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Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW. Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (GL-11-2T and ZH2-Y79) were isolated from the seawater collected from the West Pacific Ocean and the East China Sea, respectively. Cells were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Cells grew in the medium containing 0.5–7.5 % NaCl (w/v, optimum, 1.0–3.0 %), at pH 6.0–8.0 (optimum, pH 6.5–7.0) and at 4–40 °C (optimum, 30 °C). H2S production occurred in marine broth supplemented with sodium thiosulphate. The almost-complete 16S rRNA gene sequences of the two isolates were identical, and exhibited the highest similarity to
Pseudoruegeria aquimaris
JCM 13603T (97.5 %), followed by
Ruegeria conchae
TW15T (97.2%),
Shimia aestuarii
DSM 15283T (97.1 %) and
Ruegeria lacuscaerulensis
ITI-1157T (97.0 %). Phylogenetic analysis revealed that the isolates were affiliated with the family
Roseobacteraceae
and represented an independent lineage. The sole isoprenoid quinone was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and cyclo-C19 : 0
ω8c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content was 62.3 mol%. The orthologous average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among the genomes of strain GL-11-2T and the reference strains were 73.2–79.0, 20.3–22.5 and 66.0–80.8 %, respectively. Strains GL-11-2ᵀ and ZH2-Y79 possessed complete metabolic pathways for thiosulphate oxidation, dissimilatory nitrate reduction and denitrification. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that the isolates represent a novel genus and species of the family
Roseobacteraceae
, belonging to the class
Alphaproteobacteria
, for which the name Thiosulfatihalobacter marinus gen. nov., sp. nov. (type strain, GL-11–2T=KCTC 82723T=MCCC M20691T) is proposed.
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Affiliation(s)
- Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Wen-Ting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Li-Li Guo
- College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
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2
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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3
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Baek J, Kim JH, Sukhoom A, Kim W. Ruegeria sediminis sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2020; 70:3055-3061. [PMID: 32195650 DOI: 10.1099/ijsem.0.004128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain, designated CAU 1488T, was isolated from tidal flat sediment, and its taxonomic position was investigated using a polyphasic approach. The organism grew optimally at a temperature of 30 °C, at pH 7.0-7.5 and in the presence of 0-6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1488T forms a lineage distinct from Ruegeria marisrubri ZGT 118T (97.9 %), Ruegeria marina ZH17T (97.6 %), Ruegeria lacuscaerulensis ITI 1157T (97.5 %), Ruegeria pomeroyi DSS-3T (97.1 %), Ruegeria profundi ZGT108T (97.0 %), Ruegeria intermedia CC-GIMAT-2T (96.8 %), Ruegeria atlantica CECT 4292T (96.7 %) and Ruegeria kandeliae J95T (95.9 %). Genome sequencing revealed that CAU 1488T had a genome size of 4.23 Mbp and a G+C content of 63.2 mol%. Overall genome related indexes including average nucleotide identity and digital DNA-DNA hybridization values were 75.0-83.0 % and 26.2 %, which are below the cutoffs of 95 and 70 %, respectively, indicating that strain CAU 1488T represents a distinct species from the members of the genus Ruegeria. The predominant quinone was ubiquinone-10 (Q-10). The major fatty acids were summed feature 8 (C18 : 1 ω7c/ω6c; 60.7 %) and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and unidentified aminolipids. On the basis of phenotypic, chemotaxonomic and genomic data, strain CAU 1488T constitutes a novel species of the genus Ruegeria, for which the name Ruegeria sediminis sp. nov. is proposed. The type strain is CAU 1488T (=KCTC 62996T=NBRC 113693T).
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Affiliation(s)
- Jihye Baek
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
| | - Ampaitip Sukhoom
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea
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4
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Zhang S, Liu WX, Liu NH, He XY, Su HN, Li CY, Zhang YZ, Song XY, Zhang XY. Antarcticimicrobium sediminis gen. nov., sp. nov. , isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. Int J Syst Evol Microbiol 2020; 70:2624-2631. [PMID: 32134379 DOI: 10.1099/ijsem.0.004083] [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: 01/28/2023] Open
Abstract
A Gram-stain-negative, aerobic, non-flagellated and rod- or ovoid-shaped bacterium, designated as strain S4J41T, was isolated from Antarctic intertidal sediment. The isolate grew at 0-37 °C and with 0.5-10 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed Tween 80 and gelatin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S4J41T constituted a distinct phylogenetic line within the family Rhodobacteraceae and was closely related with some species in the genera Ruegeria, Phaeobacter, Pseudopuniceibacterium, Sulfitobacter, Puniceibacterium and Poseidonocella with 98.6-95.7 % 16S rRNA gene sequence similarities. The major cellular fatty acids were C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C18 : 0 and the major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. The sole respiratory quinone was Q-10. The genomic DNA G+C content of strain S4J41T was 60.3 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain S4J41T is considered to represent a novel species in a new genus within the family Rhodobacteraceae, for which the name Antarcticimicrobium sediminis gen. nov., sp. nov. is proposed. The type strain is S4J41T (=MCCC 1K03508T=KCTC 62793T). Moreover, the transfer of Ruegeria lutea Kim et al. 2019 to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov. (type strain 318-1T=JCM 30927T=KCTC 72105T) is also proposed.
