpine glacier cryoconite. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Cr7-14T was related to members of the genus Nocardioides and shared highest 16S rRNA gene sequence similarities with the type strains of Nocardioides furvisabuli (98.6 %), Nocardioides ganghwensis (98.2 %), Nocardioides oleivorans (98.1 %) and Nocardioides exalbidus (97.6 %). The predominant cellular fatty acids of strain Cr7-14T were C17 : 1ω8c (39.5 %) and iso-C16 : 0 (32.4 %). The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were galactose and rhamnose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, four unknown glycolipids and two unknown polar lipids. The genomic DNA G+C content was 71.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species, Nocardioides alpinus sp. nov., is proposed, with Cr7-14T ( = DSM 23325T = LMG 26053T = CGMCC 1.10697T) as the type strain.
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Affiliation(s)
- De-Chao Zhang
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Peter Schumann
- DSMZ – Deutsche Sammlung für Mikroorganismen und Zellkulturen GmbH, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Mersiha Redzic
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Franz Schinner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
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Kim JM, Lee SH, Jung JY, Jeon CO. Marinobacterium lutimaris sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2010; 60:1828-1831. [DOI: 10.1099/ijs.0.016246-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, moderately halophilic bacterium, designated strain AN9T, was isolated from a tidal flat of the Taean coast in South Korea. Cells were catalase- and oxidase-positive short rods that were motile by means of a single polar flagellum. Growth of strain AN9T was observed at 15–40 °C (optimum, 25–30 °C) and at pH 6.0–8.0 (optimum, pH 6.5–7.5). Strain AN9T contained ubiquinone Q-8 as the predominant isoprenoid quinone and C10 : 0 3-OH (31.7 %), C18 : 1
ω7c (24.8 %), C16 : 0 (14.7 %) and summed feature 3 (comprising C16 : 1
ω7c and/or iso-C15 : 0 2-OH, 10.72 %) as the major fatty acids. The G+C content of the genomic DNA of strain AN9T was 58 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AN9T was related to members of the genus Marinobacterium and was related most closely to Marinobacterium litorale IMCC1877T (96.8 % similarity). On the basis of chemotaxonomic and molecular data, strain AN9T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium lutimaris sp. nov. is proposed. The type strain is AN9T (=KACC 13703T =DSM 22012T).
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Affiliation(s)
- Jeong Myeong Kim
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Se Hee Lee
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Ji Young Jung
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
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Yoon JH, Park S, Kang SJ, Lee JS, Lee KC, Oh TK. Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 60:1334-1338. [DOI: 10.1099/ijs.0.015354-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, non-motile and rod- or coccoid-shaped bacterial strain, MDN22T, was isolated from a soil sample from Korea. Strain MDN22T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MDN22T was phylogenetically most closely related to the genera Nocardioides and Marmoricola. In the neighbour-joining phylogenetic tree, strain MDN22T was most closely related to Nocardioides jensenii KCTC 9134T, with which it exhibited 98.3 % 16S rRNA gene sequence similarity. The strain exhibited 93.1–96.9 % and 95.3–95.9 % 16S rRNA gene sequence similarities to the type strains of other species of the genera Nocardioides and Marmoricola, respectively. The chemotaxonomic properties of strain MDN22T were consistent with those of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 and C17 : 1. The DNA G+C content was 68.7 mol%. DNA–DNA relatedness data and differential phenotypic properties suggested that strain MDN22T could be differentiated from N. jensenii and Nocardioides dubius. On the basis of the data obtained, strain MDN22T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daedukensis sp. nov., is proposed. The type strain is MDN22T (=KCTC 19601T=CCUG 57505T).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Sooyeon Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Jung-Sook Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Keun Chul Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Republic of Korea
