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Lee BM, Choi JY, Lee SY, Rho A, Yun S, Lee WS, Cho BC, Hwang CY. Description of Qipengyuania profunda sp. nov., isolated from deep seawater of the Amundsen Sea (Antarctica), and reclassification of Qipengyuania aerophila Liu et al. 2022 as a later heterotypic synonym of Qipengyuania pacifica Tareen et al. 2022. Int J Syst Evol Microbiol 2025; 75. [PMID: 40095852 DOI: 10.1099/ijsem.0.006713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2025] Open
Abstract
Gram-stain-negative, aerobic, rod-shaped bacterial strains, designated HL-TH1T and HL-TH5, were isolated from deep seawater (1127 m depth) of the Amundsen Sea, Antarctica. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strains HL-TH1T and HL-TH5 were members of the genus Qipengyuania with close relatives Qipengyuania aerophila GH25T (99.3%), Qipengyuania pacifica NZ-96T (99.3%), Qipengyuania profundimaris G39T (99.1%) and Qipengyuania citrea RE35F/1T (98.8%). The complete genome sequences of strains HL-TH1T and HL-TH5 comprised a chromosome of 3.2 Mbp and a plasmid of 0.1 Mbp, with DNA G+C content of 64.1%. The whole genome-based comparisons using the average nt identity and digital DNA-DNA hybridization values revealed that both strains belonged to the same genomic species but were clearly discriminated (79.4-85.8% and 21.9-29.3%, respectively) from their close relatives in the genus Qipengyuania. Both strains showed optimal growth at 30 °C, pH 6.5-7.0 and 1.5-2.5% sea salts. The major fatty acids of both strains were C18:1 ω6c and/or C18:1 ω7c (37.8-38.4%), C17:1 ω6c (18.1-19.7%) and C16:1 ω6c and/or C16:1 ω7c (12.3-16.7%). The major isoprenoid quinone was ubiquinone-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified lipids. Hence, we propose that strains HL-TH1T and HL-TH5 are assigned to a novel species belonging to the genus Qipengyuania, for which the name Qipengyuania profunda sp. nov. is proposed. The type strain is HL-TH1T (=KCCM 90517T=JCM 36585T). In addition, Q. aerophila GH25T and Q. pacifica NZ-96T were found to be the same species based on a polyphasic approach. Therefore, we propose the reclassification of Q. aerophila as a later heterotypic synonym of Q. pacifica.
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Affiliation(s)
- Bo Min Lee
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Jy Young Choi
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Su Yeon Lee
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Ami Rho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Sukyoung Yun
- Division of Glacier and Earth Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Won Sang Lee
- Division of Glacier and Earth Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Chung Yeon Hwang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
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Wang Y, You H, Bu YX, Zhou P, Xu L, Fu GY, Xu XW. Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov., two novel Erythrobacteraceae members isolated from deep-sea environments. Int J Syst Evol Microbiol 2024; 74. [PMID: 38546450 DOI: 10.1099/ijsem.0.006313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Two Gram-stain-negative, rod-shaped and non-motile strains, designated as DY56-A-20T and G39T, were isolated from deep-sea sediment of the Pacific Ocean and deep-sea seawater of the Indian Ocean, respectively. Strain DY56-A-20T was found to grow at 15-37 °C (optimum, 28 °C), at pH 6.0-10.0 (optimum, pH 6.5-7.0) and in 0.5-6.0 % (w/v) NaCl (optimum, 1.0-2.0 %), while strain G39T was found to grow at 10-42 °C (optimum, 35-40 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.0) and in 0-12.0 % (w/v) NaCl (optimum, 1.0-2.0 %). The 16S rRNA gene sequence identity analysis indicated that strain DY56-A-20T had the highest sequence identity with Qipengyuania marisflavi KEM-5T (97.6 %), while strain G39T displayed the highest sequence identity with Qipengyuania citrea H150T (98.8 %). The phylogenomic reconstruction indicated that both strains formed independent clades within the genus Qipengyuania. The digital DNA-DNA hybridization and average nucleotide identity values between strains DY56-A-20T/G39T and Qipengyuania/Erythrobacter type strains were 17.8-23.8 % and 70.7-81.1 %, respectively, which are below species delineation thresholds. The genome DNA G+C contents were 65.0 and 63.5 mol% for strains DY56-A-20T and G39T, respectively. The predominant cellular fatty acids (>10 %) of strain DY56-A-20T were C17 : 1 ω6c, summed feature 8 and summed feature 3, and the major cellular fatty acids of strain G39T were C17 : 1 ω6c and summed feature 8. The major polar lipids in both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified polar lipid. The only respiratory quinone present in both strains was ubiquinone-10. Based on those genotypic and phenotypic results, the two strains represent two novel species belonging to the genus Qipengyuania, for which the names Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov. are proposed. The type strain of Q. benthica is DY56-A-20T (=MCCC M27941T=KCTC 92309T), and the type strain of Q. profundimaris is G39T (=MCCC M30353T=KCTC 8208T).
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Affiliation(s)
- Yuan Wang
- Ocean College, Zhejiang University, Zhoushan 316021, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Hao You
- Ocean College, Zhejiang University, Zhoushan 316021, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Yu-Xin Bu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Peng Zhou
- Ocean College, Zhejiang University, Zhoushan 316021, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd, Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Ge-Yi Fu
- 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
- 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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Tang MLY, Lau SCK. Effects of chlorination on the survival of sewage bacteria in seawater microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13216. [PMID: 37990630 PMCID: PMC10866060 DOI: 10.1111/1758-2229.13216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
Chlorination is a commonly used disinfection method in sewage treatment process. However, resistant bacteria may survive chlorination and enter the receiving aquatic environment upon effluent discharge. There has been limited research on the effects of chlorination on bacterial survival in seawater. To address this knowledge gap, microcosm experiments were conducted to simulate the discharge of chlorinated effluents into coastal seawater. The results revealed that bacterial communities in seawater-based effluents survived better in seawater than those in freshwater-based effluents. High chlorine dosages could significantly reduce the viable bacterial populations and their chance of regrowth in seawater. Additionally, faecal indicator bacteria (FIB) that entered the viable but non-culturable (VBNC) state under chlorination tended to persist in the VBNC state without resuscitation during seawater incubation. Because of the prevalence of VBNC indicator bacteria, qPCR quantification of FIB was more effective than conventional culture-based methods in tracing viable pathogenic chlorine-resistant bacteria, although the correlation strength varied depending on the type of effluent. This study sheds light on how chlorine dosages and the intrinsic properties of effluents affect bacterial survival in seawater and highlights the potential and limitations of using FIB in monitoring the health risks associated with the discharge of chlorinated effluents.