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Affiliation(s)
- Shan Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Wei-Xiong Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266003, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, PR China
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5
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Sun YY, Dang YR, He XY, Wang JM, Liu NH, Sun ML, Li CY, Chen XL, Zhang YZ, Song XY, Yang J, Zhang XY. Fluviibacterium aquatile gen. nov., sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2020; 70:105-111. [DOI: 10.1099/ijsem.0.003722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yuan-Yuan Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Yan-Ru Dang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan He
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Jing-Mei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Mei-Ling Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Chun-Yang Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao 266003, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
| | - Xi-Ying Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, PR China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, School of Life Science, Shandong University, Qingdao 266237, PR China
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6
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Yan YQ, Hao YX, He RH, Du ZJ. Mucilaginibacter gilvus sp. nov., isolated from Antarctic soil. Int J Syst Evol Microbiol 2019; 69:3885-3890. [PMID: 31490112 DOI: 10.1099/ijsem.0.003702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile, rod-shaped, cold-tolerant bacterium, designated F01003T, was isolated from soil sampled near Happiness Bay on the west coast of Antarctica. Strain F01003T was found to grow at 4-30 °C (optimum, 25 °C), pH 5.5-8.0 (pH 6.5-7.0) and in the presence of 0-1 % NaCl (0 %, w/v). Cells were oxidase-positive and catalase-positive. Strain F01003T contained menaquinone 7 (MK-7) as the predominant respiratory quinone. The main cellular fatty acids included summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0. Phosphatidylethanolamine and an unidentified aminolipid were identified as the major polar lipids. The DNA G+C content of strain F01003T was 44.8 mol%. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence revealed that strain F01003T was most closely related to the genus Mucilaginibacter and exhibited the highest sequence similarity to Mucilaginibacter phyllosphaerae LMG 29118T (97.3 %). On the basis of the evidence presented in this polyphasic taxonomic study, strain F01003T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibactergilvus sp. nov. is proposed. The type strain is F01003T (=KCTC 62991T=CCTCC AB 2019023T).
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Affiliation(s)
- Yu-Qi Yan
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Yong-Xin Hao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Rui-Han He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China.,College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University, Weihai 264209, PR China.,SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
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7
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Kim J, Kim DY, Yang KH, Kim S, Lee SS. Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea. Int J Syst Evol Microbiol 2019; 69:2854-2861. [PMID: 31274408 DOI: 10.1099/ijsem.0.003568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile, mesophilic, short rod-shaped, aerobic bacterium designated as 318-1T was isolated from a marine sediment collected from Masan Bay, South Korea. Strain 318-1T grew optimally at pH 6-7, at 30 °C and in the presence of 2-3 % (w/v) NaCl, tolerant of up to 8 % (w/v) NaCl, and accumulated poly-β-hydroxybutyrate (PHB). A comparative analysis of 16S rRNA gene sequences revealed that strain 318-1T formed a distinct phyletic lineage in the genus Ruegeria (family Rhodobacteraceae, class Alphaproteobacteria) and showed high sequence similarity to Ruegeria halocynthiae DSM 27839T (96.5 %) and Shimia haliotis DSM 28453T (96.3 %). Comparing the genome sequence of 318-1T with those of the type strains of seven species of the genus Rugeria and two species of the genus Shimia, the values obtained were below the thresholds with analysis of average nucleotide identities (ANI, 71.6-76.8 %) and in silico DNA-DNA hybridisation, Genome-to-Genome Distance Calculator (GGDC, 18.5-20.6 %). The DNA G+C content was 65.75 mol%. Chemotaxonomic data [predominant quinone ubiquinone Q10; polar lipid profile consisting of major compounds phosphatidylcholine (PC), phosphatidylglycerol (PG), an unidentified aminolipid and an unidentified lipid; major fatty acids summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c)] supported the affiliation of strain 318-1T to the genus Ruegeria. Genomic, chemotaxonomic, and phenotypic differentiation of strain 318-1T from the members of the genus Ruegeria support it as a novel species. On the basis of the results in this study, a novel species, Ruegeria lutea sp. nov., is proposed. The type strain is 318-1T (=JCM 30927T=KEMB 7306-525T=KCTC 72105T).
