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Hong M, Luo X, Fan R, An L, Li Q, Zhang X, Xu M, Lan Y, Shi H, Li M. Croceibacterium selenioxidans sp. nov. , isolated from seleniferous soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 36920984 DOI: 10.1099/ijsem.0.005726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
A Gram-negative, aerobic bacterial strain, designated LX-88T, was isolated from seleniferous soil in Enshi, Hubei Province, PR China. Strain LX-88Toxidized elemental selenium to selenite, and produced carotenoids but not bacteriochlorophyll. The isolate grew optimally at 28 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Phylogenetic analysies of the organism's 16S rRNA and bacterial core gene set sequences indicated that LX-88T belongs to the genus Croceibacterium, and has the highest degree of 16S rRNA gene sequence similarity to Croceibacterium soli MN-1T (97.4 %). The LX-88T genome was 3.4 Mbp and had a G+C content of 63.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values showed low relatedness (below 95 and 70 %, respectively) between strain LX-88T and other strains in the genus Croceibacterium. Ubiquinone-10 was the predominant quinone. The polar lipid profile was dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). These physiological and biochemical tests facilitated the differentiation of strain LX-88T from other members of the genus Croceibacterium. The results of this multifaceted taxonomic study indicate that strain LX-88T represents a novel species in the genus Croceibacterium, for which the name Croceibacterium selenioxidans sp. nov. is proposed. The type strain is LX-88T (=MCCC 1K08007T=LMG 32570T).
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Affiliation(s)
- Mengjuan Hong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiong Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Rongrong Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lijin An
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Qiushi Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiaoyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingzhu Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yan Lan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Heli Shi
- Enshi Tobacco Company of Hubei Province, Enshi, Hubei 445000, PR China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Tarquinio F, Attlan O, Vanderklift MA, Berry O, Bissett A. Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds. Front Microbiol 2021; 12:703014. [PMID: 34621247 PMCID: PMC8491609 DOI: 10.3389/fmicb.2021.703014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Affiliation(s)
- Flavia Tarquinio
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Océane Attlan
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Sciences et Technologies, Université de la Réunion, Saint-Denis, France
| | - Mathew A Vanderklift
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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3
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Ren WT, Cheng H, Wang CS, Xu XW, Zhou P, Wu YH. Physiological and genomic features of Henriciella with the description of Henriciella mobilis sp. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34296989 DOI: 10.1099/ijsem.0.004889] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains M65T, M69 and JN25 were isolated from seawater of the West Pacific Ocean. Cells of the three strains were Gram-stain-negative, aerobic and rod-shaped. Cells were motile by means of flagella. On the basis of the results of 16S rRNA gene sequence analysis, strains M65T, M69 and JN25 showed the highest 16S rRNA gene sequence similarity to Henriciella algicola MCS27T (98.8 %), followed by Henriciella marina DSM 19595T (98.4 %), Henriciella barbarensis MCS23T (98.4 %), Henriciella pelagia LA220T (98.3 %), Henriciella aquimarina P38T (98.1 %) and Henriciella litoralis SD10T (97.8 %). The 16S rRNA gene sequence similarities among the isolates were 100 %. Phylogenetic analyses revealed that the isolates fell within a cluster comprising the Henriciella species and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between strain M65T and the type strains of Henriciella species were 73.9-85.8 % and 19.9-22.4 %, respectively. The sole respiratory quinone detected in the three isolates was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major polar lipids were glucuronopyranosyldiglyceride, monoglycosyldiglyceride and one unidentified glycolipid. The DNA G+C content was 61.3-61.4 mol%. Phylogenetic distinctiveness, chemotaxonomic differences, together with phenotypic properties, revealed that the isolates could be differentiated from the Henriciella species with validly published names. Therefore, it is proposed that strains M65T, M69 and JN25 represent a novel species of the genus Henriciella, for which the name Henriciella mobilis sp. nov. (type strain, M65T=CGMCC 1.15927T=KCTC 52576T) is proposed.
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Affiliation(s)
- Wen-Ting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Chun-Sheng Wang
- 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
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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Azpiazu-Muniozguren M, Martinez-Ballesteros I, Gamboa J, Seoane S, Alonso R, Laorden L, Garaizar J, Bikandi J. Altererythrobacter muriae sp. nov., isolated from hypersaline Añana Salt Valley spring water, a continental thalassohaline-type solar saltern. Int J Syst Evol Microbiol 2021; 71. [PMID: 33666546 DOI: 10.1099/ijsem.0.004734] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel salt-tolerant alpha-proteobacterium, designated SALINAS58T, was isolated from Santa Engracia hypersaline spring water in the Añana Salt Valley, Álava, Spain. The isolate was Gram-negative, aerobic, non-motile, catalase-positive, oxidase-negative, rod-shaped and formed orange colonies on marine agar. Optimal growth was observed at pH 6.0-6.5, at 30 °C and in the presence of 1% (w/v) NaCl. The main cellular fatty acids (>20%) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The major respiratory quinone was ubiquinone Q-10 and the major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidilglycerol, four unidentified glycolipids and one unidentified phospholipid. Strain SALINAS58T had the highest 16S rRNA gene sequence similarity to Altererythrobacter marensis MSW-14T (96.6%), Altererythrobacter aquaemixtae JSSK-8T (96.5%) and Pontixanthobacter luteolus SW-109T (96.5%) followed by Altererythrobacter atlanticus 26DY36T (96.4%). Results of the phylogenetic analysis, based on 16S rRNA gene sequences, and phylogenetic approaches based on whole genome nucleotide differences, showed that strain SALINAS58T could be distinguished from recognized species of the genus Altererythrobacter. The genomic DNA G+C content was 61.4 mol%. Digital DNA-DNA hybridization, average nucleotide identity and average aminoacid identity values between the genome of strain SALINAS58T and A. marensis MSW-14T were 18.4, 73.1 and 68.1%, respectively. Based on data from this polyphasic characterization, strain SALINAS58T (=CECT 30029T=LMG 31726T) is considered to be classified as representing a novel species in the genus Altererythrobacter, for which the name Altererythrobacter muriae sp. nov. is proposed.
