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Wu N, Wu Y, Liu L, Zhang Q, Lv Y, Yuan Y, He J, Shen Q. Peiella sedimenti gen. nov., sp. nov., a novel taxon within the family Caulobacteraceae isolated from sediment of a river. Int J Syst Evol Microbiol 2024; 74. [PMID: 38634749 DOI: 10.1099/ijsem.0.006344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
A Gram-stain-negative bacterium, designated XZ-24T, was isolated from sediment of a river in Mianyang city, Sichuan province, PR China. Cells (1.0-2.0 µm long and 0.4-0.5 µm in width) were strictly aerobic, non-spore-forming, rod shaped, prosthecate and motile by means of a polar flagellum. Growth occurred at 10-37 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum pH 7.0) and with 0-3.0 % (w/v) NaCl (optimum 1.0 % NaCl). The results of phylogenetic analysis based on genomes and 16S rRNA gene sequences indicated that XZ-24T formed a distinct phyletic branch within the family Caulobacteraceae and was most closely related to members of the genera Brevundimonas, Caulobacter and Phenylobacterium with 95.3-96.5 % 16S rRNA gene sequence similarities. The average amino acid identities (AAI) between XZ-24T and species of the family Caulobacteraceae were 47.0-64.5 %, which were below the genus boundary (70 %). The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω7c 11-methyl and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), the isoprenoid quinone was Q-10, and the major polar lipids were 1,2-di-O-acyl-3-O-α-d-glucopyranuronosyl glycerol; 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d glucopyranuronosyl] glycerol and phosphatidylglycerol. The genome size of XZ-24T was 2.64 Mb with a DNA G+C content of 68.9 %. On the basis of the evidence presented in this study, strain XZ-24T represents a novel species of a novel genus in the family Caulobacteraceae, for which the name Peiella sedimenti gen. nov., sp. nov. (Type strain XZ-24T=CCTCC AB 20 23 094T=KCTC 8038T) is proposed.
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Affiliation(s)
- Ningning Wu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yan Wu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Le Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Qi Zhang
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Yu Lv
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Ye Yuan
- Cuiying Honors College, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Jian He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Qirong Shen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
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Ren T, Zhang C, Jin CZ, Jin FJ, Li T, Oh HM, Lee HG, Jin L. Description of Hymenobacter sediminicola sp. nov., isolated from contaminated sediment. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01846-9. [PMID: 37237242 DOI: 10.1007/s10482-023-01846-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
A polyphasic taxonomic study was conducted on two Gram-negative, non-sporulating, non-motile bacterial strains, S2-20-2T and S2-21-1, isolated from a contaminated freshwater sediment in China. Comparative 16S rRNA gene sequence studies revealed a clear affiliation of two strains with Bacteroidetes, which showed the highest pairwise sequence similarities with Hymenobacter duratus BT646T (99.3%), Hymenobacter psychrotolerans Tibet-IIU11T (99.3%), Hymenobacter kanuolensis T-3T (97.6%), Hymenobacter swuensis DY53T (96.9%), Hymenobacter tenuis POB6T (96.8%), Hymenobacter seoulensis 16F7GT (96.7%), and Hymenobacter rigui KCTC 12533T (96.5%). The phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Hymenobacter. Major fatty acids were identified as iso-C15:0, anteiso-C15:0, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c/t) and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). Major cellular polar lipids were identified as phosphatidylethanolamine, three unidentified aminolipids, an unidentified aminophosopholipid and an unidentified lipid. The respiratory quinone was detected as MK-7 and the genomic DNA G + C content was determined to be 57.9% (genome) for type strain S2-20-2T and 57.7 mol% (HPLC) for strain S2-21-1. The observed ANI and dDDH values between strain S2-20-2T and its closely related strains were 75.7-91.4% and 21.2-43.9%, respectively. Based on physiological, biochemical, genetic and genomic characteristics, we propose that strains S2-20-2T and S2-21-1 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter sediminicola sp. nov. is proposed. The type strain is S2-20-2T (= CGMCC 1.18734T = JCM 35801T).