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Affiliation(s)
- Jinsoo Kim
- Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea.,Research & Development Institute of Inventory Co. Ltd., 8-3, Yeoseori-gil, Daedeok-myeon Anseong-si, Gyeonggi-go 17542, Republic of Korea
| | - Da-Young Kim
- Life Science Major, Division of Bio-Convergence, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Keun-Hyeok Yang
- Department of Architectural Engineering, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Sungchul Kim
- Research & Development Institute of Inventory Co. Ltd., 8-3, Yeoseori-gil, Daedeok-myeon Anseong-si, Gyeonggi-go 17542, Republic of Korea.,Department of Environmental Energy Engineering, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
| | - Sang-Seob Lee
- Life Science Major, Division of Bio-Convergence, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea.,Department of Life Science, Graduate School, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, Republic of Korea
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8
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Phylogenetic Analysis and Screening of Antimicrobial and Antiproliferative Activities of Culturable Bacteria Associated with the Ascidian Styela clava from the Yellow Sea, China. BIOMED RESEARCH INTERNATIONAL 2019; 2019:7851251. [PMID: 31559313 PMCID: PMC6735190 DOI: 10.1155/2019/7851251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Accepted: 07/28/2019] [Indexed: 01/01/2023]
Abstract
Over 1,000 compounds, including ecteinascidin-743 and didemnin B, have been isolated from ascidians, with most having bioactive properties such as antimicrobial, antitumor, and enzyme-inhibiting activities. In recent years, direct and indirect evidence has shown that some bioactive compounds isolated from ascidians are not produced by ascidians themselves but by their symbiotic microorganisms. Isolated culturable bacteria associated with ascidians and investigating their potential bioactivity are an important approach for discovering novel compounds. In this study, a total of 269 bacteria were isolated from the ascidian Styela clava collected from the coast of Weihai in the north of the Yellow Sea, China. Phylogenetic relationships among 183 isolates were determined using their 16S rRNA gene sequences. Isolates were tested for antimicrobial activity against seven indicator strains, and an antiproliferative activity assay was performed to test for inhibition of human hepatocellular carcinoma Bel 7402 and human cervical carcinoma HeLa cell proliferation. Our results showed that the isolates belonged to 26 genera from 18 families in four phyla (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes). Bacillus and Streptomyces were the most dominant genera; 146 strains had potent antimicrobial activities and inhibited at least one of the indicator strains. Crude extracts from 29 strains showed antiproliferative activity against Bel 7402 cells with IC50 values below 500 μg·mL-1, and 53 strains showed antiproliferative activity against HeLa cells, with IC50 values less than 500 μg·mL-1. Our results suggest that culturable bacteria associated with the ascidian Styela clava may be a promising source of novel bioactive compounds.
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9
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Chen L, Hu JS, Xu JL, Shao CL, Wang GY. Biological and Chemical Diversity of Ascidian-Associated Microorganisms. Mar Drugs 2018; 16:md16100362. [PMID: 30275404 PMCID: PMC6212887 DOI: 10.3390/md16100362] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 11/16/2022] Open
Abstract
Ascidians are a class of sessile filter-feeding invertebrates, that provide unique and fertile niches harboring various microorganisms, such as bacteria, actinobacteria, cyanobacteria and fungi. Over 1000 natural products, including alkaloids, cyclic peptides, and polyketides, have been isolated from them, which display diverse properties, such as antibacterial, antifungal, antitumor, and anti-inflammatory activities. Strikingly, direct evidence has confirmed that ~8% of natural products from ascidians are actually produced by symbiotic microorganisms. In this review, we present 150 natural products from microorganisms associated with ascidians that have been reported up to 2017.
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Affiliation(s)
- Lei Chen
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Jin-Shuang Hu
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Jia-Lei Xu
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
| | - Chang-Lun Shao
- Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Guang-Yu Wang
- Department of Bioengineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
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10
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Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393-2411. [DOI: 10.1099/ijsem.0.002833] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Joseph S. Wirth
- Department of Microbiology, University of Georgia, Athens, GA, USA
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11
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Zhang L, Wang KL, Yin Q, Liang JY, Xu Y. Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel. Int J Syst Evol Microbiol 2018; 68:2653-2658. [PMID: 29949499 DOI: 10.1099/ijsem.0.002894] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped and motile bacterium, designated strain J95T, was isolated from the rhizosphere soil of a mangrove plant Kandeliacandel (L.) Druce in Mai Po Nature Reserve, Hong Kong. Growth of strain J95T was observed at pH 5.0-8.5 (optimum, 6.0-7.0), between 10-40 °C (30-37 °C) and in the presence of 0-9 % (w/v) NaCl (0.5-3 %). Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone and C18 : 1ω7c and C19 : 0 cycloω8c as the major fatty acids. The major polar lipids were lipid, aminolipid, phospholipid, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The genomic contained a circular chromosome of 5.48 Mb with a DNA G+C content of 65.7 mol%. The genome included 5299 genes. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain J95T belongs to the genus Ruegeria with highest sequence similarity (96.8 %) to the type strain Ruegeria marina ZH17T. The combined phenotypic, chemotaxonomic and phylogenetic data suggested that strain J95T represents a novel species of the genus Ruegeria, for which the name Ruegeria kandeliae sp. nov. is proposed. The type strain is J95T (=MCCC 1K03284T=DSM 104293T).