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Hwang CY, Bae GD, Yih W, Cho BC. Marivita cryptomonadis gen. nov., sp. nov. and Marivita litorea sp. nov., of the family Rhodobacteraceae, isolated from marine habitats. Int J Syst Evol Microbiol 2009; 59:1568-75. [DOI: 10.1099/ijs.0.005462-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Choi DH, Hwang CY, Cho BC. Pelagibius litoralis gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from coastal seawater. Int J Syst Evol Microbiol 2009; 59:818-23. [DOI: 10.1099/ijs.0.002774-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kim KH, Roh SW, Chang HW, Nam YD, Yoon JH, Jeon CO, Oh HM, Bae JW. Nocardioides basaltis sp. nov., isolated from black beach sand. Int J Syst Evol Microbiol 2009; 59:42-7. [DOI: 10.1099/ijs.0.65785-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Park SC, Baik KS, Kim MS, Chun J, Seong CN. Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment. Int J Syst Evol Microbiol 2008; 58:2619-23. [DOI: 10.1099/ijs.0.65835-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kim MK, Park MJ, Im WT, Yang DC. Aeromicrobium ginsengisoli sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol 2008; 58:2025-30. [PMID: 18768598 DOI: 10.1099/ijs.0.64871-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain Gsoil 098(T), a Gram-positive, non-spore-forming, non-motile coccus, was isolated from soil from a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Gsoil 098(T) belongs to the family Nocardioidaceae, and the highest degrees of sequence similarity were found with Aeromicrobium marinum T2(T) (99.0%), A. panaciterrae Gsoil 161(T) (98.9%), A. alkaliterrae KSL-107(T) (98.4%), A. fastidiosum KCTC 9576(T) (98.1%) and A. erythreum NRRL B-3381(T) (97.5%). Chemotaxonomic analysis revealed that strain Gsoil 098(T) possesses menaquinone MK-9(H(4)) and predominant fatty acids C(16 : 0), 10-methyl C(18:0) and C(18:0). DNA-DNA hybridization results and physiological and biochemical tests clearly demonstrated that strain Gsoil 098(T) represents a distinct species. Based on these data, Gsoil 098(T) (=KCTC 19207(T) =JCM 14732(T) =GBS 39(T)) should be classified as the type strain of a novel Aeromicrobium species, for which the name Aeromicrobium ginsengisoli sp. nov. is proposed.
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Affiliation(s)
- Myung Kyum Kim
- Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University, 1 Seocheon-dong, Giheung-gu, Yongin, Gyunggi-do 446-701, Republic of Korea
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Kim HM, Choi DH, Hwang CY, Cho BC. Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton. Int J Syst Evol Microbiol 2008; 58:2056-64. [DOI: 10.1099/ijs.0.65569-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kim YG, Hwang CY, Cho BC. Pelagicola litoralis gen. nov., sp. nov., isolated from coastal water in Korea. Int J Syst Evol Microbiol 2008; 58:2102-6. [DOI: 10.1099/ijs.0.65820-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Nocardioides halotolerans sp. nov., isolated from soil on Bigeum Island, Korea. Syst Appl Microbiol 2008; 31:24-9. [PMID: 18191931 DOI: 10.1016/j.syapm.2007.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 10/30/2007] [Indexed: 11/21/2022]
Abstract
A strictly aerobic, Gram-positive, motile, coccoid-shaped, halotolerant actinobacterium (10% NaCl, w/v), designated MSL-23T, was isolated from a soil sample on Bigeum Island, Korea. Results of 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Nocardioides, with the highest sequence similarity (95.63%) being to Nocardioides kribbensis KCTC 19038T. The major menaquinone was MK-8(H4), and the predominant cellular fatty acids were i-C16:0, ai-C17:0, C18:1 omega 9c and 10-methyl-C16:0. The DNA G+C content was 69.7 mol%. The 16S rRNA gene sequence of strain MSL 23T and its chemotaxonomic properties showed it to be unique in the genus Nocardioides. Phenotypic characteristics distinguished strain MSL-23T from other Nocardioides species. On the basis of the phenotypic, chemotaxonomic and phylogenetic data strain MSL-23T represents a novel species, for which the name Nocardioides halotolerans sp. nov. is proposed, with MSL-23T (=KCTC 19274T=DSM 19273T) as the type strain.