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Affiliation(s)
- Maia Azpiazu-Muniozguren
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Ilargi Martinez-Ballesteros
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | | | - Sergio Seoane
- Plant Biology and Ecology Department, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Rodrigo Alonso
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Lorena Laorden
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Javier Garaizar
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Joseba Bikandi
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
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5
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Gao Y, Li G, Fang C, Shao Z, Wu YH, Xu XW. Tsuneonella suprasediminis sp. nov., isolated from the Pacific Ocean. Int J Syst Evol Microbiol 2021; 71. [PMID: 33528355 DOI: 10.1099/ijsem.0.004678] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped and aerobic bacterial strain, named Ery12T, was isolated from the overlying water of the Lau Basin in the Southwest Pacific Ocean. Strain Ery12T showed high 16S rRNA gene sequences similarity to Tsuneonella flava MS1-4T (99.9 %), T. mangrovi MCCC 1K03311T (98.1 %), Altererythrobacter ishigakiensis NBRC 107699T (97.3 %) and exhibited ≤97.0 % sequence similarity with other type strains of species with validly published names. Growth was observed in media with 0-10.0 % NaCl (optimum 0-1.0 %, w/v), pH 5.0-9.5 (optimum 6.0-7.0) and 10-42 °C (optimum 30-37 °C). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were sphingoglycolipid, phosphatidyglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified glycolipids, one unidentified aminoglycolipid and one unidentified lipid. The DNA G+C content was 60.8 %. The ANI and in silico DDH values between strain Ery12T and the type strains of its closely related species were 71.0- 91.8 % and 19.5- 44.6 %, respectively. According to the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain Ery12T represents a novel species of the genus Tsuneonella, for which the name Tsuneonella suprasediminis is proposed. The type strain is Ery12T (=CGMCC 1.16500 T=MCCC 1A04421T=KCTC 62388T). We further propose to reclassify Altererythrobacter rhizovicinus and Altererythrobacter spongiae as Pelagerythrobacter rhizovicinus comb. nov. and Altericroceibacterium spongiae comb. nov., respectively.
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Affiliation(s)
- Yan Gao
- China Ocean Mineral Resources Research and Development Association, Beijing, 100000, PR China.,Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Guangyu Li
- Marine Culture Collection of China, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, 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
| | - Zongze Shao
- Marine Culture Collection of China, Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China
| | - Yue-Hong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China.,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.,School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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Sun J, Guo J, Lin TH, Feng X, Zhang R. Pseudopontixanthobacter vadosimaris gen. nov., sp. nov., isolated from shallow sea near Kueishan Island. Int J Syst Evol Microbiol 2020; 70:6444-6449. [PMID: 33174831 DOI: 10.1099/ijsem.0.004552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A Gram-stain-negative and aerobic bacterial strain, designated as JL3514T, was isolated from surface water of the hydrothermal system around Kueishan Island. The isolate formed red colonies and cells were non-flagellated, rod-shaped and contained methanol-soluble pigments. Growth was observed at 10-50 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and in the presence of 0-9 % (w/v) NaCl (optimum, 2 %). Strain JL3514T was positive for catalase and weakly positive for oxidase. Results of 16S rRNA gene sequence analyses showed highest similarities to species in the family Erythrobacteraceae, namely Croceibacterium atlanticum (96.1 %), Pelagerythrobacter marensis (96.0 %), Tsuneonella rigui (96.0 %) and Altericroceibacterium xinjiangense (96.0 %). Phylogenetic analysis based on core gene sequences revealed that the isolate formed a distinct branch with the related species and it had a lower average amino acid identity value than the suggested threshold for genera boundaries. The major fatty acids (>5 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, C17 : 1 ω6c, C14 : 0 2-OH and C12 : 0. The dominant polar lipids comprised diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, two unidentified lipids and one unidentified phospholipid. The main respiratory quinones were ubiquinone-10 (95.7 %) and ubiquinone-9 (4.3 %). The DNA G+C content from the genome was 63.0 mol%. Based on the presented data, we consider strain JL3514T to represent a novel genus of the family Erythrobacteraceae, with the name Pseudopontixanthobacter vadosimaris gen. nov., sp. nov. The type strain is JL3514T (=KCTC 62623T=MCCC 1K03561T).
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Affiliation(s)
- Jia Sun
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Jiaying Guo
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xuejin Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Rui Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, PR China.,State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR 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: 290] [Impact Index Per Article: 72.5] [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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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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Song ZM, Wang KL, Yin Q, Chen CC, Xu Y. Algoriphagus kandeliae sp. nov., isolated from mangrove rhizosphere soil. Int J Syst Evol Microbiol 2020; 70:1672-1677. [PMID: 31935174 DOI: 10.1099/ijsem.0.003954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Strain XY-J91T, a Gram-stain-negative, reddish orange, non-spore-forming and short-rod-shaped marine bacterium, was isolated from rhizosphere soil of the mangrove plant Kandelia candel (L.) Druce in Mai Po Nature Reserve, Hong Kong. The strain showed growth at 15-50 °C (optimum 40 °C), at pH 5.5-9.5 (optimum 7.0-8.0) and with 0-8 % (w/v) NaCl (optimum 1-2 %). The only respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified phospholipid. The G+C content of strain XY-J91T was 40.4 mol%. Strain XY-J91T exhibited highest 16S rRNA gene sequence similarities to the type strains of Algoriphagus marincola SW-2T (96.66 %), Algoriphagus taiwanensis CC-PR-82T (96.21%), Algoriphagus ornithinivorans JC2052T (96.16%), Algoriphagus confluentis HJM-2T (95.73%) and Algoriphagus zhangzhouensis 12C11T (95.52 %). Based on the phylogenetic, phenotypic and chemotaxonomic evidence presented, strain XY-J91T represents a novel species of the genus Algoriphagus, for which the name Algoriphagus kandeliae sp. nov. is proposed. The type strain is XY-J91T (=MCCC 1K03612T=KCTC 72216T).