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Affiliation(s)
- Lv Zhang
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Kai-Ling Wang
- 2Institute of Materia Medica, Dali University, Dali 671000, PR China.,3School of Pharmacy and Chemistry, Dali University, Dali 671000, PR China
| | - Qi Yin
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Jin-You Liang
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Ying Xu
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
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12
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Arahal DR, Lucena T, Rodrigo-Torres L, Pujalte MJ. Ruegeria denitrificans sp. nov., a marine bacterium in the family Rhodobacteraceae with the potential ability for cyanophycin synthesis. Int J Syst Evol Microbiol 2018; 68:2515-2522. [PMID: 29944092 DOI: 10.1099/ijsem.0.002867] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Strain CECT 5091T, an aerobic, marine, Gram-reaction- and Gram-stain-negative, chemoheterotrophic bacterium was isolated from oysters harvested off the Spanish Mediterranean coast. Analysis of the 16S rRNA gene sequence placed the strain within the genus Ruegeria, in the family Rhodobacteraceae, with 16S rRNA gene similarities of 98.7, 98.7 and 98.4 % to Ruegeria conchae, Ruegeria atlanticaand Ruegeria arenilitoris, respectively. Average nucleotide identities (ANI) and in silico DNA-DNA hybridization (DDH) were determined, comparing the genome sequence of CECT 5091T with those of the type strains of 12 species of the genus Ruegeria: the values obtained were always below the thresholds (95-96 % ANI, 70 % in silico DDH) used to define genomic species, proving that CECT 5091T represents a novel species of the genus Ruegeria. The strain was slightly halophilic and mesophilic, with optimum growth at 26 °C, pH 7.0 and 3 % salinity, it required sodium and magnesium ions for growth and was able to reduce nitrate to dinitrogen. Carbon sources for growth include some carbohydrates (d-ribose, d-glucose, l-rhamnose, N-acetyl-d-glucosamine) and multiple organic acids and amino acids. The major cellular fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), representing 70 % of the total fatty acids. Carbon monoxide oxidation, cyanophycin synthetic ability and phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine production are predicted from genome annotation, while bacteriochlorophyll a production was absent. The DNA G+C content of the genome was 56.7 mol%. We propose the name Ruegeriadenitrificans sp. nov. and strain CECT 5091T (=5OM10T=LMG 29896T) as the type strain for the novel species.
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain
| | - Teresa Lucena
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain
| | - María J Pujalte
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Spain
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13
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Zhang G, Haroon MF, Zhang R, Dong X, Wang D, Liu Y, Xun W, Dong X, Stingl U. Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea. Int J Syst Evol Microbiol 2017; 67:4624-4631. [PMID: 29022541 DOI: 10.1099/ijsem.0.002344] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two moderately halophilic marine bacterial strains of the family Rhodobacteraceae, designated ZGT108T and ZGT118T, were isolated from the brine-seawater interface at Erba Deep in the Red Sea (Saudi Arabia). Cells of both strains were aerobic, rod-shaped, non-motile, and Gram-stain-negative. The sequence similarity of the 16S rRNA genes of strains ZGT108T and ZGT118T was 94.9 %. The highest 16S rRNA gene sequence similarity of strain ZGT108T to its closest relative, Ruegeria conchae JCM 17315T, was 98.9 %, while the 16S rRNA gene of ZGT118T was most closely related to that of Ruegeria intermedia LMG 25539T (97.7 % similarity). The sizes of the draft genomes as presented here are 4 258 055 bp (strain ZGT108T) and 4 012 109 bp (strain ZGT118T), and the G+C contents of the draft genomes are 56.68 mol% (ZGT108T) and 62.94 mol% (ZGT108T). The combined physiological, biochemical, phylogenetic and genotypic data supported placement of both strains in the genus Ruegeria and indicated that the two strains are distinct from each other as well as from all other members in the genus Ruegeria. This was also confirmed by low DNA-DNA hybridization values (<43.6 %) and low ANI values (<91.8 %) between both strains and the most closely related Ruegeria species. Therefore, we propose two novel species in the genus Ruegeria to accommodate these novel isolates: Ruegeriaprofundi sp. nov. (type strain ZGT108T=JCM 19518T=ACCC 19861T) and Ruegeriamarisrubri sp. nov. (type strain ZGT118T=JCM 19519T=ACCC 19862T).