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Nocardioides islandiensis sp. nov., isolated from soil in Bigeum Island Korea. Antonie van Leeuwenhoek 2007; 93:401-6. [DOI: 10.1007/s10482-007-9217-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 12/04/2007] [Indexed: 10/22/2022]
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Lee DW, Hyun CG, Lee SD. Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand. Int J Syst Evol Microbiol 2007; 57:2960-2963. [DOI: 10.1099/ijs.0.65127-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a novel actinobacterium (designated SBS-12T), which was isolated from beach sand on Jeju Island, Republic of Korea, was determined following a polyphasic taxonomic characterization. Cells of the organism were Gram-positive, catalase-positive, oxidase-negative and non-motile rods. The organism contained ll-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H4) as predominant menaquinone, and had a polar lipid profile containing phosphatidylglycerol and phosphatidylinositol, iso-C16 : 0 as the major fatty acid and a DNA G+C content of 73.1 mol%. A neighbour-joining tree based on 16S rRNA gene sequences showed that the organism occupies a distinct phylogenetic position within the radiation including representatives of the family Nocardioidaceae. High levels of 16S rRNA gene sequence similarity were found with Nocardioides kribbensis (97.2 %), Nocardioides aquiterrae (96.9 %), Nocardioides pyridinolyticus (96.6 %) and Nocardioides aquaticus (96.3 %). The combination of morphological and chemotaxonomic characteristics was consistent with classification in the genus Nocardioides, but the isolate can be differentiated from all Nocardioides species with validly published names by a range of physiological properties. The name Nocardioides marinisabuli sp. nov. is proposed for this novel organism, with the type strain SBS-12T (=JBRI 2003T=KCCM 42681T=DSM 18965T).
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Affiliation(s)
- Dong Wan Lee
- Department of Science Education, Cheju National University, Jeju 690-756, Republic of Korea
| | - Chang-Gu Hyun
- Laboratory for Microbial Diversity and Biotechnology, Jeju Biodiversity Research Institute and Jeju Hi-Tech Industry Development Institute, Jeju 690-121, Republic of Korea
| | - Soon Dong Lee
- Department of Science Education, Cheju National University, Jeju 690-756, Republic of Korea
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Yoon JH, Kang SJ, Lee SY, Oh TK. Nocardioides terrigena sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007; 57:2472-2475. [DOI: 10.1099/ijs.0.65079-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, rod- or coccoid-shaped bacterial strain, DS-17T, was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-17T grew optimally at around pH 8.0 and 30 °C in the presence of 0.5–1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-17T belonged to the genus Nocardioides. The chemotaxonomic properties of strain DS-17T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0, C17 : 1
ω8c and C17 : 0 were the major fatty acids. The DNA G+C content was 71.5 mol%. Strain DS-17T exhibited 16S rRNA gene sequence similarity values of 94.5–96.9 % to the type strains of recognized Nocardioides species. Strain DS-17T could be distinguished from recognized Nocardioides species by differences in phenotypic characteristics. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DS-17T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides terrigena sp. nov. is proposed. The type strain is DS-17T (=KCTC 19217T=JCM 14582T).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Soo-Young Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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Abstract
A Gram-positive, slightly halophilic, rod-shaped bacterium, designated CL-DD14(T), was isolated from seawater of the East Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CL-DD14(T) belongs to the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between strain CL-DD14(T) and the type strains of recognized species of the genus Nocardioides were low (94.1-97.1 %). Strain CL-DD14 (T) grew over the pH range 6-9 and temperature range 10-40 degrees C. The strain grew at NaCl concentrations of 0.5-8 % (w/v) with optimum growth at 1-3 % and no growth was observed after 3 weeks on nutrient agar without any salts. It contained ll-diaminopimelic acid as the diamino acid in the cell wall. The major isoprenoid quinone was MK-8(H(4)) and the major cellular fatty acids were iso-C(16 : 0) and 10-methyl C(17 : 0). The DNA G+C content was 72.9 mol%. On the basis of phenotypic and phylogenetic data, strain CL-DD14(T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides marinus sp. nov. is proposed. The type strain is CL-DD14(T) (=KCCM 42321(T)=DSM 18248(T)).