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Affiliation(s)
- Zhi-Man Song
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Kai-Ling Wang
- School of Pharmacy and Chemistry, Dali University, Dali 671000, PR China.,Institute of Materia Medica, Dali University, Dali 671000, PR China
| | - Qi Yin
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, PR China
| | - Cheng-Chun Chen
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
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10
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Li HP, Yao D, Shao KZ, Han QQ, Gou JY, Zhao Q, Zhang JL. Altererythrobacter rhizovicinus sp. nov., isolated from rhizosphere soil of Haloxylon ammodendron. Int J Syst Evol Microbiol 2020; 70:680-686. [DOI: 10.1099/ijsem.0.003817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hui-Ping Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Dan Yao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Kun-Zhong Shao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Qing-Qing Han
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Jing-Yi Gou
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Qi Zhao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
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11
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Park S, Park JM, Yoon JH. Altererythrobacter aquimixticola sp. nov., isolated from sediment sampled at the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2019; 69:2408-2414. [PMID: 31150323 DOI: 10.1099/ijsem.0.003494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and coccoid-, ovoid- or rod-shaped bacterial strain, designated SSKS-13T, was isolated from sediment sampled at the junction between the ocean and a freshwater spring at Jeju island, Republic of Korea. Strain SSKS-13T grew optimally at 37 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain SSKS-13T fell within the clade comprising the type strains of Altererythrobacter species, clustering with the type strains of Altererythrobacter lauratis, Altererythrobacter palmitatis and Altererythrobacter buctensis having 16S rRNA gene sequence similarities of 97.2-97.6 %. Strain SSKS-13T exhibited 16S rRNA gene sequence similarities of less than 97.0 % to the type strains of the other recognized species. Strain SSKS-13T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain SSKS-13T were phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C content of strain SSKS-13T was 64.6 mol%. The mean DNA-DNA relatedness values of strain SSKS-13T with the type strains of A. lauratis, A. palmitatis and A. buctensis were 11.7-25.3 %. Differential phenotypic properties, together with the phylogenetic and genetic data, proved that strain SSKS-13T is distinct from recognized Altererythrobacter species. On the basis of the data presented here, strain SSKS-13T is considered to represent a novel species of the genus Altererythrobacter, for which the name Altererythrobacter aquimixticola sp. nov. is proposed. The type strain is SSKS-13T (=KACC 19863T=KCTC 62900T=NBRC 113545T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Ji-Min Park
- 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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Meng FX, Li G, Fang C, Wu YH, Cheng H, Chen Y, Wang CS, Shao Z, Xu XW. Altererythrobacter aerophilus sp. nov., isolated from deep-sea water of the north-west Pacific. Int J Syst Evol Microbiol 2019; 69:1689-1695. [PMID: 30942688 DOI: 10.1099/ijsem.0.003377] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped bacterium, designated Ery1T, was isolated from deep-sea seawater collected from the Mariana Trench and subjected to a polyphasic investigation for taxonomy. Strain Ery1T was able to grow in medium containing 0-10 % NaCl (w/v; optimum, 0-1.0 %), pH 5.0-9.5 (optimum, pH 6.0-7.0) and at temperatures between 10-45 °C (optimum, 30-40 °C). The comparison of 16S rRNA gene sequences revealed that strain Ery1T showed highest similarity to Altererythrobacterxinjiangensis S3-63T (97.7 %) and Altererythrobacterrigui WW3T (97.6 %), and exhibited less than 97.5 % sequence similarity to other type strains of the species with validly published names. Phylogenetic analyses indicated that strain Ery1T fell within the cluster comprising the Altererythrobacter species and formed a coherent clade with Altererythrobacterxinjiangensis and Altererythrobactersoli. The OrthoANIu and in silico DNA-DNA hybridization values between strain Ery1T and the reference strains were 73.8-75.9 % and 19.2-20.1 %, respectively. Strain Ery1T contained Q-10 as the major respiratory quinone and Q-11 in a minor amount. The major fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C18 : 1ω7c 11-methyl and C14 : 0 2-OH. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidyglycerol, phatidylethanolamine, phosphatidylcholine and three unidentified glycolipids. Differential phenotypic properties, chemotaxonomic differences, phylogenetic distinctiveness, together with the genomic data demonstrated that strain Ery1T represents a novel species of the genus Altererythrobacter, for which named as Altererythrobacter aerophilus sp. nov. with the type strain Ery1T (=KCTC 62387T=CGMCC 1.16499T=MCCC 1A10037T).
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Affiliation(s)
- Fan-Xu Meng
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,2Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Guangyu Li
- 3Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China
| | - Chen Fang
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,2Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Yue-Hong Wu
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,2Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Hong Cheng
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,2Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Yanwu Chen
- 3Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China
| | - Chun-Sheng Wang
- 1Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China.,2Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Zongze Shao
- 3Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, PR China
| | - Xue-Wei Xu
- 2Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China.,1Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration, Hangzhou 310012, PR China
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13
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Kang H, Kim H, Joh K. Altererythrobacter maritimus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2019; 69:1566-1572. [PMID: 30856089 DOI: 10.1099/ijsem.0.003336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A rod-shaped, Gram-staining-negative and orange-pigmented bacterium, designated strain HME9302T, was isolated from seawater of the Yellow Sea in the Republic of Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HME9302T formed a lineage within the genus Altererythrobacter, and was most closely related to Altererythrobacter aurantiacus O30T with 96.7 % sequence similarity. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and four unidentified lipids. The DNA G+C content was 60.8 mol%. On the basis of the evidence presented in this study, strain HME9302T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter maritimus sp. nov. is proposed with the type strain HME9302T (=KCTC 32463T=KACC 17617T=CECT 8417T).