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Affiliation(s)
- Guishan Zhang
- Red Sea Research Center, King Abdulah University of Science and Technology, Thuwal Jeddah 23955-6900, Saudi Arabia.,Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mohamed Fauzi Haroon
- Red Sea Research Center, King Abdulah University of Science and Technology, Thuwal Jeddah 23955-6900, Saudi Arabia
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoyan Dong
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Dandan Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Weibing Xun
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ulrich Stingl
- Red Sea Research Center, King Abdulah University of Science and Technology, Thuwal Jeddah 23955-6900, Saudi Arabia.,University of Florida, UF/IFAS, Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, Davie, FL 33314, USA
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14
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Giebel HA, Klotz F, Voget S, Poehlein A, Grosser K, Teske A, Brinkhoff T. Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill. Stand Genomic Sci 2016; 11:81. [PMID: 27777651 PMCID: PMC5064897 DOI: 10.1186/s40793-016-0201-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 10/04/2016] [Indexed: 10/24/2022] Open
Abstract
The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community. The draft genome comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and energy source and is able to grow on several hydroxylated and substituted aromatic compounds. Based on 16S rRNA gene comparison the closest described and validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is lacking several phenotypic and genomic characteristics specific for the genus Phaeobacter. Phylogenomic analyses based on the whole genome support extensive genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially by using the secretion system type IV. Our physiological observations are consistent with the genomic and phylogenomic analyses and support that strain O3.65 is a novel species of a new genus within the Rhodobacteraceae.
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Affiliation(s)
- Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Franziska Klotz
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Katrin Grosser
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina, Chapel Hill, NC USA
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
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15
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Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZP. Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake. Int J Syst Evol Microbiol 2015; 65:4550-4556. [DOI: 10.1099/ijsem.0.000611] [Citation(s) in RCA: 11] [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-stain-negative bacterium, strain TS-T30T, was isolated from a saline lake (Lake Tuosu) in Qaidam basin, Qinghai province, China, and its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, non-motile, 0.8–1.4 μm wide and 1.9–4.0 μm long. Strain TS-T30T was strictly heterotrophic and aerobic. Catalase- and oxidase-positive. Growth was observed in the presence of 0.5–11.0 % (w/v) NaCl (optimum 3.0 %), and at 10–35 °C (optimum 25 °C) and pH 6.5–10.0 (optimum pH 8.5). Strain TS-T30T contained C18 : 1ω7c as the only predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content was 62 mol% (T
m). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T30T formed a distinct lineage that was independent of other most closely related genera: Lutimaribacter (95.2–95.9 % 16S rRNA gene sequence similarities), Poseidonocella (95.4 %), Ruegeria (92.8–94.9 %), Marivita (93.6–94.9 %), Seohaeicola (94.7 %), Sediminimonas (94.7 %), Shimia (93.9–94.7 %), Oceanicola (92.6–94.5 %) and Roseicyclus (94.5 %). The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and an unknown aminolipid; phosphatidylcholine was not detected. These data demonstrated that strain TS-T30T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Lacimonas salitolerans gen. nov., sp. nov. is proposed. The type strain of the type species is TS-T30T ( = CGMCC 1.12477T = NBRC 110969T).
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Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100089, PR China
| | - Yu-Guang Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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16
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Pontivivens insulae gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015; 65:2896-2902. [DOI: 10.1099/ijs.0.000352] [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-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated GYSW-23T, was isolated from seawater off Geoje island in the South Sea, South Korea. Strain GYSW-23T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain GYSW-23T forms a distinct evolutionary lineage independent of other taxa of the family Rhodobacteraceae. It exhibited 16S rRNA gene sequence similarity values of 94.0, 93.5, 93.4 and 93.4 % to the type strains of Roseovarius aestuarii, Ruegeria marina, Roseovarius pacificus and Oceanicola litoreus, respectively, and 93.6 % to ‘Actibacterium atlanticum’ 22II-S11-z10. Strain GYSW-23T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain GYSW-23T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain GYSW-23T were distinguishable from those of the phylogenetically related taxa. The DNA G+C content of strain GYSW-23T was 60.6 mol%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain GYSW-23T is considered to represent a novel species of a new genus in the family Rhodobacteraceae, for which the name Pontivivens insulae gen. nov., sp. nov. is proposed. The type strain of Pontivivens insulae is GYSW-23T ( = KCTC 42458T = CECT 8812T).