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Affiliation(s)
- Dong Han Choi
- Marine Environmental Research Department, Korea Ocean Research and Development Institute, Ansan 426-744, Republic of Korea
| | - Hye Min Kim
- School of Earth and Environmental Sciences, Seoul National University, Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Jae-Hoon Noh
- Marine Environmental Research Department, Korea Ocean Research and Development Institute, Ansan 426-744, Republic of Korea
| | - Byung Cheol Cho
- School of Earth and Environmental Sciences, Seoul National University, Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
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An DS, Im WT, Lee ST, Yoon MH. Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2007; 57:2143-2146. [PMID: 17766888 DOI: 10.1099/ijs.0.64806-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain designated Gsoil 616T was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-positive, strictly aerobic, non-motile, non-spore-forming and rod- or coccoid-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Nocardioides in the family Nocardioidaceae but was clearly separated from established species of this genus. The 16S rRNA gene sequence similarities between strain Gsoil 616T and the type strains of Nocardioides species with validly published names ranged from 91.8 to 96.1 %. The G+C content of the genomic DNA was 73 mol%. Phenotypic and chemotaxonomic data [major menaquinone MK-8(H4) and major fatty acid iso-C16 : 0] supported the affiliation of strain Gsoil 616T to the genus Nocardioides. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate from other Nocardioides species. Therefore, strain Gsoil 616T represented a novel species within the genus Nocardioides, for which the name Nocardioides panacihumi sp. nov. is proposed. The type strain is Gsoil 616T (=KCTC 19187T =DSM 18660T).
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MESH Headings
- Actinomycetales/classification
- Actinomycetales/genetics
- Actinomycetales/isolation & purification
- Actinomycetales/physiology
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Genes, rRNA
- Korea
- Molecular Sequence Data
- Panax
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Vitamin K 2/analysis
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Affiliation(s)
- Dong-Shan An
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Wan-Taek Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Sung-Taik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Min-Ho Yoon
- Department of BioEnvironmental Chemistry, College of Agriculture and Life Sciences, Chungnam National University, Gung-dong 22, Yuseong-gu, Daejeon 305-764, Republic of Korea
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Yoon JH, Kang SJ, Lee CH, Oh TK. Nocardioides insulae sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007; 57:136-140. [PMID: 17220455 DOI: 10.1099/ijs.0.64612-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, rod-shaped or coccoid bacterial strain, DS-51T, was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-51T grew optimally at pH 8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-51T forms a distinct line of descent within the radiation enclosed by the genus Nocardioides. The chemotaxonomic properties of strain DS-51T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0 was the major fatty acid. The DNA G+C content was 71.1 mol%. The 16S rRNA gene sequence of strain DS-51T had similarity levels of 92.5–95.1 % with the sequences of the type strains of Nocardioides species. Strain DS-51T could be distinguished from other Nocardioides species by differences in some phenotypic characteristics. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain DS-51T represents a novel species of the genus Nocardioides, for which the name Nocardioides insulae sp. nov. is proposed. The type strain is DS-51T (=KCTC 19180T=DSM 17944T).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Choong-Hwan Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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Nocardioides exalbidus sp. nov., a novel actinomycete isolated from lichen in Izu-Oshima Island, Japan. ACTA ACUST UNITED AC 2007. [DOI: 10.3209/saj.saj210103] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Abstract
A Gram-positive, rod-shaped, yellow-pigmented actinomycete, designated strain SBS-26T, was isolated from a sample of black sand from Samyang Beach on Jeju Island (Republic of Korea) and was subjected to polyphasic characterization to unravel its taxonomic status. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the organism belongs to the genus Nocardioides but forms a distinct branch at the base of a Nocardioides ganghwensis–Nocardioides oleivorans cluster. The 16S rRNA gene sequence of strain SBS-26T showed the highest levels of similarity to those of N. ganghwensis JC2055T (97.7 %) and N. oleivorans DSM 16090T (97.6 %). The levels of 16S rRNA gene sequence similarity between strain SBS-26T and other members of the genera Nocardioides and Marmoricola were in the range 93.0–96.2 %. The following chemotaxonomic characteristics support the phylogenetic association of strain SBS-26T with members of the genus Nocardioides: ll-diaminopimelic acid as the principal diamino acid of the peptidoglycan, MK-8(H4) as the major menaquinone, iso-C16 : 0 as the predominant fatty acid and a DNA G+C content of 69.1 mol%. The polar lipids contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain SBS-26T represents a novel species of the genus Nocardioides, for which the name Nocardioides furvisabuli sp. nov. is proposed. The type strain is strain SBS-26T (=JCM 13813T=NRRL B-24465T).