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Affiliation(s)
- Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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14
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Park S, Park JM, Oh TK, Yoon JH. Altererythrobacter insulae sp. nov., a lipolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1009-1015. [PMID: 30702417 DOI: 10.1099/ijsem.0.003260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A lipolytic, Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated BPTF-M16T, was isolated from tidal flat sediment on the Yellow Sea in the Republic of Korea. Strain BPTF-M16T grew optimally at 30 °C and in the presence of 2.0-3.0 % (w/v) NaCl. A phylogenetic tree of 16S rRNA gene sequences showed that strain BPTF-M16T fell within the clade comprising the type strains of Altererythrobacter species. Strain BPTF-M16T exhibited 16S rRNA gene sequence similarity values of 98.0 and 97.1 % to the type strains of Altererythrobacterishigakiensis and Altererythrobactermarinus, respectively, and of less than 97.0 % to the type strains of the other recognized species. Strain BPTF-M16T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain BPTF-M16T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and one unidentified glycolipid. Mean DNA-DNA relatedness values of strain BPTF-M16T with the type strains of A. ishigakiensis and A. marinus were 22 and 13 %, respectively. The average nucleotide identity value between strain BPTF-M16T and the type strain of A. ishigakiensis was 76.80 %. Differential phenotypic properties, together with the phylogenetic and genetic data, revealed that strain BPTF-M16T is separated from recognized Altererythrobacter species. On the basis of the data presented here, strain BPTF-M16T is considered to represent a novel species of the genus Altererythrobacter, for which the name Altererythrobacter insulae sp. nov. is proposed. The type strain is BPTF-M16T (=KCTC 62421T=KACC 19609T=NBRC 113190T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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15
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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: 3.2] [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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16
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Ma H, Ren H, Huang L, Luo Y. Altererythrobacter flavus sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2018; 68:2265-2270. [DOI: 10.1099/ijsem.0.002822] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Hao Ren
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Lingfeng Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Yuanrong Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
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17
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Kandeliimicrobium roseum gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from mangrove rhizosphere soil. Int J Syst Evol Microbiol 2018; 68:2158-2164. [DOI: 10.1099/ijsem.0.002773] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Zhang L, Wang KL, Yin Q, Liang JY, Xu Y. Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel. Int J Syst Evol Microbiol 2018; 68:2653-2658. [PMID: 29949499 DOI: 10.1099/ijsem.0.002894] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped and motile bacterium, designated strain J95T, was isolated from the rhizosphere soil of a mangrove plant Kandeliacandel (L.) Druce in Mai Po Nature Reserve, Hong Kong. Growth of strain J95T was observed at pH 5.0-8.5 (optimum, 6.0-7.0), between 10-40 °C (30-37 °C) and in the presence of 0-9 % (w/v) NaCl (0.5-3 %). Chemotaxonomic analysis showed ubiquinone-10 as the predominant respiratory quinone and C18 : 1ω7c and C19 : 0 cycloω8c as the major fatty acids. The major polar lipids were lipid, aminolipid, phospholipid, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The genomic contained a circular chromosome of 5.48 Mb with a DNA G+C content of 65.7 mol%. The genome included 5299 genes. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain J95T belongs to the genus Ruegeria with highest sequence similarity (96.8 %) to the type strain Ruegeria marina ZH17T. The combined phenotypic, chemotaxonomic and phylogenetic data suggested that strain J95T represents a novel species of the genus Ruegeria, for which the name Ruegeria kandeliae sp. nov. is proposed. The type strain is J95T (=MCCC 1K03284T=DSM 104293T).
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Affiliation(s)
- Lv Zhang
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Kai-Ling Wang
- 2Institute of Materia Medica, Dali University, Dali 671000, PR China.,3School of Pharmacy and Chemistry, Dali University, Dali 671000, PR China
| | - Qi Yin
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Jin-You Liang
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Ying Xu
- 1Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
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Siddaramappa S, Viswanathan V, Thiyagarajan S, Narjala A. Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales. Microb Genom 2018; 4. [PMID: 29620507 PMCID: PMC5989583 DOI: 10.1099/mgen.0.000172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C40 carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.
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Affiliation(s)
- Shivakumara Siddaramappa
- 1Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Vandana Viswanathan
- 1Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India.,2Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Saravanamuthu Thiyagarajan
- 1Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
| | - Anushree Narjala
- 1Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Bengaluru 560100, Karnataka, India
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Wu YH, Yan J, Fang C, Huo YY, Ma WL, Zhang DM, Wang CS, Xu XW. Gracilimonas amylolytica sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2018; 68:1713-1718. [PMID: 29611802 DOI: 10.1099/ijsem.0.002734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated LA399T, was isolated from deep-sea sediment collected from the Pacific Ocean. Cells of strain LA399T grew in the medium containing 0-10.0 % of NaCl (w/v; optimum 3.0-5.0 %), pH 6.5-8.0 (optimum 7.0) and 20-40 °C (optimum 37 °C). Aesculin, gelatin, starch and Tween 80 were hydrolysed. Strain LA399T was closely related to Gracilimonas halophila WDS2C40T (97.0 % sequence similarity), Gracilimonas mengyeensis YIM J14T (96.4 %), Gracilimonas rosea CL-KR2T (96.4 %) and Gracilimonas tropica DSM 19535T (96.0 %), and exhibited equal or less than 96.0 % sequence similarity to other type strains of species with validly published names. Phylogenetic analyses revealed that strain LA399T clustered with the clade comprising the Gracilimonas species and formed an independent lineage. Strain LA399T contained menaquinone 7 as the sole isoprenoid quinone and iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c/10-methyl C16 : 0) as the predominant cellular fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and three unidentified glycolipids. The DNA G+C content was 45.3 mol%. According to the phylogenetic, chemotaxonomic and phenotypic data, it represents a novel species of the genus Gracilimonas, for which the name Gracilimonas amylolytica is proposed. The type strain is LA399T (=CGMCC 1.16248T=KCTC 52885T).
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Affiliation(s)
- Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Jing Yan
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China.,School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Wei-Lin Ma
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - De-Min Zhang
- School of Marine Sciences, Ningbo University, Ningbo 315211, PR China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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Complete Genome Sequence of Altererythrobacter sp. Strain B11, an Aromatic Monomer-Degrading Bacterium, Isolated from Deep-Sea Sediment under the Seabed off Kashima, Japan. GENOME ANNOUNCEMENTS 2018; 6:6/12/e00200-18. [PMID: 29567747 PMCID: PMC5864952 DOI: 10.1128/genomea.00200-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Altererythrobacter sp. strain B11 is an aromatic monomer-degrading bacterium newly isolated from sediment under the seabed off Kashima, Japan, at a depth of 2,100 m. Here, we report the complete nucleotide sequence of the genome of strain B11.