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Affiliation(s)
- Mandy Lok Yi Tang
- Department of Ocean ScienceHong Kong University of Science and TechnologyHong KongChina
| | - Stanley Chun Kwan Lau
- Department of Ocean ScienceHong Kong University of Science and TechnologyHong KongChina
- Center for Ocean Research in Hong Kong and MacauHong Kong University of Science and TechnologyHong KongChina
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Comparative Genomics Reveals Genetic Diversity and Metabolic Potentials of the Genus Qipengyuania and Suggests Fifteen Novel Species. Microbiol Spectr 2022; 10:e0126421. [PMID: 35446150 PMCID: PMC9241875 DOI: 10.1128/spectrum.01264-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Members of the genus Qipengyuania are heterotrophic bacteria frequently isolated from marine environments with great application potential in areas such as carotenoid production. However, the genomic diversity, metabolic function, and adaption of this genus remain largely unclear. Here, 16 isolates related to the genus Qipengyuania were recovered from coastal samples and their genomes were sequenced. The phylogenetic inference of these isolates and reference type strains of this genus indicated that the 16S rRNA gene was insufficient to distinguish them at the species level; instead, the phylogenomic reconstruction could provide the reliable phylogenetic relationships and confirm 15 new well-supported branches, representing 15 putative novel genospecies corroborated by the digital DNA-DNA hybridization and average nucleotide identity analyses. Comparative genomics revealed that the genus Qipengyuania had an open pangenome and possessed multiple conserved genes and pathways related to metabolic functions and environmental adaptation, despite the presence of divergent genomic features and specific metabolic potential. Genetic analysis and pigment detection showed that the members of this genus were identified as carotenoid producers, while some proved to be potentially aerobic anoxygenic photoheterotrophs. Collectively, the first insight into the genetic diversity and metabolic potentials of the genus Qipengyuania will contribute to better understanding of the speciation and adaptive evolution in natural environments. IMPORTANCE The deciphering of the phylogenetic diversity and metabolic features of the abundant bacterial taxa is critical for exploring their ecological importance and application potential. Qipengyuania is a genus of frequently isolated heterotrophic microorganisms with great industrial application potential. Numerous strains related to the genus Qipengyuania have been isolated from diverse environments, but their genomic diversity and metabolic functions remain unclear. Our study revealed a high degree of genetic diversity, metabolic versatility, and environmental adaptation of the genus Qipengyuania using comparative genomics. Fifteen novel species of this genus have been established using a polyphasic taxonomic approach, expanding the number of described species to almost double. This study provided an overall view of the genus Qipengyuania at the genomic level and will enable us to better uncover its ecological roles and evolutionary history.
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Wagh VS, Ram H, Dastager SG. Priestia veravalensis sp. nov., isolated from coastal sample. Arch Microbiol 2021; 203:4839-4845. [PMID: 34226954 DOI: 10.1007/s00203-021-02418-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 11/28/2022]
Abstract
The taxonomic position of two isolates, SGD-V-76T and SGD-M-37, isolated from sediment sample of Veraval coast, India, was examined using the polyphasic taxonomic approach. The morphological and chemotaxonomic characteristics of these two organisms are typical of the genus Priestia. The phylogenetic analyses performed using almost complete 16S rRNA gene sequences demonstrated that the isolate belongs to the Bacillaceae family, and forms a clade within the cluster containing Priestia flexus MTCC 2909T, Priestia aryabhattai B8W22T and Priestia megaterium KCTC 3007T and both strains showed highest similarity of > 98% with 3-29 nucleotide differences. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7 and the G + C content of strains was 37.5-37.7 mol%. However, the DNA-DNA hybridization and the phenotypic characteristics revealed that, the strain SGD-V-76T and strain SGD-M-37 are similar species but different from any known Priestia species with ANI values of 79.2, 79.3 and 79.2 and the dDDH values of 17.7, 17.8 and 18.0% respectively. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, and genomic data strain SGD-V-76T was clearly distinguished from closely related members of the Priestia genus. Based on the above data analysis strain SGD-V-76T (= DSM28242T = KCTC33802T = CIP111056T = NCIM5510T) represents a novel species of the genus Priestia, and we propose the name Priestia veravalensis sp. nov.
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Affiliation(s)
- Vasudev S Wagh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,National Collection of Industrial Microorganisms (NCIM), CSIR National Chemical Laboratory, Pune, 411008, India
| | - Hari Ram
- National Collection of Industrial Microorganisms (NCIM), CSIR National Chemical Laboratory, Pune, 411008, India
| | - Syed G Dastager
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. .,National Collection of Industrial Microorganisms (NCIM), CSIR National Chemical Laboratory, Pune, 411008, India.
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6
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Liu Y, Pei T, Deng MR, Zhu H. Qipengyuania soli sp. nov., Isolated from Mangrove Soil. Curr Microbiol 2021; 78:2806-2814. [PMID: 34047831 DOI: 10.1007/s00284-021-02538-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/05/2021] [Indexed: 11/26/2022]
Abstract
A novel Gram-stain-negative, non-motile, and rod-shaped bacterial strain, designated as 6D36T, was isolated from mangrove soil and characterized by using a polyphasic taxonomic approach. Strain 6D36T was found to grow at 10-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, 7.0) and in 0-8% (w/v) NaCl (optimum, 3%). The predominant cellular fatty acids of strain 6D36T were summed feature 8 (C19:1 ω7c and/or C18:1 ω6c) and C17:1 ω6c; the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and sphingoglycolipid; the sole respiratory quinone was Q-10. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6D36T fell into the genus Qipengyuania and was closely related to "Erythrobacter mangrovi" MCCC 1K03690T (98.5%), Qipengyuania citrea CGMCC 1.8703T (97.6%), and Qipengyuania pelagi JCM 17468T (97.4%). The phylogenomic analysis indicated that strain 6D36T formed an independent branch distinct from reference-type strains of species within this genus. The digital DNA-DNA hybridization and average nucleotide identity values between strain 6D36T and the three type strains above were, respectively, 20.2-21.3% and 79.5-81.5%, of which were far below their respective threshold for species definition, implying that the strain represents a novel genospecies. The genomic DNA G + C content was 63.3%. Based on phenotypic and genotypic characteristics, strain 6D36T is concluded to represent a novel species of the genus Qipengyuania, for which the name Qipengyuania soli sp. nov., is proposed. The type strain of the species is 6D36T (= GDMCC 1.1977T = KCTC 82333T).