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17
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Ascidiaceihabitans donghaensis gen. nov., sp. nov., isolated from the golden sea squirt Halocynthia aurantium. Int J Syst Evol Microbiol 2014; 64:3970-3975. [DOI: 10.1099/ijs.0.066399-0] [Citation(s) in RCA: 11] [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-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated RSS1-M3T, was isolated from a golden sea squirt (Halocynthia aurantium) collected from the East Sea, South Korea. Strain RSS1-M3T grew optimally at 30 °C, at pH 7.0–8.0 and in presence of 2.0 % (w/v) NaCl. Strain RSS1-M3T exhibited the highest 16S rRNA gene sequence similarity (96.55 %) to the type strain of
Pelagicola litoralis
. Neighbour-joining and maximum-likelihood phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSS1-M3T clustered with the type strains, or proposed type strains, of
Planktotalea frisia
,
Pacificibacter maritimus
,
Roseovarius marinus
and
Halocynthiibacter namhaensis
, showing sequence similarity of 94.88–96.32 %. Strain RSS1-M3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The polar lipid profile of strain RSS1-M3T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminolipid and one unidentified lipid as major components, could be distinguished from those of the phylogenetically related genera. The DNA G+C content of strain RSS1-M3T was 55.8 mol%. On the basis of the phylogenetic, chemotaxonomic and phenotypic properties, strain RSS1-M3T is considered to represent a novel species of a new genus within the class
Alphaproteobacteria
, for which the name Ascidiaceihabitans donghaensis gen. nov., sp. nov. is proposed. The type strain is RSS1-M3T ( = KCTC 42118T = CECT 8599T).
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18
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Kim YO, Park S, Nam BH, Kim DG, Yoon JH. Pseudopelagicola gijangensis gen. nov., sp. nov., isolated from the sea squirt Halocynthia roretzi. Int J Syst Evol Microbiol 2014; 64:3447-3452. [DOI: 10.1099/ijs.0.062067-0] [Citation(s) in RCA: 13] [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-stain-negative, aerobic, non-motile, rod-shaped bacterial strain, designated YSS-7T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea of South Korea. Strain YSS-7T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain YSS-7T clustered with the type strains of
Pelagicola litoralis
,
Planktotalea frisia
,
Pacificibacter maritimus
and
Roseovarius marinus
. Strain YSS-7T exhibited the highest 16S rRNA gene sequence similarity (97.7 %) to the type strain of
Pelagicola litoralis
and sequence similarity of more than 96.0 % to the type strains of some other species. Strain YSS-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids of strain YSS-7T were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and an unidentified lipid. The fatty acid and polar lipid profiles of strain YSS-7T were different from those of the type strains of phylogenetically related species. The DNA G+C content of strain YSS-7T was 55.5 mol%. Other phenotypic properties demonstrated that strain YSS-7T is distinguished from phylogenetically related species. On the basis of the data presented, strain YSS-7T is considered to represent a novel genus and species, for which the name Pseudopelagicola gijangensis gen. nov., sp. nov. is proposed. The type strain of Pseudopelagicola gijangensis is YSS-7T ( = KCTC 42049T = CECT 8540T).
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Affiliation(s)
- Young-Ok Kim
- Biotechnology Research Division, National Fisheries Research and Development Institute (NFRDI), Gijang, Busan 619-705, South Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Fisheries Research and Development Institute (NFRDI), Gijang, Busan 619-705, South Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Fisheries Research and Development Institute (NFRDI), Gijang, Busan 619-705, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
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Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC. Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014. Int J Syst Evol Microbiol 2014; 64:3897-3903. [PMID: 25180090 DOI: 10.1099/ijs.0.066142-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, strictly aerobic, rod- or oval-shaped, motile, non-spore-forming bacterium, designated strain CC-AMHB-3(T), was isolated from coastal surface seawater off Hualien, Taiwan. The novel strain showed high pairwise 16S rRNA gene sequence similarities to Ruegeria mobilis NBRC 101030(T) (96.5%), Ruegeria scottomollicae LMG 24367(T) (96.4%), Phaeobacter aquaemixtae SSK6-1(T) (96.2%), Phaeobacter daeponensis TF-218(T) (96.2%), Cribrihabitans marinus CZ-AM5(T) (96.1%) and other species of the family Rhodobacteraceae (≤ 95.9%). However, strain CC-AMHB-3(T) formed a distinct phyletic lineage associated with C. marinus CZ-AM5(T) during phylogenetic analyses. The polar lipid profile of strain CC-AMHB-3(T) included major amounts of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine; moderate amounts of phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid; and trace amounts of an unidentified lipid and an unidentified phospholipid, which was qualitatively almost in line with that of C. marinus CZ-AM5(T) but remarkably distinct as compared with the type species of the genera Ruegeria (Ruegeria atlantica JCM 21234(T)) and Phaeobacter (Phaeobacter gallaeciensis JCM 21319(T)). In line with the fatty acid profile of C. marinus CZ-AM5(T), the major (>5% of total) fatty acids of strain CC-AMHB-3(T) were C(18:1)ω7c and/or C(18:1)ω6c (summed feature 8), 11-methyl C(18:1)ω7c and C(16:0). The DNA G+C content was 66.7 mol%. Ubiquinone-10 (Q-10) was the sole respiratory quinone. Thus, based on the results of the polyphasic study presented here, strain CC-AMHB-3(T) is considered to represent a novel species of the genus Cribrihabitans, for which the name Cribrihabitans neustonicus sp. nov. is proposed; the type strain is CC-AMHB-3(T) ( = JCM 19537(T) =BCRC 80695(T)). In addition, an emended description of the genus Cribrihabitans is also proposed.