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Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial. Front Microbiol 2018; 9:366. [PMID: 29545788 PMCID: PMC5838024 DOI: 10.3389/fmicb.2018.00366] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 11/27/2022] Open
Abstract
Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
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Affiliation(s)
- Shumeng Kou
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gilles Vincent
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
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Fang C, Wu YH, Xamxidin M, Wang CS, Xu XW. Maribacter cobaltidurans sp. nov., a heavy-metal-tolerant bacterium isolated from deep-sea sediment. Int J Syst Evol Microbiol 2017; 67:5261-5267. [DOI: 10.1099/ijsem.0.002458] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chen Fang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Maripat Xamxidin
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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Liao H, Li Y, Zhang M, Lin X, Lai Q, Tian Y. Altererythrobacter mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2017; 67:4851-4856. [DOI: 10.1099/ijsem.0.002393] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hu Liao
- Key Laboratory of the Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Yuqian Li
- Key Laboratory of the Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Mengjia Zhang
- Key Laboratory of the Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coast and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
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Yuan N, Zeng Y, Feng H, Yu Z, Huang Y. Altererythrobacter xixiisoli sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2017; 67:3655-3659. [PMID: 28879849 DOI: 10.1099/ijsem.0.002198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, coccoid, yellow, non-motile, aerobic bacterium, designated strain S36T, was isolated from soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain S36T could represent a novel species of genus Altererythrobacter showing highest similarity to Altererythrobacter atlanticus 26DY36T (96.31 % 16S rRNA gene sequence similarity). The temperature, pH and NaCl concentration ranges for growth were 10-37 °C (optimum 32 °C), pH 5.0-10.0 (optimum pH 7.0) and 0.5-3 % (optimum 1 %, w/v), respectively. The predominant respiratory quinone of strain S36T was Q-10. The major fatty acids were C16 : 0, C17 : 1ω6c, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 62.7 mol%. These data all support the affiliation of strain S36T to the genus Altererythrobacter. The polar lipids profile of strain S36T comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and two unidentified glycolipids. The results of physiological and biochemical tests allowed differentiation of strain S36T from other members of the genus Altererythrobacter. Therefore, strain S36T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter xixiisoli sp. nov. is proposed; the type strain is S36T (=CGMCC 1.12804T=NBRC 110413T).
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Affiliation(s)
- Nate Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yanhua Zeng
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Hao Feng
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhiliang Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yili Huang
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
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Altererythrobacter aquiaggeris sp. nov., isolated from water of an estuary bank. Int J Syst Evol Microbiol 2017; 67:3410-3416. [DOI: 10.1099/ijsem.0.002128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Park S, Jung YT, Choi SJ, Yoon JH. Altererythrobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:3446-3451. [DOI: 10.1099/ijsem.0.002136] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] 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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Wu YH, Cheng H, Huo YY, Jin XB, Wang CS, Xu XW. Henriciella pelagia sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:3020-3025. [DOI: 10.1099/ijsem.0.002066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Ying-Yi Huo
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xiong-Bin Jin
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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29
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Wu YH, Cheng H, Xu L, Jin XB, Wang CS, Xu XW. Physiological and genomic features of a novel violacein-producing bacterium isolated from surface seawater. PLoS One 2017. [PMID: 28640915 PMCID: PMC5481030 DOI: 10.1371/journal.pone.0179997] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Strains JW1T and JW3, isolated from surface seawater of the Arabian Sea, were subjected to polyphasic taxonomic analysis. Cells of both strains were Gram-stain-negative, aerobic, and rod-shaped. They formed violet pigment and produced violacein. On the basis of 16S rRNA gene sequence analysis, strains JW1T and JW3 showed high 16S rRNA gene sequence similarity with Pseudoalteromonas byunsanensis JCM12483T (98.2%), P. shioyasakiensis SE3T (97.8%), P. arabiensis JCM 17292T (97.3%), and P. gelatinilytica NH153T (97.1%). The 16S rRNA gene sequence similarity between JW1T and JW3 was 100%. Phylogenetic analyses revealed that both strains fell within the cluster of the genus Pseudoalteromonas and represented an independent lineage. The average nucleotide identity and in silico DNA-DNA hybridization values between JW1T and type strains of the closely related Pseudoalteromonas species were 70.9–83.3% and 20.0–26.4%, respectively. The sole respiratory quinone in both strains is ubiquinone 8 (Q-8). The principal fatty acids are summed feature 3 (C16:1ω7c and/or iso-C15:0 2OH), C18:1ω7c, and C16:0. The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, one unidentified glycolipid, one unidentified aminolipid, and one unidentified phospholipid. The DNA G+C content was 43.3 mol%. Differential phylogenetic distinctiveness, chemotaxonomic differences, and phenotypic properties indicated that strains JW1T and JW3 could be differentiated from the Pseudoalteromonas species with validly published names. Therefore, it is proposed that strains JW1T and JW3 represent a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas amylolytica sp. nov. (type strain, JW1T = CGMCC 1.15681T = KCTC 52406T = MCCC 1K02162T) is proposed.
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Affiliation(s)
- Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China
| | - Xiong-Bin Jin
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, P. R. China
- * E-mail:
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Liang X, Lin H, Wang K, Liao Y, Lai Q, Xu Y, Wang C. Altererythrobacter salegens sp. nov., a slightly halophilic bacterium isolated from surface sediment. Int J Syst Evol Microbiol 2017; 67:909-913. [PMID: 27926820 DOI: 10.1099/ijsem.0.001708] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped and slightly halophilic bacterium, strain XY-R17T, was isolated from the surface sediment of Mai Po Inner Deep Bay Ramsar Site birdwatch in Hong Kong. The 16S rRNA gene sequence of strain XY-R17T exhibited 96.5 % similarity to that of the type strain of Altererythrobacter atlanticus. Optimal growth occurred at pH 7.0-7.5, 3-8 % (w/v) NaCl and at 30 °C. The major respiratory quinone was ubiquinone-10. The principal fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), 11-methyl C18 : 1ω7c and C17 : 1ω6c .The polar lipid profile consisted of the major compounds sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and two unknown lipids. The DNA G+C content was 64.7 mol%. Based on its phenotypic properties, chemotaxonomic characteristics and phylogenetic distinctiveness, strain XY-R17T should be designated as a novel species of the genus Altererythrobacter. Therefore, the name Altererythrobacter salegens sp. nov. (type strain XY-R17T=KCTC 52267T=MCCC 1K01500T) is proposed.