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Affiliation(s)
- Yang Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Tao Pei
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Ming-Rong Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470-4495. [PMID: 32726199 PMCID: PMC7660246 DOI: 10.1099/ijsem.0.004293] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Oceanography, Hohai University, Nanjing 210000, PR China
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Xue-Wei Xu
- 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 200030, PR China
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Park S, Chen S, Yoon JH. Erythrobacter insulae sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2020; 70:1470-1477. [DOI: 10.1099/ijsem.0.003824] [Citation(s) in RCA: 7] [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-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a tidal flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus
Erythrobacter
. JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of
Erythrobacter longus
,
Erythrobacter aquimaris
,
Erythrobacter nanhaisediminis
,
Erythrobacter vulgaris
,
Erythrobacter seohaensis
,
Erythrobacter litoralis
and
Erythrobacter citreus
and 93.7–96.6 % to the type strains of the other species of the genus
Erythrobacter
. The ANI and dDDH values between JBTF-M21T and the type strains of
E. longus
,
E. nanhaisediminis
,
E. seohaensis
and
E. litoralis
were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of
E. aquimaris
,
E. vulgaris
and
E. citreus
were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus
Erythrobacter
with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus
Erythrobacter
, for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Siyu Chen
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Lee SD, Kim YJ, Kim IS. Erythrobacter suaedae sp. nov., isolated from a rhizosphere mudflat of a halophyte (Suaeda japonica). Int J Syst Evol Microbiol 2019; 69:3287-3292. [DOI: 10.1099/ijsem.0.003625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Soon Dong Lee
- Present address: R&D Center, BioPS Co., Ltd., Daedeuk Valley Campus, Hannam University, Daejon 34054, Republic of Korea
- Faculty of Science Education, Jeju National University, Jeju 63243, Republic of Korea
| | - Young-Ju Kim
- Ilseong Landscaping Co., Ltd., Jeju 63242, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daej on 34054, Republic of Korea
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Park S, Won SM, Yoon JH. Erythrobacter marisflavi sp. nov., isolated from isolated from estuary water. Int J Syst Evol Microbiol 2019; 69:2696-2702. [DOI: 10.1099/ijsem.0.003510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sung Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Quéré G, Intertaglia L, Payri C, Galand PE. Disease Specific Bacterial Communities in a Coralline Algae of the Northwestern Mediterranean Sea: A Combined Culture Dependent and -Independent Approach. Front Microbiol 2019; 10:1850. [PMID: 31555220 PMCID: PMC6722220 DOI: 10.3389/fmicb.2019.01850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/26/2019] [Indexed: 12/02/2022] Open
Abstract
Crustose coralline red algae (CCA) are important components of marine ecosystems thriving from tropical waters and up to the poles. They fulfill important ecological services including framework building and induction of larval settlement. Like other marine organisms, CCAs have not been spared by the increase in marine disease outbreaks. The white-band syndrome has been recently observed in corallines from the Mediterranean Sea indicating that the disease threat has extended from tropical to temperate waters. Here, we examined the microbiome and the pathobiome of healthy and diseased Neogoniolithon brassica-florida coralline algae in the Mediterranean Sea by combining culture-dependent and -independent approaches. The coralline white-band syndrome was associated with a distinct pathobiome compared to healthy tissues and showed similarities with the white-band syndrome described in the Caribbean Sea. A sequence related to the genus Hoeflea, order Rhizobiales, characterized the white-band disease pathobiome described by amplicon sequencing. No representative of this genus was isolated by culture. We, however, successfully isolated an abundant member of the healthy CCA microbiome, an Alphaproteobateria of the family Rhodobacteraceae. In conclusion, we did not identify a potential causative agent of the disease, but through the complementarity of culture dependent and independent approaches we characterized the healthy microbiome of the coralline and the possible opportunistic bacteria colonizing diseased tissues.
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Affiliation(s)
- Gaëlle Quéré
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France.,UMR 9220 ENTROPIE, 'Ecologie Marine Tropicale des Océans Pacifique et Indien', IRD, CNRS, Université de La Réunion, Noumea, New Caledonia
| | - Laurent Intertaglia
- Plateforme Bio2Mar, CNRS, Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls-sur-Mer, France
| | - Claude Payri
- UMR 9220 ENTROPIE, 'Ecologie Marine Tropicale des Océans Pacifique et Indien', IRD, CNRS, Université de La Réunion, Noumea, New Caledonia
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls-sur-Mer, France
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12
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Setiyono E, Heriyanto, Pringgenies D, Shioi Y, Kanesaki Y, Awai K, Brotosudarmo THP. Sulfur-Containing Carotenoids from A Marine Coral Symbiont Erythrobacter flavus Strain KJ5. Mar Drugs 2019; 17:E349. [PMID: 31212714 PMCID: PMC6627997 DOI: 10.3390/md17060349] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/21/2019] [Accepted: 05/29/2019] [Indexed: 12/15/2022] Open
Abstract
Erythrobacter flavus strain KJ5 (formerly called Erythrobacter sp. strain KJ5) is a yellowish marine bacterium that was isolated from a hard coral Acropora nasuta in the Karimunjawa Islands, Indonesia. The complete genome sequence of the bacterium has been reported recently. In this study, we examined the carotenoid composition of this bacterium using high-performance liquid chromatography coupled with ESI-MS/MS. We found that the bacterium produced sulfur-containing carotenoids, i.e., caloxanthin sulfate and nostoxanthin sulfate, as the most abundant carotenoids. A new carotenoid zeaxanthin sulfate was detected based on its ESI-MS/MS spectrum. The unique presence of sulfated carotenoids found among the currently known species of the Erythrobacter genus were discussed.
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Affiliation(s)
- Edi Setiyono
- Ma Chung Research Center for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 465151, Indonesia; (E.S.); (H.); (Y.S.)
| | - Heriyanto
- Ma Chung Research Center for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 465151, Indonesia; (E.S.); (H.); (Y.S.)
| | - Delianis Pringgenies
- Department of Coastal Resource Management, Universitas Diponegoro, Jl. Prof. Soedarto Tembalang, Semarang 50275, Indonesia;
| | - Yuzo Shioi
- Ma Chung Research Center for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 465151, Indonesia; (E.S.); (H.); (Y.S.)
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan;
| | - Koichiro Awai
- Department of Biological Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan;
| | - Tatas Hardo Panintingjati Brotosudarmo
- Ma Chung Research Center for Photosynthetic Pigments (MRCPP) and Department of Chemistry, Universitas Ma Chung, Villa Puncak Tidar N01, Malang 465151, Indonesia; (E.S.); (H.); (Y.S.)