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Affiliation(s)
- Asif Hameed
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Mariyam Shahina
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Chiu-Chung Young
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan, ROC
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Park S, Park JM, Kang CH, Yoon JH. Confluentimicrobium lipolyticum gen. nov., sp. nov., a novel lipolytic alphaproteobacterium isolated from the junction between the ocean and a freshwater spring, and emended description of Actibacterium mucosum Lucena et al. 2012. Antonie van Leeuwenhoek 2014; 106:969-77. [DOI: 10.1007/s10482-014-0266-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/20/2014] [Indexed: 11/29/2022]
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21
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Aquimixticola soesokkakensis gen. nov., sp. nov., a novel lipolytic alphaproteobacterium isolated from the junction between the ocean and a freshwater spring, and reclassification of Roseovarius marinus as Pacificibacter marinus comb. nov. and emended description of the genus Pacificibacter. Antonie van Leeuwenhoek 2014; 106:647-55. [DOI: 10.1007/s10482-014-0235-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/08/2014] [Indexed: 11/26/2022]
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22
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Chen Z, Liu Y, Liu LZ, Zhong ZP, Liu ZP, Liu Y. Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system. Int J Syst Evol Microbiol 2014; 64:1257-1263. [DOI: 10.1099/ijs.0.059576-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, strain CZ-AM5T, was isolated from an aerated biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated by using a polyphasic approach. Cells of strain CZ-AM5T were non-spore-forming rods, 0.5–0.8 µm wide and 1.2–2.0 µm long, and motile by means of one or two polar or lateral flagella. Strain CZ-AM5T was strictly aerobic, heterotrophic, oxidase-negative and catalase-positive. Growth occurred at 15–40 °C (optimum, 30–35 °C), at pH 6.5–10.5 (optimum, pH 7.0–7.5) and in the presence of 0–12.0 % (w/v) NaCl (optimum, 4.0 %). The predominant fatty acid was C18 : 1ω7c (80.3 %). Ubiquinone 10 (Q-10) was the sole respiratory quinone. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. The DNA G+C content was 60.4 mol%. Strain CZ-AM5T showed the highest 16S rRNA gene sequence similarity (96.5 %) to
Phaeobacter caeruleus
LMG 24369T; it exhibited 16S rRNA gene sequence similarity of 95.0–96.5, 95.2–96.3, 96.2, 94.6–95.7 and 94.8–95.8 % to members of the genera
Phaeobacter
,
Ruegeria
,
Citreimonas
,
Leisingera
and
Donghicola
, respectively. However, phylogenetic trees based on 16S rRNA gene sequences showed that strain CZ-AM5T did not join any of the above genera, but formed a distinct lineage in the trees. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain CZ-AM5T is considered to represent a novel genus and species of the family
Rhodobacteraceae
, for which the name Cribrihabitans marinus gen. nov., sp. nov. is proposed. The type strain of Cribrihabitans marinus is CZ-AM5T ( = CGMCC 1.13219T = JCM 19401T).
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Affiliation(s)
- Zhu Chen
- R&D Center of Marine Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Liang-Zi Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Liu
- R&D Center of Marine Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
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23
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Kim YO, Park S, Nam BH, Jung YT, Kim DG, Yoon JH. Ruegeria meonggei sp. nov., an alphaproteobacterium isolated from ascidian Halocynthia roretzi. Antonie van Leeuwenhoek 2014; 105:551-8. [PMID: 24380959 DOI: 10.1007/s10482-013-0107-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/21/2013] [Indexed: 10/25/2022]
Abstract
A Gram-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated MA-E2-3(T), was isolated from an ascidian (Halocynthia roretzi) collected from the South Sea, South Korea. Strain MA-E2-3(T) was found to grow optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MA-E2-3(T) fell within the clade comprising Ruegeria species, clustering consistently with the type strain of Ruegeria halocynthiae, with which it exhibited 98.2 % sequence similarity. Sequence similarities to the type strains of the other recognized Ruegeria species were 94.7-97.7 %. Strain MA-E2-3(T) was found to contain Q-10 as the predominant ubiquinone and C18:1 ω7c as the predominant fatty acid. The major polar lipids of strain MA-E2-3(T) were identified as phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain MA-E2-3(T) was determined to be 58.0 mol%. Mean DNA-DNA relatedness values between strain MA-E2-3(T) and the type strains of four phylogenetically closely related Ruegeria species were in the range of 13-23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MA-E2-3(T) is separated from other Ruegeria species. On the basis of the data presented, strain MA-E2-3(T) (=KCTC 32450(T) = CECT 8411(T)) represents a novel species of the genus Ruegeria, for which the name Ruegeria meonggei sp. nov. is proposed.