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Affiliation(s)
- Soon Dong Lee
- Department of Science Education, Cheju National University, Jeju 690-756, Republic of Korea
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Yoon JH, Lee JK, Jung SY, Kim JA, Kim HK, Oh TK. Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium. Int J Syst Evol Microbiol 2006; 56:1783-1787. [PMID: 16902008 DOI: 10.1099/ijs.0.64120-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, rod- or coccoid-shaped andN-hexanoyl-l-homoserine lactone-degrading bacterial strain, A2-4T, was isolated from a soil in Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain A2-4Tgrew optimally at pH 7.0–8.0 and 30 °C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A2-4Tis most closely related to members of the genusNocardioides. Strain A2-4Tpossessed chemotaxonomic properties indicative of members of the genusNocardioides; the cell-wall peptidoglycan type was based onll-diaminopimelic acid, MK-8(H4) was the predominant menaquinone and iso-C16 : 0was the predominant fatty acid. The DNA G+C content was 72.1 mol%. The 16S rRNA gene sequence of strain A2-4Twas 98.3–99.1 % similar to those of the type strains ofNocardioides simplex,Nocardioides aromaticivoransandNocardioides nitrophenolicusand 93.8–96.3 % similar to those of the type strains of otherNocardioidesspecies. Strain A2-4Tcould be distinguished from the three phylogenetic relatives,N. nitrophenolicus,N. aromaticivoransandN. simplex, by DNA–DNA relatedness (25–42 %) and by differences in some phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, the strain represents a novel species of the genusNocardioides, for which the nameNocardioides kongjuensissp. nov. is proposed. The type strain is A2-4T(=KCTC 19054T=JCM 12609T).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon 305-600, Korea
| | - Jung-Kee Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon 305-600, Korea
| | - Seo-Youn Jung
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon 305-600, Korea
| | - Jung-Ae Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon 305-600, Korea
| | - Ha-Kun Kim
- Department of Genetic Engineering, Paichai University, Taejon 302-735, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon 305-600, Korea
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Kim S, Jeong H, Kim S, Chun J. Clostridium ganghwense sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2006; 56:691-693. [PMID: 16585678 DOI: 10.1099/ijs.0.63791-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, strictly anaerobic, halophilic, motile, sporulating and rod-shaped bacterium, designated strain HY-42-06T, was isolated from tidal flat sediment from Ganghwa Island in South Korea. The isolate produced glycerol, ethanol and CO2 as fermentation end-products from glucose. Strain HY-42-06T grew optimally at 35 °C, pH 7·5 and 3 % (w/v) artificial sea salts. No growth was observed in the absence of sea salts. In phylogenetic analyses based on 16S rRNA gene sequence, strain HY-42-06T showed a distinct phyletic line within the members of cluster I of the order Clostridiales. The closest phylogenetic neighbour to strain HY-42-06T was Clostridium novyi ATCC 17861T (94·91 % 16S rRNA gene sequence similarity). Several phenotypic characters readily differentiate the tidal flat isolate from phylogenetically related clostridia. On the basis of polyphasic evidence, strain HY-42-06T should be classified as a representative of a novel species, for which the name Clostridium ganghwense sp. nov. is proposed. The type strain is HY-42-06T (=IMSNU 40127T=KCTC 5146T=JCM 13193T).
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Affiliation(s)
- Seil Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Hyunyoung Jeong
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Sanggoo Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
| | - Jongsik Chun
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
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45
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Yoon JH, Lee CH, Oh TK. Aeromicrobium alkaliterrae sp. nov., isolated from an alkaline soil, and emended description of the genus Aeromicrobium. Int J Syst Evol Microbiol 2005; 55:2171-2175. [PMID: 16166727 DOI: 10.1099/ijs.0.63582-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic, non-motile bacterial strain, KSL-107(T), was isolated from an alkaline soil from Korea and subjected to a polyphasic taxonomic study. Strain KSL-107(T) grew optimally at 25 degrees C and pH 7.0-7.5. Strain KSL-107(T) had a cell-wall peptidoglycan based on ll-2,6-diaminopimelic acid. It contained MK-9(H(4)) as the predominant menaquinone and C(16:0), C(16:0) 2-OH and 10-methyl C(18:0) as the major fatty acids. The DNA G+C content was 71.5 mol%. Comparative 16S rRNA gene sequence analyses showed that strain KSL-107(T) was phylogenetically affiliated to the genus Aeromicrobium of the family Nocardioidaceae. Similarity values between the 16S rRNA gene sequence of strain KSL-107(T) and those of type strains of Aeromicrobium species were in the range 97.9-98.2%. The isolate could be distinguished from other Aeromicrobium species by levels of DNA-DNA relatedness and differences in some phenotypic characteristics. On the basis of the data presented, it is suggested that strain KSL-107(T) (=KCTC 19073(T)=DSM 16824(T)) represents a novel Aeromicrobium species, for which the name Aeromicrobium alkaliterrae sp. nov. is proposed. An emended description of the genus Aeromicrobium is also proposed.