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13
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Fang C, Wu YH, Sun C, Wang H, Cheng H, Meng FX, Wang CS, Xu XW. Erythrobacter zhengii sp. nov., a bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2019; 69:241-248. [DOI: 10.1099/ijsem.0.003136] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chen Fang
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Yue-Hong Wu
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Cong Sun
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
- 2College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Hong Wang
- 3Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, 18 Chao Wang Road, Hangzhou 310014, PR China
| | - Hong Cheng
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Fan-Xu Meng
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Chun-Sheng Wang
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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14
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Xing T, Liu Y, Wang N, Xu B, Liu K, Shen L, Gu Z, Guo B, Zhou Y, Liu H. Erythrobacter arachoides sp. nov., isolated from ice core. Int J Syst Evol Microbiol 2017; 67:4235-4239. [DOI: 10.1099/ijsem.0.002290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tingting Xing
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yongqin Liu
- University of Chinese Academy of Sciences, Beijing, PR China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, PR China
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Ninglian Wang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, PR China
- College of Urban and Environmental Science, Northwest University, Xi’an, 710069, PR China
| | - Baiqing Xu
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, PR China
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Keshao Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Liang Shen
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Zhengquan Gu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Bixi Guo
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yuguang Zhou
- Institute of Microbiology, China General Microbiological Culture Collection Center, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Hongcan Liu
- Institute of Microbiology, China General Microbiological Culture Collection Center, Chinese Academy of Sciences, Beijing, 100101, PR China
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15
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Park S, Jung YT, Choi SJ, Yoon JH. Erythrobacter aquimixticola sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:2964-2969. [DOI: 10.1099/ijsem.0.002055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Yong-Taek Jung
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Su Jung Choi
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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16
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Isolation and characterization of the first phage infecting ecologically important marine bacteria Erythrobacter. Virol J 2017; 14:104. [PMID: 28592325 PMCID: PMC5463345 DOI: 10.1186/s12985-017-0773-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/01/2017] [Indexed: 11/24/2022] Open
Abstract
Background Erythrobacter comprises a widespread and ecologically significant genus of marine bacteria. However, no phage infecting Erythrobacter spp. has been reported to date. This study describes the isolation and characterization of phage vB_EliS-R6L from Erythrobacter. Methods Standard virus enrichment and double-layer agar methods were used to isolate and characterize the phage. Morphology was observed by transmission electron microscopy, and a one-step growth curve assay was performed. The phage genome was sequenced using the Illumina Miseq platform and annotated using standard bioinformatics tools. Phylogenetic analyses were performed based on the deduced amino acid sequences of terminase, endolysin, portal protein, and major capsid protein, and genome recruitment analysis was conducted using Jiulong River Estuary Virome, Pacific Ocean Virome and Global Ocean Survey databases. Results A novel phage, vB_EliS-R6L, from coastal waters of Xiamen, China, was isolated and found to infect the marine bacterium Erythrobacter litoralis DSM 8509. Morphological observation and genome analysis revealed that phage vB_EliS-R6L is a siphovirus with a 65.7-kb genome that encodes 108 putative gene products. The phage exhibits growth at a wide range of temperature and pH conditions. Genes encoding five methylase-related proteins were found in the genome, and recognition site predictions suggested its resistance to restriction-modification host systems. Genomic comparisons and phylogenetic analyses indicate that phage vB_EliS-R6L is distinct from other known phages. Metagenomic recruitment analysis revealed that vB_EliS-R6L-like phages are widespread in marine environments, with likely distribution in coastal waters. Conclusions Isolation of the first Erythrobacter phage (vB_EliS-R6L) will contribute to our understanding of host-phage interactions, the ecology of marine Erythrobacter and viral metagenome annotation efforts.
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17
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Erythrobacter alti sp. nov., a marine alphaproteobacterium isolated from seawater. Arch Microbiol 2017; 199:1133-1139. [DOI: 10.1007/s00203-017-1384-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
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18
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Zhuang L, Liu Y, Wang L, Wang W, Shao Z. Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 2016. [PMID: 26220886 DOI: 10.1099/ijsem.0.000481] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, motile, rod-shaped, orange-pigmented bacterium able to degrade polycyclic aromatic hydrocarbons was isolated from deep-sea sediment of the Atlantic Ocean and subjected to a polyphasic taxonomic study. The strain, designated s21-N3T, could grow at 4–37 °C (optimum 28 °C), at pH 5–10 (optimum pH 7–8) and with 1–7 % (w/v) NaCl (optimum 2–3 %). Strain s21-N3T was positive for nitrate reduction, denitrification, aesculin hydrolysis, oxidase and catalase, but negative for indole production and urease. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain s21-N3T formed a distinct branch within the genus Erythrobacter, sharing high similarities with three closely related strains, Erythrobacter marinus HWDM-33T (98.67 %), ‘Erythrobacter luteus’ KA37 (97.80 %) and Erythrobacter gangjinensis K7-2T (97.59 %). The similarities between strain s21-N3T and other type strains of recognized species within the genus Erythrobacter ranged from 95.00 to 96.47 %. The digital DNA–DNA hybridization values and average nucleotide identity (ANI) values between strain s21-N3T and the three closely related strains Erythrobacter marinus HWDM-33T, ‘Erythrobacter luteus’ KA37 and Erythrobacter gangjinensis K7-2T were 18.60, 18.00 and 18.50 % and 74.24, 72.49 and 72.54 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and summed feature 3 (C16 : 1ω7c/ω6c). The respiratory lipoquinone was identified as Q-10. The major polar lipids comprised sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The G+C content of the chromosomal DNA was determined to be 58.18 mol%. The combined genotypic and phenotypic distinctiveness demonstrated that strain s21-N3T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter atlanticus sp. nov. is proposed, with the type strain s21-N3T ( = MCCC 1A00519T = KCTC 42697T).
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Affiliation(s)
- Lingping Zhuang
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Lin Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Wanpeng Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA; Key Laboratory of Marine Genetic Resources of Fujian Province; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China
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19
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Lei X, Zhang H, Chen Y, Li Y, Chen Z, Lai Q, Zhang J, Zheng W, Xu H, Zheng T. Erythrobacter luteus sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2015; 65:2472-2478. [PMID: 25911535 DOI: 10.1099/ijs.0.000283] [Citation(s) in RCA: 22] [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 Gram-staining-negative, orange-pigmented, aerobic bacterial strain, designated KA37T, was isolated from a mangrove sediment sample collected from Yunxiao mangrove National Nature Reserve, Fujian Province, China. Growth was observed at 4-37 °C, 0-3% (w/v) NaCl and pH 5-10. Mg2+ ions were required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Erythrobacter, which belongs to the family Erythrobacteraceae. Strain KA37T was most closely related to Erythrobacter gangjinensis KCTC 22330T (96.9% sequence similarity), followed by Erythrobacter marinus KCTC 23554T (96.8%); similarity to other members of the genus was below 96.6%. The major fatty acids were C17 : 1ω6c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Strain KA37T did not produce bacteriochlorophyll a. The predominant respiratory quinone was ubiquinone 10 (Q-10). The polar lipids of strain KA37T were sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, five unknown lipids and one unidentified phospholipid. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence, the novel strain most appropriately belongs to the genus Erythrobacter, but can be distinguished readily from species of the genus Erythrobacter with validly published names. The name Erythrobacter luteus sp. nov. is proposed, with strain KA37T ( = MCCC 1F01227T = KCTC 42179T) as the type strain.
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Affiliation(s)
- Xueqian Lei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Huajun Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Yao Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Yi Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Zhangran Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Qiliang Lai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, PR China
| | - Jingyan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Wei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Hong Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Tianling Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, PR China
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20
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Erythrobacter lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2014; 64:4184-4190. [DOI: 10.1099/ijs.0.067728-0] [Citation(s) in RCA: 19] [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-negative, non-motile, coccoid- or oval-shaped bacterial strain, designated S-5T, belonging to the class
Alphaproteobacteria
, was isolated from a tidal flat sediment of the Yellow Sea, Korea and was subjected to a polyphasic taxonomic study. Strain S-5T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining analysis based on 16S rRNA gene sequences showed that strain S-5T fell within the clade comprising the species of the genus
Erythrobacter
, clustering with the type strains of
Erythrobacter pelagi
,
Erythrobacter citreus
and
Erythrobacter seohaensis
with which it exhibited the highest 16S rRNA gene sequence similarity (96.0–96.7 %). The DNA G+C content was 66.0 mol%. Strain S-5T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 1ω6c as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid and two unidentified lipids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain S-5T is distinguishable from other species of the genus
Erythrobacter
. On the basis of the data presented, strain S-5T is considered to represent a novel species of the genus
Erythrobacter
, for which the name Erythrobacter
lutimaris sp. nov. is proposed. The type strain is S-5T ( = KCTC 42109T = CECT 8624T).