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Affiliation(s)
- Xiaoyan Liang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China.,Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Huina Lin
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Kailing Wang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China.,Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Yunjing Liao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of State Oceanic Administration, Xiamen 361005, PR China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, PR China
| | - Changyun Wang
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, PR China
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Yuan CG, Chen X, Jiang Z, Chen W, Liu L, Xian WD, Asem MD, Zhi XY, Li WJ. Altererythrobacter lauratis sp. nov. and Altererythrobacter palmitatis sp. nov., isolated from a Tibetan hot spring. Antonie van Leeuwenhoek 2017; 110:1077-1086. [PMID: 28470566 DOI: 10.1007/s10482-017-0882-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
Two Gram-negative, moderately thermophilic, yellow-pigmented, rod-shaped and motile bacterial strains, designated YIM 75003T and YIM 75004T, were isolated from sediment samples collected from the Tagejia hot spring in Tibet, western China. The taxonomic affiliation of the two strains was investigated by a polyphasic approach. Pairwise comparison of the 16S rRNA gene sequences showed that strains YIM 75003T and YIM 75004T are closely related to Altererythrobacter buctense M0322T (97.2 and 97.1% respectively), while sharing 99.9% sequence similarity against each other. Optimum growth of the two strains was observed at 37-45 °C, pH 8.0 and in the presence of 1-6% NaCl (w/v). Their predominant respiratory quinone was found to be ubiquinone 10. The major fatty acids in both the strains were identified as summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) and summed feature 4 (C17:1 anteiso B and/or iso I). Their major polar lipid profiles were found to be diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The DNA G+C contents of strains YIM 75003T and YIM 75004T were determined to be 61.3 and 60.1 mol%, respectively. The DNA-DNA hybridization values between strains YIM 75003T and YIM 75004T, and between the two strains and their closely related phylogenetic neighbour A. buctense M0322T (=CGMCC 1.12871T) were less than 70%. Based on the morphological and physiological properties, phylogenetic analyses, chemotaxonomic characteristics and DNA-DNA relatedness values, the two strains can be distinguished from each other and from their phylogenetically closely related strain. Strains YIM 75003T and YIM 75004T are, therefore, considered to represent two novel species of the genus Altererythrobacter, for which the names Altererythrobacter lauratis sp. nov. (type strain YIM 75003T = KCTC 52606T = CCTCC AB2016268T) and Altererythrobacter palmitatis sp. nov. (type strain YIM 75004T = KCTC 52607T = CCTCC AB2016270T) are proposed.
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Affiliation(s)
- Chang-Guo Yuan
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Xing Chen
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Zhao Jiang
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Wei Chen
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao-Yang Zhi
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China.
| | - Wen-Jun Li
- Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People's Republic of China. .,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Zhao Q, Li HR, Han QQ, He AL, Nie CY, Wang SM, Zhang JL. Altererythrobacter soli sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 2017; 67:454-459. [PMID: 27902308 DOI: 10.1099/ijsem.0.001652] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An alkaliphilic strain designed MN-1T was isolated from a desert sand sample collected from Tengger desert, north-western China. To delineate its taxonomic position, this Gram-stain-negative, rod-shaped, strictly aerobic bacterium was subjected to a polyphasic taxonomic study. Growth was observed at temperatures from 4 to 37 °C (optimum 30-32 °C), at salinities from 0 to 2 % (optimum 1 %) and at pH from 6.5 to 12.0 (optimum 7.0-9.0). Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain MN-1T was a member of the genus Altererythrobacterbut could be distinguished from recognized species of this genus. Compared to the reference strains, the novel strain was flagellated and motile by means of polar flagella. The predominant respiratory quinone was ubiquinone-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid, one unidentified phospholipid and four unidentified lipids. The predominant fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. These chemotaxonomic traits were in agreement with the characteristics of the genus Altererythrobacter. Strain MN-1T was most closely related to Altererythrobacter xinjiangensis S3-63T (96.9 % 16S rRNA gene sequence similarity), followed by Altererythrobacter dongtanensis JM27T (96.4 %) and Altererythrobacter marinus H32T (96.1 %). The G+C content of the genomic DNA of strain MN-1T was 67.0 mol%. On the basis of data from this polyphasic taxonomic study, strain MN-1T is proposed as the type strain of a novel species of the genus Altererythrobacter, named as Altererythrobacter soli sp. nov. (=KCTC 52135T=MCCC 1K02066T).
