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Kumar P, Verma A, Yadav P, Das J, Kumar L, Krishnamurthi S. Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:172995. [PMID: 38719044 DOI: 10.1016/j.scitotenv.2024.172995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/20/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
The taxonomic position and genomic characteristics of a nitrogen fixing and polymer degrading marine bacterium, strain SAOS 164 isolated from a mangrove sediment sample was investigated. Sequence analysis based on 16S rRNA gene identified it as a member of family Halieaceae with closest similarity to Haliea salexigens DSM 19537T (96.3 %), H. alexandrii LZ-16-2T (96.2 %) and Parahaliea maris HSLHS9T (96.0 %) but was distantly related to the genera Haliea, Parahaliea and Halioglobus in phylogenetic trees. In order to ascertain the exact taxonomic position, phylogeny based on RpoBC proteins, whole genome, core and orthologous genes, and comparative analysis of metabolic potential retrieved the strain in an independent lineage clustering along with the genera Halioglobus, Pseudohalioglobus and Seongchinamella. Further, various genome based delimitation parameters represented by mol % GC content, percentage of conserved proteins (POCP), and amino acid identity (AAI) along with chemotaxonomic markers (i.e. fatty acids and polar lipids) supported the inferences of genome based phylogeny and indicated that the strain SAOS 164 belongs to a novel genus. The genome was mapped to 4.8 Mb in size with 65.1 % DNA mol% G + C content. In-silico genomic investigation and phenotyping revealed diverse metabolite genes/pathways related to polymer hydrolysis, nitrogen fixation, light induced growth, carbohydrate, sulfur, phosphorus and amino acid metabolism, virulence factors, defense mechanism, and stress-responsive elements facilitating survival in the mangrove habitat. Based on polyphasic taxonomic approach including genome analyses, a novel genus Mangrovimicrobium sediminis gen. nov. sp. nov. (=SAOS 164T = MTCC 12907T = KCTC 52755T = JCM 32136T) is proposed. Additionally, the reclassification of Halioglobus pacificus (=DSM 27932T = KCTC 23430T = S1-72T) to Pseudhalioglobus pacificus comb. nov. is also proposed.
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Affiliation(s)
- Pravin Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India; Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden; Umeå Marine Sciences Centre, Hörnefors, Sweden
| | - Pooja Yadav
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Joyasree Das
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Lalit Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India.
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Zhu W, Zhou J, Lu S, Yang J, Lai XH, Jin D, Pu J, Huang Y, Liu L, Li Z, Xu J. Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov. J Microbiol 2021; 60:137-146. [PMID: 34826100 PMCID: PMC8622105 DOI: 10.1007/s12275-022-1428-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/02/2022]
Abstract
Four novel Gram-negative, mesophilic, aerobic, motile, and cocci-shaped strains were isolated from tick samples (strains 546T and 573) and respiratory tracts of marmots (strains 1318T and 1311). The 16S rRNA gene sequencing revealed that strains 546T and 573 were 97.8% identical to Roseomonas wenyumeiae Z23T, whereas strains 1311 and 1318T were 98.3% identical to Roseomonas ludipueritiae DSM 14915T. In addition, a 98.0% identity was observed between strains 546T and 1318T. Phylogenetic and phylogenomic analyses revealed that strains 546T and 573 clustered with R. wenyumeiae Z23T, whereas strains 1311 and 1318T grouped with R. ludipueritiae DSM 14915T. The average nucleotide identity between our isolates and members of the genus Roseomonas was below 95%. The genomic G+C content of strains 546T and 1318T was 70.9% and 69.3%, respectively. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the major polar lipids, with Q-10 as the predominant respiratory quinone. According to all genotypic, phenotypic, phylogenetic, and phylogenomic analyses, the four strains represent two novel species of the genus Roseomonas, for which the names Roseomonas haemaphysalidis sp. nov. and Roseomonas marmotae sp. nov. are proposed, with 546T (= GDMCC 1.1780T = JCM 34187T) and 1318T (= GDMCC 1.1781T = JCM 34188T) as type strains, respectively.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, P. R. China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China. .,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China. .,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China.
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Jiang S, Lian FB, Sun YY, Zhang XK, Du ZJ. Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34398727 DOI: 10.1099/ijsem.0.004959] [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 Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3-0.4 µm wide, 2.0-2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4-40 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, pH 7.5-8.0) and at NaCl concentrations of 1.0-10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c; 60.7 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9-95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2-80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae. Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner-Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae, for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).
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Affiliation(s)
- Shan Jiang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Feng-Bai Lian
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - You-Yang Sun
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiao-Kui Zhang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong 264209, PR China.,State key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
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Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2020; 70:4061-4090. [DOI: 10.1099/ijsem.0.004245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Li SH, Song J, Kang I, Hwang J, Cho JC. Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater. J Microbiol 2020; 58:463-471. [PMID: 32462487 DOI: 10.1007/s12275-020-0206-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 11/29/2022]
Abstract
A Gram-stain-negative, rod-shaped, obligately aerobic, nonflagellated, and chemoheterotrophic bacterium, designated IMCC3088T, was isolated from coastal seawater of the Yellow Sea. The 16S rRNA gene sequence analysis indicated that this strain belonged to the family Halieaceae which shared the highest sequence similarities with Luminiphilus syltensis NOR5-1BT (94.5%) and Halioglobus pacificus S1-72T (94.5%), followed by 92.3-94.3% sequence similarities with other species within the aforementioned family. Phylogenetic analyses demonstrated that strain IMCC3088T was robustly clustered with Luminiphilus syltensis NOR5-1BT within the family Halieaceae. However, average amino acid identity (AAI), percentages of conserved proteins (POCP), average nucleotide identity (ANI), and alignment fraction (AF) between strain IMCC3088T and Luminiphilus syltensis NOR5-1BT were 54.5%, 47.7%, 68.0%, and 16.5%, respectively, suggesting that they belonged to different genera. Whole-genome sequencing of strain IMCC3088T revealed a 3.1 Mbp genome size with a DNA G + C content of 51.7 mol%. The genome encoded diverse metabolic pathways including sulfur oxidation, phenol degradation, and proteorhodopsin phototrophy. Mono-unsaturated fatty acids were found to be the predominant cellular fatty acid components in the strain. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were the primarily identified polar lipids, and ubiquinone-8 was identified as a major respiratory quinone. The taxonomic data collected herein suggested that strain IMCC3088T represented a novel genus and species of the family Halieaceae, for which the name Aequoribacter fuscus gen. nov., sp. nov. is proposed with the type strain (= KACC 15529T = NBRC 108213T).
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Affiliation(s)
- Shan-Hui Li
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jaeho Song
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Ilnam Kang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Juchan Hwang
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2020; 70:2960-2966. [PMID: 32471528 DOI: 10.1099/ijsem.0.004156] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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