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21
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Citrimicrobium luteum gen. nov., sp. nov., aerobic anoxygenic phototrophic bacterium isolated from the gut of a sea cucumber Stichopus japonicus. J Microbiol 2014; 52:819-24. [PMID: 25163838 DOI: 10.1007/s12275-014-4136-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 07/17/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
A Gram-stain negative, yellow-pigmented, motile, pleomorphic bacterium, designated strain CBA4602(T), was isolated from the gut of the sea cucumber Stichopus japonicus, which was collected from Jeju Island in the Republic of Korea. In a phylogenetic analysis based on the 16S rRNA gene, strain CBA4602(T) belonged to the order Sphingomonadales in the class Alphaproteobacteria. The 16S rRNA gene sequence similarity between strain CBA4602(T) and 'Citromicrobium bathyomarinum' JF-1, the most closely related strain having nonvalidly published name, was 98.4%, followed by 95.2-96.7% identities with sequence of the other closest strains in the genus Erythrobacter. Strain CBA4602(T) had bacteriochlorophyll a and carotenoids. Strain CBA4602(T) grew in 0-10% (w/v) NaCl, at 10-42°C and pH 6.0-8.0, with optimal growth in 1-2% NaCl, at 30-37°C and pH 7.0. Strain CBA4602(T) was positive for catalase and oxidase activities and was able to hydrolyse gelatine and Tween 20 and 40, but not starch, Tween 80 or L-tyrosine. The G+C content of genomic DNA from strain CBA4602(T) was 68.0 mol% and Q-10 was the major detected isoprenoid quinone. The polar lipids were three unidentified phospholipids, three unidentified glycolipids, and two unidentified lipids. The dominant fatty acids were anteiso-C15:0, C16:0, anteiso-C17:0 and C18:0. As considering the current taxonomic status of the genus 'Citromicrobium' and polyphasic taxonomic analyses, strain CBA4602(T) represents a novel genus and species. The name Citrimicrobium luteum is proposed for the type strain CBA4602(T) (=KACC 17668(T) =JCM 19530(T)).
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22
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Yoon BJ, Lee DH, Oh DC. Erythrobacter jejuensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:1421-1426. [DOI: 10.1099/ijs.0.038349-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, yellow-pigmented, non-motile, strictly aerobic, rod-shaped bacterium, designated strain CNU001T, was isolated from seawater collected on the coast of Jeju Island, South Korea, and subjected to a polyphasic taxonomic study. The temperature, pH and NaCl ranges for growth were 10–30 °C, pH 6.0–10.0 and 2.0–5.0 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNU001T belonged to the genus
Erythrobacter
in the family
Erythrobacteraceae
, with
Erythrobacter longus
DSM 6997T (96.6 % sequence similarity),
Erythrobacter gaetbuli
SW-161T (96.3 %),
Erythrobacter vulgaris
022 2-10T (96.2 %),
Erythrobacter nanhaisediminis
T30T (96.1 %) and other members of the genus
Erythrobacter
(<96.0 %) identified as the novel strain’s closest relatives. The major cellular fatty acids were C18 : 1ω7c and C17 : 1ω6c. The polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid and six other unidentified lipids. The major respiratory quinone was ubiquinone-10 (UQ-10) and the genomic DNA G+C content of the novel strain was 58.9 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU001T represents a novel species within the genus
Erythrobacter
, for which the name Erythrobacter jejuensis sp. nov. is proposed. The type strain is CNU001T ( = KCTC 23090T = JCM 16677T).
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Affiliation(s)
- Byoung-Jun Yoon
- The Research Institute for Basic Sciences, Jeju National University, Jeju 690-756, Republic of Korea
- Department of Biology, College of Natural Science, Jeju National University, Jeju 690-756, Republic of Korea
| | - Dong-Heon Lee
- The Research Institute for Basic Sciences, Jeju National University, Jeju 690-756, Republic of Korea
| | - Duck-Chul Oh
- The Research Institute for Basic Sciences, Jeju National University, Jeju 690-756, Republic of Korea
- Department of Biology, College of Natural Science, Jeju National University, Jeju 690-756, Republic of Korea
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Erythrobacter westpacificensis sp. nov., a marine bacterium isolated from the Western Pacific. Curr Microbiol 2012; 66:385-90. [PMID: 23241657 DOI: 10.1007/s00284-012-0287-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
Abstract
A novel Gram-negative, orange-pigmented bacterial strain JLT2008(T) was isolated from the surface seawater of the Western Pacific and subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JLT2008(T) belonged to the genus Erythrobacter, sharing the highest similarity (96.6 %) with Erythrobacter gangjinensis K7-2(T) and the lowest similarity (94.9 %) with Erythrobacter litoralis DSM 8509(T). Strain JLT2008(T) did not contain bacteriochlorophyll a, and the predominant respiratory lipoquinone was ubiquinone-10. The major fatty acids were C(18:1) ω7c, C(16:0), C(16:1) ω7c/C(16:1) ω6c. The prominent polar lipids were sphingoglycolipid, phosphatidylethanolamine, and phosphatidylglycerol. The genomic G + C content was 60.1 mol %. Based on the polyphasic taxonomic data, a novel species within the genus Erythrobacter, and with the name Erythrobacter westpacificensis sp. nov., is proposed. The type strain is JLT2008(T) (=CGMCC 1.10993(T) = JCM 18014(T)).
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Jung YT, Park S, Oh TK, Yoon JH. Erythrobacter marinus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2012; 62:2050-2055. [DOI: 10.1099/ijs.0.034702-0] [Citation(s) in RCA: 27] [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-negative, non-motile, ovoid to rod-shaped bacterium, designated strain HWDM-33T, was isolated from seawater of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HWDM-33T grew optimally at pH 7–8, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HWDM-33T clustered with
Erythrobacter gangjinensis
K7-2T, with which it shared 96.9 % sequence similarity. Strain HWDM-33T exhibited 94.2–95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized species of the genus
Erythrobacter
. Strain HWDM-33T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, C17 : 1ω6c, and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain HWDM-33T was 66.1 mol%. Differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain HWDM-33T was separate from
E. gangjinensis
and other recognized species of the genus
Erythrobacter
. On the basis of the data presented here, strain HWDM-33T represents a novel species of the genus
Erythrobacter
, for which the name Erythrobacter marinus sp. nov. is proposed. The type strain is HWDM-33T ( = KCTC 23554T = CCUG 60528T).
