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Zhang DF, He W, Shao Z, Ahmed I, Zhang Y, Li WJ, Zhao Z. Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 37970897 DOI: 10.1099/ijsem.0.006156] [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: 11/19/2023] Open
Abstract
The families Paracoccaceae and
Roseobacteraceae
comprise metabolically, phenotypically and genotypically diverse members, and their descriptions rely heavily on 16S rRNA gene analysis. Hundreds of genera have been reported within the two families and misclassifications have been a reoccurring problem, even when the taxonomies have been established based on genome-scale phylogenetic reconstructions. In this study, we conducted a comprehensive phylotaxonomic assessment of the families Paracoccaceae and
Roseobacteraceae
based on four ubiquitous gene sets, bac120 (120 genes in Bacteria), rhodo268 (268 genes in ‘
Rhodobacteraceae
’, defined in this study), rp1 (16 ribosomal protein genes in Prokaryote) and rp2 (23 ribosomal protein genes in Prokaryote), using two tree-inferring applications and two approaches (supermatrix and consensus). The results suggested that the four supermatrix trees based on bac120 and rhodo268 shared a high proportion of common nodes (>88.4 %) and the topology was reproducible among all the trees within most of the genera. The evolutionary distance (ED) analysis showed significant overlapping between the intergeneric and intrageneric comparisons, implying that the proposal of some genera seemed to be unnecessary. In addition, the bac120 gene set and the FastTree program were found to be the most cost-effective way to conduct phylogenomic analysis of the families Paracoccaceae and
Roseobacteraceae
. An ED threshold of 0.21–0.23 based on either bac120 or rhodo268 was proposed as one standard for later genus delimitation in these families. A comprehensive phylogenetic framework is presented in this study and the proposed genus definition will help to establish a more reasonable taxonomy in the families Paracoccaceae and
Roseobacteraceae
.
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Affiliation(s)
- Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
| | - Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
| | - Zongze Shao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Iftikhar Ahmed
- National Agricultural Research Centre (NARC), Land Resources Research Institute (LRRI), National Culture Collection of Pakistan (NCCP), Islamabad, Pakistan
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China
| | - Wen-Jun Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
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Cao WR, Shang DD, Liu BT, Hu YH, Sun XK, Sun YY, Jiang MY, Du ZJ. Ruegeria haliotis sp. nov., Isolated from the Gut of the Abalone Haliotis rubra. Curr Microbiol 2021; 78:2151-2159. [PMID: 33792761 DOI: 10.1007/s00284-021-02450-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/10/2021] [Indexed: 11/27/2022]
Abstract
A Gram-stain-negative, aerobic, non-motile, white-pigmented, short rod-shaped, and alginate-degrading bacterium, designated B1Z28T, was isolated from the gut of the abalone Haliotis rubra obtained at Weihai, China. Strain B1Z28T was found to grow at 4-35 °C, pH 6.5-9.0, and in the presence of 0.5-8.0% (w/v) NaCl. Cells were positive for oxidase and catalase activity. The 16S rRNA-based phylogenetic analysis revealed that the nearest phylogenetic neighbors of strain B1Z28T were Tritonibacter scottomollicae MCCC 1A06440T (98.1%), Ruegeria faecimaris KCTC 23044T (98.0%), and Ruegeria meonggei KCTC 32450T (97.8%). Based on phylogenomic analysis, the average nucleotide identity (ANI) values between strain B1Z28T and the neighbor strains were 71.6, 77.2, and 78.1%, respectively; the digital DNA-DNA hybridization (dDDH) values based on the draft genomes between strain B1Z28T and its closest neighbors were 20.5, 20.8, and 21.6%, respectively. Ubiquinone-10 (Q-10) was detected as the predominant respiratory quinone. The dominant cellular fatty acids were Summed feature 8 (contained C18:1 ω7c and/or C18:1 ω6c). The polar lipids included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phospholipid (PL), aminolipid (AL), and three unidentified lipids. Based on the phylogenetic and phenotypic characteristics, strain B1Z28T is considered to represent a novel species of the genus Ruegeria, for which the name Ruegeria haliotis sp. nov. is proposed. The type strain is B1Z28T (= KCTC 72686T = MCCC 1H00393T).
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Affiliation(s)
- Wen-Rui Cao
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Bang-Tao Liu
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Yi-Hao Hu
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xun-Ke Sun
- Marine College, Shandong University, Weihai, 264209, People's Republic of China
| | - Yuan-Yuan Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
| | - Ming-Yu Jiang
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, People's Republic of China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
- Marine College, Shandong University, Weihai, 264209, People's Republic of China.
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Dai D, Li Y, He W, Qin F, Zheng J, Sun M, Zhang D. Oceanomicrobium pacificus gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from seawater of tropical western Pacific. Antonie van Leeuwenhoek 2021; 114:303-311. [PMID: 33548023 DOI: 10.1007/s10482-021-01523-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
The Gram-stain-negative, aerobic, ovoid or rod-shaped bacterial strain, designated KN286T, was isolated from seawater of tropical western Pacific. Growth occurred between 15 and 40 °C (optimally at 30-35 °C), pH 6-9 (optimally at 7.0) and in the presence of 0.5-5.0% (w/v) NaCl (optimally between 2.0 and 3.0%). Strain KN286T contained Q-10 as the major respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, three phospholipids, three glycolipids, and three unidentified polar lipids. The predominant cellular fatty acid was summed feature 8 (composed of C18:1ω7c and/or C18:1ω6c). Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain KN286T was a member of the family Rhodobacteraceae and formed a distinct lineage. Strain KN286T has a genome size of 3.25 Mbp and a G + C content of 65.0 mol%. It encoded with some genes for carbohydrate-active enzymes, such as GH20 (Glycoside Hydrolase Family 20) and PL1 (Polysaccharide Lyase Family 1) and did not encode with a set of genes for reduction of nitrate to nitrite (nitrate reductase gamma subunit, respiratory nitrate reductase alpha N-terminal and respiratory nitrate reductase beta C-terminal). Based on phylogenetic analyses with single-copy orthologous clusters, low isDDH value (19.6%), low ANI (72.4%) and low AAI (65.7%) results, differential chemotaxonomic and physiological properties, strain KN286T represents a novel species of a novel genus of the family Rhodobacteraceae, for which the name Oceanomicrobium pacificus gen. nov., sp. nov. is proposed. The type strain of Oceanomicrobium pacificus is KN286T (=CGMCC 1.17118T = KCTC 72430T).
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Affiliation(s)
- Dadong Dai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Yangjie Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenxuan He
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Qin
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
| | - Dechao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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