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Affiliation(s)
- Tingting Ren
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Chengxiao Zhang
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Chun-Zhi Jin
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Feng-Jie Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Taihua Li
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Hee-Mock Oh
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Long Jin
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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Jin CZ, Wu XW, Zhuo Y, Yang Y, Li T, Jin FJ, Lee HG, Jin L. Genomic insights into a free-living, nitrogen-fixing but non nodulating novel species of Bradyrhizobium sediminis from freshwater sediment: Three isolates with the smallest genome within the genus Bradyrhizobium. Syst Appl Microbiol 2022; 45:126353. [PMID: 36030678 DOI: 10.1016/j.syapm.2022.126353] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022]
Abstract
Three bacterial strains isolated from a sediment sample collected at a water depth of 4 m from the Huaihe River in China were characterized. Phylogenetic investigation of the 16S rRNA gene and concatenated housekeeping gene sequences assigned the three novel strains in a highly supported lineage distinct from the published Bradyrhizobium species. The sequence similarities of the concatenated housekeeping genes of the three novel strains support their distinctiveness with the type strains of named species. Average nucleotide identity values of the genome sequences (79.9-82.5%) were below the threshold value of 95-96% for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium erythrophlei, Bradyrhizobium jicamae, Bradyrhizobium lablabi, Bradyrhizobium mercantei, Bradyrhizobium elkanii and Bradyrhizobium japonicum. The complete genomes of strains S2-20-1T, S2-11-2 and S2-11-4 consist of single chromosomes of size 5.55, 5.45 and 5.47 Mb, respectively. These strains lack a symbiosis island, key nodulation and photosystem genes. Based on the data presented here, the three strains represent a novel species for which the name Bradyrhizobium sediminis sp. nov. is proposed for S2-20-1T as the type strain. Those three strains are proposed as novel species in free-living Bradyrhizobium isolates with the smallest genomes so far within the genus Bradyrhizobium. A number of functional differences between the three isolates and other published genomes indicate that the genus Bradyrhizobium is extremely heterogeneous and has roles within the community including non-symbiotic nitrogen fixation.
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Affiliation(s)
- Chun-Zhi Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China; Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Xue-Wen Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Ye Zhuo
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Yizi Yang
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 210-037, China
| | - Taihua Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Feng-Jie Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China
| | - Hyung-Gwan Lee
- Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Long Jin
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China.
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Gao JL, Sun P, Sun YC, Xue J, Wang G, Wang LW, Du Y, Zhang X, Sun JG. Caulobacter endophyticus sp. nov., an endophytic bacterium harboring three lasso peptide biosynthetic gene clusters and producing indoleacetic acid isolated from maize root. Antonie van Leeuwenhoek 2021; 114:1213-1224. [PMID: 34002321 DOI: 10.1007/s10482-021-01593-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/08/2021] [Indexed: 11/30/2022]
Abstract
A novel Gram-stain-negative, aerobic and rod-shaped bacterium with a single polar flagellum or a stalk at the end of the cell, was isolated from maize roots in the Fangshan District of Beijing, People's Republic of China. The new strain designated 774T produced indole acetic acid (IAA). The 16S rRNA gene sequence analysis indicated that strain 774T belongs to the genus Caulobacter and is closely related to Caulobacter flavus RHGG3T, Caulobacter zeae 410Tand Caulobacter radices 695T, all with sequence similarities of 99.9%. The genome size of strain774T was 5.4 Mb, comprising 5042 predicted genes with a DNA G+C content of 68.7%.Three striking lasso peptide biosynthetic gene clusters and two IAA synthesis genes belonging to the TPM pathway were also found in the genome of strain 774T. The average nucleotide identity values and digital DNA-DNA hybridization values of the strain774T with its closely phylogenetic neighbours were less than 91.5% and 45.0%, respectively, indicating a new Caulobacter species. The major fatty acids of strain774T were identified as C16: 0 (27.7%), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) (12.6%) and summed feature 8 (C18: 1ω7c and/or C18: 1ω6c) (42.9%).The major polar lipids consisted of phosphatidyl-glycerol and glycolipids. The predominant ubiquinone was identified as Quinone 10. Based on the polyphasic characterization, strain 774T represents a novel species of the genus Caulobacter, for which the name Caulobacter endophyticus sp. nov. is proposed with 774T (= CGMCC 1.16558T = DSM 106777T) as the type strain.
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Affiliation(s)
- Jun-Lian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Pengbo Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.,Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Yu-Chen Sun
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China.,College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Jing Xue
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Li-Wei Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Yunpeng Du
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Xiuhai Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China.
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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