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Affiliation(s)
- Young-Ok Kim
- Biotechnology Research Division, National Fisheries Research and Development Institute (NFRDI), Gijang, Busan, 619-705, South Korea
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24
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Dogs M, Voget S, Teshima H, Petersen J, Davenport K, Dalingault H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Standfest S, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Klenk HP, Göker M, Brinkhoff T. Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Stand Genomic Sci 2013; 9:334-50. [PMID: 24976890 PMCID: PMC4062626 DOI: 10.4056/sigs.4448212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.
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Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sonja Standfest
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
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25
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Kämpfer P, Arun AB, Rekha PD, Busse HJ, Young CC, Glaeser SP. Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. Int J Syst Evol Microbiol 2013; 63:2538-2544. [DOI: 10.1099/ijs.0.047910-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus
Ruegeria
with 97.4 % similarity to
Ruegeria lacuscaerulensis
ITI-1157T, and a lower sequence similarity to all other species of the genus
Ruegeria
. Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2T clustered within the genus
Ruegeria
. Robust tree topology for the genus
Ruegeria
including the new strain was only obtained by including all
Rhodobacteraceae
type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2T represents a novel species of the genus
Ruegeria
, for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2T ( = CCUG 59209T = LMG 25539T = CCM 7758T).
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Affiliation(s)
- P. Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - A. B. Arun
- Yenepoya Research Center, Yenepoya University, University Road., Deralakatee, Mangalore, Karnataka state, India
| | - P. D. Rekha
- Yenepoya Research Center, Yenepoya University, University Road., Deralakatee, Mangalore, Karnataka state, India
| | - H.-J. Busse
- Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - C.-C. Young
- Department of Soil and Environmental Sciences, National Chung-Hsing University, Taichung 402, Taiwan
| | - S. P. Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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26
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Lee J, Whon TW, Shin NR, Roh SW, Kim J, Park SK, Kim MS, Shin KS, Lee JS, Lee KC, Kim YO, Bae JW. Ruegeria conchae sp. nov., isolated from the ark clam Scapharca broughtonii. Int J Syst Evol Microbiol 2012; 62:2851-2857. [DOI: 10.1099/ijs.0.037283-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A slightly halophilic, Gram-negative, strictly aerobic, non-motile rod, designated TW15T, was isolated from an ark clam in South Korea. Growth occurred at 10–37 °C, with 1–5 % (w/v) NaCl and at pH 7.0–10.0. Optimal growth occurred at 25–30 °C, with 2 % (w/v) NaCl and at pH 8.0. Strain TW15T exhibited both oxidase and catalase activities. The major fatty acids of strain TW15T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c) and 11-methyl C18 : 1ω7c. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The polar lipids of strain TW15T comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid and five unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain TW15T was most closely related to
Ruegeria lacuscaerulensis
DSM 11314T (98.0 % 16S rRNA gene sequence similarity). DNA–DNA relatedness with closely related strains was <52±3 %. The DNA G+C content was 55.7 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain TW15T represents a novel species of the genus
Ruegeria
, for which the name Ruegeria conchae sp. nov. is proposed. The type strain is TW15T ( = KACC 15115T = JCM 17315T).
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Affiliation(s)
- Jina Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Seong Woon Roh
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Jandi Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Seong-Kyu Park
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
| | - Kee-Sun Shin
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Keun Chul Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Fisheries Research and Development Institute (NFRDI), Gijang, Busan 619-705, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul 130-701, Republic of Korea
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27
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Two new cholic acid derivatives from the marine ascidian-associated bacterium Hasllibacter halocynthiae. Molecules 2012; 17:12357-64. [PMID: 23090017 PMCID: PMC6268207 DOI: 10.3390/molecules171012357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/08/2012] [Accepted: 10/17/2012] [Indexed: 11/26/2022] Open
Abstract
The investigation of secondary metabolites in liquid cultures of a recently discovered marine bacterium, Hasllibacter halocynthiae strain KME 002T, led to the isolation of two new cholic acid derivatives. The structures of these compounds were determined to be 3,3,12-trihydroxy-7-ketocholanic acid (1) and 3,3,12-trihydroxy-7-deoxycholanic acid (2) through HRFABMS and NMR data analyses.
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28
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Christie-Oleza JA, Piña-Villalonga JM, Guerin P, Miotello G, Bosch R, Nogales B, Armengaud J. Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of theRuegeriagenus. Environ Microbiol 2012; 15:133-47. [DOI: 10.1111/j.1462-2920.2012.02812.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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