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Choong-Hwan Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, South Korea
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Yoon JH, Lee CH, Oh TK. Nocardioides dubius sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 2005; 55:2209-2212. [PMID: 16166734 DOI: 10.1099/ijs.0.63748-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, rod- or coccus-shaped bacterial strain, KSL-104T, was isolated from an alkaline soil from Korea and its taxonomic position was investigated by a polyphasic approach. Strain KSL-104Tgrew optimally at pH 7·0–8·0 and 30 °C. It was characterized chemotaxonomically as having a cell-wall peptidoglycan type based onll-2,6-diaminopimelic acid with MK-8(H4) as the predominant menaquinone. The major fatty acid was iso-C16 : 0and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The DNA G+C content was 70·6 mol%. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain KSL-104Tjoined the cluster comprisingNocardioides jenseniiandMarmoricola aurantiacus. The cellular fatty acid profile of strain KSL-104Twas different from that ofM. aurantiacus. Strain KSL-104Tand the type strain ofN. jenseniiexhibited a 16S rRNA gene sequence similarity value of 97·1 % and a mean DNA–DNA relatedness value of 13 %. Levels of 16S rRNA gene sequence similarity between strain KSL-104Tand the type strains of otherNocardioidesspecies were in the range 94·0–96·5 %. On the basis of phenotypic, phylogenetic and genetic data, strain KSL-104T(=KCTC 9992T=JCM 13008T) represents a novel species of the genusNocardioides, for which the nameNocardioides dubiussp. nov. is proposed.
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Choong-Hwan Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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Schippers A, Schumann P, Spröer C. Nocardioides oleivorans sp. nov., a novel crude-oil-degrading bacterium. Int J Syst Evol Microbiol 2005; 55:1501-1504. [PMID: 16014472 DOI: 10.1099/ijs.0.63500-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crude-oil-degrading strain BAS3Trepresents a novelNocardioidesspecies, according to a taxonomic study. The 16S rRNA gene sequence of strain BAS3Twas most similar to that ofNocardioides ganghwensis(IMSNU 14028T; 99 % similarity), but the DNA–DNA relatedness to this type strain was only 32 %. The physiological properties of strain BAS3Tdiffer from those ofN. ganghwensis(IMSNU 14028T) and other species ofNocardioides. The diamino acid in the cell-wall peptidoglycan of strain BAS3Tisll-diaminopimelic acid and the major menaquinone is MK-8(H4). The nameNocardioides oleivoranssp. nov. is proposed for the novelNocardioidesspecies, since its type strain, BAS3T(=DSM 16090T=NCIMB 14004T), is able to degrade crude oil.
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Affiliation(s)
- Axel Schippers
- Referat Geomikrobiologie, Bundesanstalt für Geowissenschaften und Rohstoffe, Stilleweg 2, D-30655 Hannover, Germany
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - Cathrin Spröer
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
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Yoon JH, Kim IG, Lee MH, Oh TK. Nocardioides kribbensis sp. nov., isolated from an alkaline soil. Int J Syst Evol Microbiol 2005; 55:1611-1614. [PMID: 16014490 DOI: 10.1099/ijs.0.63631-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-positive, rod- or coccoid-shaped bacterial strains, KSL-2T, KSL-5 and KSL-6, were isolated from an alkaline soil in Korea and subjected to a polyphasic taxonomical analysis. These isolates grew optimally at pH 9·0 and 30 °C. They were characterized chemotaxonomically as having cell wall peptidoglycan based on ll-2,6-diaminopimelic acid, MK-8(H4) as the predominant menaquinone and iso-C16 : 0 as the major fatty acid. The DNA G+C content of the isolates was 73–74 mol%. Strains KSL-2T, KSL-5 and KSL-6 were identical in their 16S rRNA gene sequences and exhibited DNA–DNA relatedness values of 88–93 %. Phylogenetic trees based on 16S rRNA gene sequences showed that the three isolates fell within the evolutionary radiation encompassed by the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between the three strains and the type strains of Nocardioides species ranged from 93·6 % (with Nocardioides albus) to 97·2 % (with Nocardioides aquiterrae). DNA–DNA relatedness levels between the three isolates and N. aquiterrae CJ-14T were 8–15 %. On the basis of phenotypic, phylogenetic and genetic data, strains KSL-2T, KSL-5 and KSL-6 were classified in the genus Nocardioides as members of a novel species for which the name Nocardioides kribbensis sp. nov. is proposed, with KSL-2T (=KCTC 19038T=DSM 16314T) as the type strain.