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, PR China
| | - Hui-Ru Li
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, PR China
| | - Qing-Qing Han
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, PR China
| | - Ao-Lei He
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, PR China
| | - Cong-Yuan Nie
- Forestry Workstation of Alxa Right Banner, Inner Mongolia Autonomous Region, Alxa 750300, Inner Mongolia, PR China
| | - Suo-Min Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, PR China
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, PR China
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Shi XL, Wu YH, Jin XB, Wang CS, Xu XW. Alteromonas lipolytica sp. nov., a poly-beta-hydroxybutyrate-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:237-242. [DOI: 10.1099/ijsem.0.001604] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xiao-Lai Shi
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Xiong-Bin Jin
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
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Kim JH, Yoon JH, Kim W. Altererythrobacter sediminis sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:5424-5429. [DOI: 10.1099/ijsem.0.001535] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
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Croceicoccus pelagius sp. nov. and Croceicoccus mobilis sp. nov., isolated from marine environments. Int J Syst Evol Microbiol 2016; 66:4506-4511. [DOI: 10.1099/ijsem.0.001381] [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
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Park S, Jung YT, Park JM, Yoon JH. Altererythrobacter confluentis sp. nov., isolated from water of an estuary environment. Int J Syst Evol Microbiol 2016; 66:4002-4008. [DOI: 10.1099/ijsem.0.001301] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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
- University of Science and Technology (UST), 113 Gwahangno, Yuseong, Daejeon, Republic of Korea
| | - Ji-Min Park
- 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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Xue H, Piao CG, Guo MW, Wang LF, Fang W, Li Y. Description of Altererythrobacter aerius sp. nov., isolated from air, and emended description of the genus Altererythrobacter. Int J Syst Evol Microbiol 2016; 66:4543-4548. [PMID: 27499156 DOI: 10.1099/ijsem.0.001388] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, yellow-pigmented, ovoid to rod-shaped, strictly aerobic bacterial strain, designated 100921-2T, was isolated from air at the foot of Xiangshan Mountain. Phylogenetic and phenotypic analysis of the organism revealed that the isolate belongs to the genus Altererythrobacter. Strain 100921-2T showed high 16S rRNA gene sequence similarity (96.01-94.70 %) to other type strains of the genus Altererythrobacter, with the highest similarity to Altererythrobactermarensis MSW-14T. Growth of strain 100921-2T was observed at 4-50 °C (optimum, 30 °C), at pH 4.5-10.0 (optimum, pH 7.0) and at salinities of 0-10 % (w/v) NaCl (optimum 0-0.5 %). The major fatty acids were C18 : 1ω7c (27.8 %), C17 : 1ω6c (23.1 %), 11-methyl C18 : 1ω7c(11.9 %), summed feature 3 (9.1 %) and C15 : 0 2-OH (7.9 %). The predominant respiratory quinone was ubiquinone-10 (Q-10). Polar lipid analysis indicated the presence of diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unknown phospholipids, five unknown polar lipids and two unknown glycolipids. The DNA G+C content of the type strain was 67.5 mol%. On the basis of the data from the polyphasic characterization, strain 100921-2T represents a novel species, for which the name Altererythrobacter aerius sp. nov. is proposed. The type strain is 100921-2T (=CFCC 14287T=KCTC 42844T).
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Affiliation(s)
- Han Xue
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Chun-Gen Piao
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Min-Wei Guo
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lai-Fa Wang
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Wei Fang
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Yong Li
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing 100091, PR China
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Feng XM, Mo YX, Han L, Nogi Y, Zhu YH, Lv J. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2016. [PMID: 26220187 DOI: 10.1099/ijsem.0.000472] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, non-motile, facultatively aerobic bacterium, designated strain M1T, was isolated from a subterrestrial sediment sample of Qiangtang Basin in Qinghai-Tibetan plateau, China. The strain formed rough yellow colonies on R2A plates. Cells were oval or short rod-shaped, catalase-positive and oxidase-negative. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family Erythrobacteraceae and showed 96.2–96.4 % 16S rRNA gene sequence similarities to its closest relatives. Chemotaxonomic analysis revealed ubiquinone-10 (Q10) as the dominant respiratory quinone of strain M1T and C17 : 1ω6c (44.2 %) and C18 : 1ω7c (13.7 %) as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, three unidentified glycolipids, one unidentified phosphoglycolipid and one unidentified lipid. The DNA G+C content of strain M1T was 73.7 mol%. On the basis of phenotypic, phylogenetic and genotypic data presented in this study, strain M1T represents a novel species of a new genus in the family Erythrobacteraceae, for which the name Qipengyuania sediminis gen. nov., sp. nov. is proposed. The type strain of the type species is M1T ( = CGMCC 1.12928T = JCM 30182T).
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Affiliation(s)
- Xiao-Min Feng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
| | - Yong-Xin Mo
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
| | - Lu Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China.,College of Resources and Environmental Science, East China Normal University, Shanghai 200241, PR China
| | - Yuichi Nogi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - You-Hai Zhu
- Oil and Gas Survey, China Geological Survey, Beijing 10029, PR China
| | - Jie Lv
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 10029, PR China
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Fidalgo C, Henriques I, Rocha J, Tacão M, Alves A. Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:10200-14. [PMID: 26875822 DOI: 10.1007/s11356-016-6208-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/29/2016] [Indexed: 05/27/2023]
Abstract
Halimione portulacoides is abundant in salt marshes, accumulates mercury (Hg), and was proposed as useful for phytoremediation and pollution biomonitoring. Endophytic bacteria promote plant growth and provide compounds with industrial applications. Nevertheless, information about endophytic bacteria from H. portulacoides is scarce. Endophytic isolates (n = 665) were obtained from aboveground and belowground plant tissues, from two Hg-contaminated sites (sites E and B) and a noncontaminated site (site C), in the estuary Ria de Aveiro. Representative isolates (n = 467) were identified by 16S rRNA gene sequencing and subjected to functional assays. Isolates affiliated with Proteobacteria (64 %), Actinobacteria (23 %), Firmicutes (10 %), and Bacteroidetes (3 %). Altererythrobacter (7.4 %), Marinilactibacillus (6.4 %), Microbacterium (10.2 %), Salinicola (8.8 %), and Vibrio (7.8 %) were the most abundant genera. Notably, Salinicola (n = 58) were only isolated from site C; Hoeflea (17), Labrenzia (22), and Microbacterium (67) only from belowground tissues. This is the first report of Marinilactibacillus in the endosphere. Principal coordinate analysis showed that community composition changes with the contamination gradient and tissue. Our results suggest that the endosphere of H. portulacoides represents a diverse bacterial hotspot including putative novel species. Many isolates, particularly those affiliated to Altererythrobacter, Marinilactibacillus, Microbacterium, and Vibrio, tested positive for enzymatic activities and plant growth promoters, exposing H. portulacoides as a source of bacteria and compounds with biotechnological applications.