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Affiliation(s)
- Yong-Taek Jung
- University of Science and Technology (UST), 113 Gwahangno, Yuseong, Daejeon 305-350, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon 306-809, Republic of Korea
| | - Sooyeon Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon 306-809, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yuseong, Daejeon 306-809, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Gyeonggi-do 440-746, Republic of Korea
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Wu HX, Lai PY, Lee OO, Zhou XJ, Miao L, Wang H, Qian PY. Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea. Int J Syst Evol Microbiol 2011; 62:1348-1353. [PMID: 21828015 DOI: 10.1099/ijs.0.029561-0] [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 novel Gram-negative, aerobic, catalase- and oxidase-positive, non-sporulating, non-motile, rod-shaped bacterium, designated strain UST081027-248(T), was isolated from seawater of the Red Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UST081027-248(T) fell within the genus Erythrobacter. Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of Erythrobacter species ranged from 95.3 % (with Erythrobacter gangjinensis) to 98.2 % (with Erythrobacter citreus). However, levels of DNA-DNA relatedness between strain UST081027-248(T) and the type strains of closely related species were below 70 %. Optimal growth of the isolate occurred in the presence of 2.0 % NaCl, at pH 8.0-9.0 and at 28-36 °C. The isolate did not produce bacteriochlorophyll a. The predominant cellular fatty acids were C(17:1)ω6c, summed feature 8 (C(18:1)ω6c and/or C(18:1)ω7c) and C(15:0) 2-OH. The genomic DNA G+C content of strain UST081027-248(T) was 60.4 mol%. Phenotypic properties and phylogenetic distinctiveness clearly indicated that strain UST081027-248(T) represents a novel species of the genus Erythrobacter, for which the name Erythrobacter pelagi sp. nov. is proposed. The type strain is UST081027-248(T) ( = JCM 17468(T) = NRRL 59511(T)).
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Affiliation(s)
- Hui-Xian Wu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China.,KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Pok Yui Lai
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - On On Lee
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Xiao-Jian Zhou
- Institute of Marine Science and Technology, Yangzhou University, No. 196, West Huayang Street, Yangzhou City, Jiangsu Province, PR China
| | - Li Miao
- Institute of Marine Science and Technology, Yangzhou University, No. 196, West Huayang Street, Yangzhou City, Jiangsu Province, PR China
| | - Hao Wang
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Pei-Yuan Qian
- KAUST Global Partnership Program, Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches. Syst Appl Microbiol 2010; 33:222-31. [PMID: 20413241 DOI: 10.1016/j.syapm.2010.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 02/20/2010] [Accepted: 02/22/2010] [Indexed: 11/21/2022]
Abstract
Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n=53) and to Halomonas aquamarina (n=14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora.
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Xu M, Xin Y, Yu Y, Zhang J, Zhou Y, Liu H, Tian J, Li Y. Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea. Int J Syst Evol Microbiol 2009; 60:2215-2220. [PMID: 19897611 DOI: 10.1099/ijs.0.014027-0] [Citation(s) in RCA: 39] [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 novel Gram-negative, orange-pigmented, slightly halophilic, rod-shaped bacterium, strain T30(T), was isolated from sediment from the South China Sea. Phylogenetic analysis showed that strain T30(T) was a member of the genus Erythrobacter, sharing highest 16S rRNA gene sequence similarities with Erythrobacter aquimaris JCM 12189(T) (99.5 %) and Erythrobacter vulgaris DSM 17792(T) (99.0 %). Levels of DNA-DNA relatedness between strain T30(T) and closely related strains of Erythrobacter species ranged from 14.5 to 56.9 %.The isolate lacked bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone. The major fatty acids of this strain were C(18 : 1) ω(38.2 %) and C(16 : 1) ω 7c /C(16 : 1) ω 6c (17.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. The DNA G+C content of strain T30(T) was 59.5 mol%. On the basis of phenotypic and phylogenetic data, a novel species, Erythrobacter nanhaisediminis sp. nov., is proposed; the type strain is T30(T) (=CGMCC 1.7715(T)=JCM 16125(T)).
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Affiliation(s)
- Mingshuang Xu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Jianli Zhang
- School of Life Science and Technology, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jiesheng Tian
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Ying Li
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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Lee YS, Lee DH, Kahng HY, Kim EM, Jung JS. Erythrobacter gangjinensis sp. nov., a marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2009; 60:1413-1417. [PMID: 19671726 DOI: 10.1099/ijs.0.015743-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-negative, aerobic, orange-pigmented bacterial strain, designated K7-2(T), was isolated from seawater of Gangjin Bay, Korea, and subjected to a polyphasic taxonomic study. Strain K7-2(T) contained ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and did not produce bacteriochlorophyll a. Major fatty acids were C(18 : 1)omega7c (51.4 %), iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (15.0 %) and C(17 : 1)omega6c (8.8 %). Major polar lipids were phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content was 61.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain K7-2(T) formed a distinct phylogenetic lineage within the cluster comprising Erythrobacter strains. Similarities between the 16S rRNA gene sequences of strain K7-2(T) and the type strains of Erythrobacter species ranged from 95.0 % (Erythrobacter litoralis DSM 8509(T)) to 96.8 % (Erythrobacter citreus RE35F/1(T)). On the basis of polyphasic taxonomic data, strain K7-2(T) (=KCTC 22330(T)=JCM 15420(T)) is classified in a novel species within the genus Erythrobacter, for which the name Erythrobacter gangjinensis sp. nov. is proposed.
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Affiliation(s)
- Young Sun Lee
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Dong-Heon Lee
- Department of Environmental Education, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Hyung-Yeel Kahng
- Department of Environmental Education, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Eun Mi Kim
- Department of Dental Hygiene, Gwangju Health College, Gwangju 506-701, Republic of Korea
| | - Jae Sung Jung
- Department of Biology, Sunchon National University, Suncheon 540-742, Republic of Korea
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Lai Q, Yuan J, Shao Z. Altererythrobacter marinus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2009; 59:2973-6. [PMID: 19628597 DOI: 10.1099/ijs.0.008193-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A taxonomic study was carried out on strain H32(T), which was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. The 16S rRNA gene sequence of strain H32(T) showed highest similarity to that of Altererythrobacter luteolus SW-109(T) (96.7 %); lower similarities were observed with other members of the genus Altererythrobacter (94.7-95.7 %) and with members of the genera Erythrobacter (94.5-96.3 %), Erythromicrobium (94.9 %) and Porphyrobacter (94.3-95.3 %). Phylogenetic analyses of all members of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that strain H32(T) formed a clade within the genus Altererythrobacter. The dominant fatty acids were C(16 : 0) (6.7 %), C(18 : 1)omega7c (44.3 %) and 11-methyl C(18 : 1)omega7c (25.4 %). The major respiratory quinone was ubiquinone 10. The DNA G+C content was 66.5 mol%. Strain H32(T) did not contain bacteriochlorophyll a. These characteristics are in good agreement with those of members of the genus Altererythrobacter. Therefore, according to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain H32(T) belongs to the genus Altererythrobacter, but can be readily distinguished from known Altererythrobacter species. It is therefore proposed that strain H32(T) represents a novel species, Altererythrobacter marinus sp. nov., with H32(T) (=CCTCC AB 208229(T) =LMG 24629(T) =MCCC 1A01070(T)) as the type strain.