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - In-Gi Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Mi-Hwa Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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Kubota M, Kawahara K, Sekiya K, Uchida T, Hattori Y, Futamata H, Hiraishi A. Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst Appl Microbiol 2005; 28:165-74. [PMID: 15830809 DOI: 10.1016/j.syapm.2004.10.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Seven strains of dibenzofuran (DF)-degrading bacteria isolated from dioxin-polluted environments were characterized. These isolates were able to grow with dibenzofuran as the sole carbon and energy source. During the growth with dibenzofuran, they produced a soluble yellow metabolite that exhibited a unique pH-dependent shift of absorption maxima. Dibenzo-p-dioxin and biphenyl were also degraded with pigment production. The isolates were strictly aerobic and chemoorganotrophic and had gram-positive, nonmotile, rod-shaped cells. Chemotaxonomic analyses showed that cells contained L,L-diaminopimeric acid in the peptidoglycan, branched-chain fatty acids as major fatty acids, and menaquinone MK-8(H4) as the sole respiratory quinone. The G + C content of the DNA of the isolates ranged from 72.0 to 72.4 mol%. The 16S rRNA gene sequences of the isolates were very similar to each other (> or = 99.8%). The phylogenetic analysis showed that the isolates formed a cluster with species of the genus Nocardioides with Nocardioides simplex and Nocardioides nitrophenolicus as their nearest neighbors. DNA-DNA hybridization studies showed that the isolates showed a hybridization level of less than 55% to any tested species of the genus Nocardioides. Based on these data, Nocardioides aromaticivorans sp. nov. is proposed for the new DF-degrading isolates. The type strain is strain H-1 (IAM 14992, JCM 11674, DSM 15131).
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Affiliation(s)
- Masahiro Kubota
- Graduate School of Fundamental Life Science, Kitasato University, Sagamihara, Kanagawa 228-8555, Japan
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Yoon JH, Kim IG, Lee MH, Lee CH, Oh TK. Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea. Int J Syst Evol Microbiol 2005; 55:809-814. [PMID: 15774667 DOI: 10.1099/ijs.0.63374-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four Gram-positive, rod- or coccus-shaped bacterial strains, KSL-1T, KSL-9, KSL-10 and KSL-12, were isolated from an alkaline serpentinite soil in Korea, and their taxonomic positions were investigated in a polyphasic study. The four strains exhibited no difference in their 16S rRNA gene sequences. Phylogenetic analyses based on 16S rRNA gene sequences showed that the four strains were phylogenetically affiliated to the genus Nocardioides. The four strains had cell-wall peptidoglycan based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone detected in the four strains was MK-8(H4). The major fatty acid components were iso-C16 : 0, 10-methyl-C18 : 0, C18 : 1
ω9c and C17 : 1
ω6c. The DNA G+C contents were 72·4–73·6 mol%. The four strains exhibited 16S rRNA gene sequence similarity levels of 94·0–96·3 % to the type strains of Nocardioides species with validly published names. DNA–DNA relatedness levels between the four strains were 85–91 %. On the basis of phenotypic properties, phylogenetic distinctiveness and genotypic relatedness, strains KSL-1T, KSL-9, KSL-10 and KSL-12 were classified in the genus Nocardioides as members of a novel species, Nocardioides alkalitolerans sp. nov. The type strain is strain KSL-1T (=KCTC 19037T=DSM 16699T).
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - In-Gi Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Mi-Hwa Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Choong-Hwan Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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