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Affiliation(s)
- Cátia Fidalgo
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- iBiMED and CESAM, Departamento de Biologia, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - Isabel Henriques
- iBiMED and CESAM, Departamento de Biologia, Campus de Santiago, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
| | - Jaqueline Rocha
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Marta Tacão
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Artur Alves
- CESAM, Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
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Srinivasan S, Joo ES, Kim EB, Jeon SH, Jung HY, Kim MK. Altererythrobacter terrae sp. nov., isolated from mountain soil. Antonie van Leeuwenhoek 2016; 109:397-404. [PMID: 26803765 DOI: 10.1007/s10482-015-0643-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/23/2015] [Indexed: 11/30/2022]
Abstract
A Gram-negative, non-motile, non-spore-forming, ovoid-shaped bacterium designated as SWU3(T) was isolated from mountain soil collected at Seoul Women's University, South Korea. Based on 16S rRNA sequence analysis, strain SWU3(T) was found to belong to the genus Altererythrobacter. It shares high sequence similarities with A. dongtanensis JM27(T) (96.6 %), A. epoxidivorans JCS350(T) (96.6 %), and A. troitsensis KMM 6042(T) (96.5 %). Growth was observed between 15 and 37 °C (optimum, 30 °C) with pH of 6-9 (optimum, pH 7.0). It could tolerate 0-2 % (w/v) NaCl. Its predominant quinone was found to be ubiquinone (Q-10). Its major cellular fatty acids were determined to be C17:1 ω6c, C18:1 ω7c, and summed featured 3 (C16:1 ω7c/C16:1 ω6c), all of which are similar characteristics to those of species within the genus Altererythrobacter. Its G + C molar content was found to be 58.4 mol%. Phylogenetic evidence, together with phenotypic characteristics showed that strain SWU3(T) represents a new species of the genus Altererythrobacter. The name Altererythrobacter terrae sp. nov. is proposed and the type strain is SWU3(T) (=KEMB 9004-128(T) = JCM 19177(T)).
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Affiliation(s)
- Sathiyaraj Srinivasan
- Division of Environmental & Life Science, Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea
| | - Eun Sun Joo
- Division of Environmental & Life Science, Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea
| | - Eun Bit Kim
- Division of Environmental & Life Science, Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea
| | - Seon Hwa Jeon
- Division of Environmental & Life Science, Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea
| | - Hee-Young Jung
- College of Agricultural and Life Sciences, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Myung Kyum Kim
- Division of Environmental & Life Science, Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, 623 Hwarangno, Nowon-gu, Seoul, 139-774, Republic of Korea.
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Honkalas V, Dabir A, Dhakephalkar PK. Life in the Anoxic Sub-Seafloor Environment: Linking Microbial Metabolism and Mega Reserves of Methane Hydrate. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:235-262. [DOI: 10.1007/10_2015_5004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Wu YH, Cheng H, Zhou P, Huo YY, Wang CS, Xu XW. Complete genome sequence of the heavy metal resistant bacterium Altererythrobacter atlanticus 26DY36T, isolated from deep-sea sediment of the North Atlantic Mid-ocean ridge. Mar Genomics 2015; 24 Pt 3:289-92. [DOI: 10.1016/j.margen.2015.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/09/2015] [Accepted: 10/09/2015] [Indexed: 10/22/2022]
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Jung YT, Park S, Lee JS, Yoon JH. Altererythrobacter aestiaquae sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:3943-3949. [DOI: 10.1099/ijs.0.066639-0] [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-stain-negative, coccoid- or oval-shaped, gliding bacterial strain, designated HDW-31T, belonging to the class
Alphaproteobacteria
, was isolated from seawater of the Yellow Sea, Korea, and was subjected to a taxonomic study using a polyphasic approach. Strain HDW-31T grew optimally at pH 7.0–8.0, at 30 °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 HDW-31T fell within the clade comprising the genus
Altererythrobacter
, clustering with the type strains of
Altererythrobacter luteolus
and
Altererythrobacter gangjinensis
, with which strain HDW-31T exhibited 97.0 and 96.0 % sequence similarity values, respectively. Sequence similarities to the type strains of the other recognized species of the genus
Altererythrobacter
were 93.5–96.0 %. The DNA G+C content was 57.9 mol% and mean DNA–DNA relatedness between strain HDW-31T and the type strain of
A. luteolus
was 5.3 %. Strain HDW-31T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0 as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, a sphingoglycolipid, two unidentified glycolipids and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain HDW-31T is distinguishable from recognized species of the genus
Altererythrobacter
. On the basis of the data presented, strain HDW-31T is considered to represent a novel species of the genus
Altererythrobacter
, for which the name Altererythrobacter aestiaquae sp. nov. is proposed. The type strain is HDW-31T ( = KCTC 42006T = CECT 8527T).
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Affiliation(s)
- Yong-Taek Jung
- University of Science and Technology (UST), 113 Gwahangno, Yuseong, Daejeon, Republic of Korea
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Sook Lee
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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Altererythrobacter oceanensis sp. nov., isolated from the Western Pacific. Antonie van Leeuwenhoek 2014; 106:1191-8. [PMID: 25245787 DOI: 10.1007/s10482-014-0288-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 09/16/2014] [Indexed: 10/24/2022]
Abstract
A Gram-stain negative, ovoid-rod shaped, strictly aerobic bacterium, strain Y2(T), was isolated from a deep-sea sediment of the Western Pacific. Phylogenetic and phenotypic properties of the organism indicated that it belongs to the genus Altererythrobacter. Strain Y2(T) shares highest 16S rRNA gene sequence similarity of 96.6 % with Erythrobacter jejuensis CNU001(T), followed by the type strains of recognized members of the genus Altererythrobacter (94.8-96.5 %). Strain Y2(T) forms a clade with E. jejuensis CNU001(T) in the cluster of species of the genus Altererythrobacter. Growth of strain Y2(T) was observed at 4-40 °C (optimum, 35-37 °C), at pH 6.0-10.0 (optimum, pH 7.0-8.0) and in the presence of 0-5 % (w/v) NaCl (optimum, 2-3 %). The major cellular fatty acids were found to be C17:1 ω6c (41.5 %), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c; 17.2 %), C17:1 ω8c (11.0 %) and C15:0 2OH (8.1 %). The major respiratory quinone was determine to be ubiquinone 10 (Q-10). The polar lipid analysis indicated the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, three unidentified phospholipids, two unidentified glycolipids, two unidentified aminolipids and three unknown lipids. The DNA G + C content of the type strain is 60.0 mol %. On the basis of the data from the polyphasic characterization, strain Y2(T) represents a novel species, for which the name Altererythrobacter oceanensis sp. nov. is proposed. The type strain is Y2(T) (=CGMCC 1.12752(T) =LMG 28109(T)).
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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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