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Affiliation(s)
- Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, PR China
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30
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Xu XW, Wu YH, Wang CS, Wang XG, Oren A, Wu M. Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2009; 59:2247-53. [DOI: 10.1099/ijs.0.004267-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Erythrobacter litoralis has been known as a bacteriochlorophyll a-containing, aerobic, anoxygenic, phototrophic bacterium. Here we announce the complete genome sequence of E. litoralis HTCC2594, which is devoid of phototrophic potential. E. litoralis HTCC2594, isolated by dilution-to-extinction culturing from seawater, could not carry out aerobic anoxygenic phototrophy and lacked genes for bacteriochlorophyll a biosynthesis and photosynthetic reaction center proteins.
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32
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33
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Kumar NR, Nair S, Langer S, Busse HJ, Kämpfer P. Altererythrobacter indicus sp. nov., isolated from wild rice (Porteresia coarctata Tateoka). Int J Syst Evol Microbiol 2008; 58:839-44. [PMID: 18398179 DOI: 10.1099/ijs.0.65523-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, non-spore-forming organism, strain MSSRF26T, was isolated from mangrove-associated wild rice in India. On the basis of 16S rRNA gene sequence similarities, strain MSSRF26T was shown to belong to the Alphaproteobacteria, most closely related to Altererythrobacter luteolus and Altererythrobacter epoxidivorans (96.1 and 95.9 % similarity to the respective type strains). Chemotaxonomic data [major ubiquinones Q-10 (91 %) and Q-9 (9 %); major polyamine spermidine, with putrescine, cadaverine and spermine detected only in trace amounts; major polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid; major fatty acid C18 : 1 omega 7c and C(14 : 0) 2-OH as hydroxylated fatty acid] supported the affiliation of MSSRF26T to the genus Altererythrobacter. Fatty acid data and physiological and biochemical tests allowed phenotypic differentiation of the isolate from described Altererythrobacter species. Strain MSSRF26T therefore represents a novel species, for which the name Altererythrobacter indicus sp. nov. is proposed, with the type strain MSSRF26T (=LMG 23789T =DSM 18604T).
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Affiliation(s)
- N Ramesh Kumar
- Microbiology Department, M S Swaminathan Research Foundation, 3rd Cross Street, Taramani Institutional Area, Chennai - 600 113, India
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Mesbah NM, Abou-El-Ela SH, Wiegel J. Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. MICROBIAL ECOLOGY 2007; 54:598-617. [PMID: 17450395 DOI: 10.1007/s00248-006-9193-y] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 11/16/2006] [Accepted: 11/26/2006] [Indexed: 05/08/2023]
Abstract
The phylogenetic diversity of the bacterial and archaeal community in the water and sediments of three large lakes of the Wadi An Natrun was investigated using 16S rRNA clone libraries. The bacterial community was diverse: 769 clones formed 345 operational taxonomic units (OTUs) defined at 99% 16S rRNA sequence identity. The bacterial community in both the water and sediments of the lakes was dominated by clones affiliated with the low G + C Gram-type-positive group, alpha-proteobacteria, and Bacteroidetes, (11-39, 11-30, and 10-37% of OTUs observed, respectively), patterns that have been observed in previously described alkaline, athalassohaline systems. However, a relatively high proportion of Firmicutess-related clones in the water of the lakes and alpha-proteobacteria in the sediments was observed. The bacterial community composition of the water and sediment of the same lake and of different lakes was significantly different (p < 0.05). Operational taxonomic units related to the gamma-proteobacteria were more abundant in the sediment of Lake Fazda, whereas the sediment of Lake UmRisha was dominated by members of the delta-proteobacteria. The proportion of gamma-proteobacterial and Bacteroidetes-affiliated OTUs were predominant in the water of Lake UmRisha and differed significantly from other lake waters (chi-squared analysis, p < or = 0.01). The more oxygenated and dilute nature of Lake Hamra was reflected in its microbial community composition, with the abundance of Bacillales sequences in the water, the absence of Halanaerobiales, Clostridiales, and Archaea in the water, and the presence of representatives of more phyla such as the Actinobacteria, Spirochaetes, and Verrucomicrobia. The archaeal community composition appeared less diverse: 589 clones resulted in 198 OTUs defined at 99% 16S rRNA sequence identity, and all sequences fell into the phylum Euryarchaeota. Phylogenetic analysis showed that many of the sequences were distantly related (83-90% 16S rRNA sequence identity) to cultured and uncultured archaea, with many clones forming clusters that branched deeply within the Euryarchaeota. Forty-two and 53% of the bacterial and archaeal clones had less than 90% 16S rRNA sequence identity to previously described sequences. This indicates that the water and sediments of the Wadi An Natrun harbor a unique and novel prokaryotic diversity that is different from what has been described among other alkaline, athalassohaline lakes.
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Affiliation(s)
- Noha M Mesbah
- Department of Microbiology, University of Georgia, Athens, GA 30602-2605, USA.
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Rathgeber C, Yurkova N, Stackebrandt E, Schumann P, Humphrey E, Beatty JT, Yurkov V. Porphyrobacter meromictius sp. nov., an appendaged bacterium, that produces Bacteriochlorophyll a. Curr Microbiol 2007; 55:356-61. [PMID: 17882507 DOI: 10.1007/s00284-007-0275-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 05/04/2007] [Indexed: 11/28/2022]
Abstract
Four Gram-negative strains (ML4(T), ML19, ML31, ML32) of nonmotile, appendaged, budding bacteria were isolated from the meromictic Mahoney Lake in British Columbia, Canada. The strains were red to brown-red in color and produced bacteriochlorophyll a incorporated into photosynthetic pigment-protein complexes. Phylogenetic analysis has placed these strains within the class Alphaproteobacteria, with the closest relatives being members of the genera Erythrobacter, Porphyrobacter, and Erythromicrobium. Morphological features warrant their inclusion within the genus Porphyrobacter and these strains can be readily distinguished from other species of this genus on the basis of a mesophilic temperature range, a broad pH range, and tolerance to extremely high NaCl and Na(2)SO(4) concentrations, in keeping with the environment from which they were isolated, a Na(2)SO(4)-dominated meromictic lake. These isolates utilize a variety of organic substrates for aerobic chemoheterotrophic growth and do not grow under anaerobic conditions, in either the presence or the absence of light. All strains require vitamin B(12), and strains ML4(T) and ML19 require biotin. The DNA G + C contents ranged from 62.2 to 64.9 mol%. Phenotypic and phyletic data support the classification of strains ML4(T), ML19, ML31, and ML32 as a novel Porphyrobacter species for which the name Porphyrobacter meromictius sp. nov. is proposed.
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Affiliation(s)
- Christopher Rathgeber
- Department of Microbiology, The University of Manitoba, 422 Buller Building, R3T 2N2, Winnipeg, MB, Canada
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Azanza MPV, Azanza RV, Vargas VMD, Hedreyda CT. Bacterial endosymbionts of Pyrodinium bahamense var. compressum. MICROBIAL ECOLOGY 2006; 52:756-64. [PMID: 16944340 DOI: 10.1007/s00248-006-9128-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 06/18/2006] [Indexed: 05/11/2023]
Abstract
The study presents evidence in support of the bacterial theory associated with the toxicity of Pyrodinium bahamense var. compressum. Bacterial endosymbionts from Philippine P. bahamense var. compressum strain Pbc MZRVA 042595 were isolated and identified via 16S rDNA sequence analysis. Taxonomic diversity of the identified culturable intracellular microbiota associated with Philippine P. bahamense var. compressum was established to be limited to the Phyla Proteobacteria, Actinobacteria, and Firmicutes. Major endosymbionts identified included Moraxella spp., Erythrobacter spp., and Bacillus spp., whereas Pseudomonas putida, Micrococcus spp., and Dietzia maris were identified as minor isolates. All identified strains except D. maris, P. putida, and Micrococcus spp. were shown to contain either saxitoxin or neo saxitoxin or both at levels < or =73 ng/10(7) bacterial cells based on high-performance liquid chromatography analysis. Paralytic shellfish poisoning-like physiologic reactions in test animals used in the mouse assay were recorded for the endosymbionts except for P. putida. The study is the first to elucidate the possible contribution of bacterial endosymbionts in the toxicity of P. bahamense var. compressum isolated in the Philippines.
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Affiliation(s)
- Ma Patricia V Azanza
- Department of Food Science and Nutrition, College of Home Economics, University of the Philippines, Diliman, Quezon City 1101, Philippines.
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37
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Yoon JH, Kang KH, Yeo SH, Oh TK. Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:1167-1170. [PMID: 15879250 DOI: 10.1099/ijs.0.63522-0] [Citation(s) in RCA: 50] [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-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109(T), was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C(18 : 1)omega7c as the major fatty acid. The DNA G + C content was 60.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109(T) is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109(T) exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94.0-96.3 %, making it possible to categorize strain SW-109(T) as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109(T) (= KCTC 12311(T) = JCM 12599(T)) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.
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MESH Headings
- Bacterial Typing Techniques
- Bacteriochlorophyll A/analysis
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Fatty Acids/analysis
- Fatty Acids/isolation & purification
- Genes, rRNA
- Gentian Violet
- Geologic Sediments/microbiology
- Growth Inhibitors/pharmacology
- Korea
- Molecular Sequence Data
- Phenazines
- Phylogeny
- Pigments, Biological
- Quinones/analysis
- Quinones/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sodium Chloride/pharmacology
- Soil Microbiology
- Sphingomonadaceae/classification
- Sphingomonadaceae/cytology
- Sphingomonadaceae/isolation & purification
- Sphingomonadaceae/physiology
- Water Microbiology
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Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Kook Hee Kang
- Department of Food and Life Science, Sungkyunkwan University, Chunchun-dong 300, Jangan-gu, Suwon, Korea
| | - Soo-Hwan Yeo
- Center for Traditional Microorganism Resources, Keimyung University, Shindang-dong, Dalseo-gu, Daegu, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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38
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Ivanova EP, Bowman JP, Lysenko AM, Zhukova NV, Gorshkova NM, Kuznetsova TA, Kalinovskaya NI, Shevchenko LS, Mikhailov VV. Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates. Syst Appl Microbiol 2005; 28:123-30. [PMID: 15830804 DOI: 10.1016/j.syapm.2004.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Four yellow-pigmented, gram-negative, chemoorganotrophic aerobic bacteria were isolated from starfish Stellaster equestris (strains 022-2-10T, 022-2-9, and 022-2-12) and soft coral (unidentified species) (strain 022-4-7) collected in the South China Sea. 16S rRNA gene sequence-based analyses of the new organisms revealed that Erythrobacter spp. were the closest relatives and shared the highest similarity of 98.7% to E. citreus, 98.5% to E. flavus, 97.9% to E. litoralis and 97.6% to E. longus. The novel organisms were tolerant to 3-6% NaCl, grew between 10 degrees C and 40 degrees C, and were not able to degrade gelatin, casein, and agar, while degraded Tween 80. Two strains (022-2-9 and 022-2-12) could weakly degrade starch. All strains produced a large pool of carotenoids and did not have Bacteriochlorophyll a. Phosphatidylethanolamine (30-36%), phosphatidylglycerol (39-46%), and phosphatidylcholine (21-27%) were the predominant phospholipids. Sphingoglycolipid was not detected. The major fatty acids were 16:0 (6-11%), 16:1omega7 (12-15%), and 18:1omega7 (46-49%). The two-hydroxy fatty acids, 13:0-2OH, 14:0-2OH, 15:0-2OH, 16:0-2OH were also present. The G + C content of the DNAs ranged from 61 to 62 mol%. The level of DNA similarity among four strains was conspecific and ranged from 94% to 98%. Even though new strains and other species of the genus had rather high level of 16S rRNA gene sequence similarities, DNA-DNA hybridization experiments showed only 33-39% of binding with the DNA of the type strains. On the basis of these results and the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the new organisms be classified as a novel species; the name Erythrobacter vulgaris sp. nov. is proposed. The type strain is 022-2-10T (= KMM 3465T = CIP 107841T).
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Affiliation(s)
- Elena P Ivanova
- Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia.
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39
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Yoon JH, Oh TK, Park YH. Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:71-75. [PMID: 15653855 DOI: 10.1099/ijs.0.63233-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, non-spore-forming, slightly halophilic strains, SW-135T and SW-161T, which were isolated from a tidal flat of the Yellow Sea in Korea, were subjected to a polyphasic taxonomic study. The two isolates lacked bacteriochlorophyll a and contained ubiquinone-10 (Q-10) as the predominant respiratory lipoquinone and C18 : 1
ω7c and C17 : 1
ω6c as the major fatty acids. The DNA G+C contents of strains SW-135T and SW-161T were 62·2 and 64·5 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains fall within the radiation of the cluster comprising Erythrobacter species. Strains SW-135T and SW-161T exhibited a 16S rRNA gene sequence similarity value of 96·9 % and a mean DNA–DNA relatedness level of 12·3 %. Sequence similarities between strains SW-135T and SW-161T and the type strains of recognized Erythrobacter species ranged from 96·7 to 98·5 %. Levels of DNA–DNA relatedness were low enough to indicate that strains SW-135T and SW-161T represent members of two species separate from all recognized Erythrobacter species. On the basis of polyphasic taxonomic data, strains SW-135T (=KCTC 12228T=DSM 16221T) and SW-161T (=KCTC 12227T=DSM 16225T) were classified as two novel Erythrobacter species, for which the names Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov. are proposed, respectively.
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Affiliation(s)
- Jung-Hoon Yoon
- 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
| | - Yong-Ha Park
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
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