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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

gen. nov., sp. nov., represented by a marine strain of the family No Access

Abstract

A Gram-stain-negative, non-motile, facultatively anaerobic, short rod-shaped bacterium, designated HB171799, was isolated from seacoast sandy soil collected at Qishui Bay, Hainan, PR China. The chemotaxonomic analysis revealed that the respiratory quinones were Q-8 and Q-7, and the major cellular fatty acids were summed feature 8 (comprising C c and/or C c), C and C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The size of the draft genome was 3.68 Mb with a DNA G+C content of 48.0 mol%. Results of phylogenetic analyses based on 16S rRNA gene and genome sequences showed that the novel isolate belonged to the family and formed a distinct subcluster at the base of the radiation of the genus . The highest sequence similarity (96.0 %) of the novel isolate was found to the type strains of JCM 18476 and DSM23425. The whole genome-based phylogeny and differences in cellular fatty acids and polar lipids readily distinguished strain HB171799 from all the closely related validly published type strains. Strain HB171799 is therefore suggested to represent a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain is HB171799 (=CGMCC 1.16727=JCM 33332).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Maribrevibacterium harenarium , Oceanospirillaceae and polyphasic taxonomy
Funding
This study was supported by the:
  • Central Public-interest Scientific Institution Basal Research Fund of CATAS from Chinese Government (Award 1630052019014)
    • Principle Award Recipient: HuiqinHuang
  • Central Public-interest Scientific Institution Basal Research Fund of CATAS from Chinese Government (Award 1630052016011)
    • Principle Award Recipient: HuiqinHuang
  • Financial Fund of Ministry of Agriculture and Rural Affairs of China (Award NFZX2021)
    • Principle Award Recipient: YonghuaHu
  • Financial Fund of Ministry of Agriculture and Rural Affairs of China (Award NHYYSWZZZYKZX2020)
    • Principle Award Recipient: YonghuaHu
© 2021 The Authors
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References

  1. Hylemon PB, Wells JS, Krieg NR, Jannasch HW. The genus Spirillum: a taxonomic study. Int J Syst Bacteriol 1973; 23:340–380 [View Article]
     [Google Scholar]
  2. Garrity GM, Bell JA, Lilburn T. Family I. Oceanospirillaceae fam. nov. Brenner D, Staley J, Garrity G. eds In Bergey’s Manual of Systematic Bacteriology, 2nd Edn, Vol 2, Part B New York: Springer;p271
     [Google Scholar]
  3. Satomi M, Kimura B, Hamada T, Harayama S, Fujii T. Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Int J Syst Evol Microbiol 2002; 52:739–747 [View Article] [PubMed]
     [Google Scholar]
  4. Dauga C, Gillis M, Vandamme P, Ageron E, Grimont F et al. Balneatrix alpaca gen. nov., sp. nov., a bacterium associated with pneumonia and meningitis in a spa therapy center. Res Microbiol 1993; 144:35–46 [View Article] [PubMed]
     [Google Scholar]
  5. Wang G, Jia Q, Li T, Dai S, Wu H et al. Bacterioplanes sanyensis gen. nov., sp. nov., a PHB–accumulating bacterium isolated from a pool of Spirulina platensis cultivation. Arch Microbiol 2014; 196:739–744
     [Google Scholar]
  6. Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM. Corallomonas stylophorae gen. nov., sp. nov., a halophilic bacterium isolated from the reef-building coral Stylophora pistillata . Int J Syst Bacteriol 2013; 63:982–988
     [Google Scholar]
  7. Cao Y, Chastain RA, Eloe EA, Nogi Y, Kato C et al. Novel psychropiezophilic Oceanospirillales species Profundimonas piezophila gen. nov., sp. nov., isolated from the deep-sea environment of the Puerto Rico Trench. Appl Environ Microbiol 2014; 80:54–60 [View Article] [PubMed]
     [Google Scholar]
  8. Lee H, Yoshizawa S, Kogure K, Kim HS, Yoon J. Pelagitalea pacifica gen. nov., sp. nov., a new marine bacterium isolated from seawater. Curr Microbiol 2015; 70:514–519 [View Article] [PubMed]
     [Google Scholar]
  9. Weisburg WG, Barns SM, Pelletier DJ, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  10. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing Ezbiocloud: A taxonomically united database of 16s rrna gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
     [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  13. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  14. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  16. Kumari P, Poddar A, Das SK. Marinomonas fungiae sp. nov., isolated from the coral Fungia echinata from the Andaman Sea. Int J Syst Bacteriol 2014; 64:487–494
     [Google Scholar]
  17. Lau KWK, Ren JP, Wai NLM, Lau SCL, Qian PY et al. Marinomonas ostreistagni sp. nov., isolated from a pearl-oyster culture pond in Sanya, Hainan province, China. Int J Syst Bacteriol 2006; 56:2271–2275
     [Google Scholar]
  18. Chun J, Rainey FA. Intergrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
     [Google Scholar]
  19. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365–8370 [View Article] [PubMed]
     [Google Scholar]
  20. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 6:673–679
     [Google Scholar]
  21. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic acids Res 1997; 5:955–964
     [Google Scholar]
  22. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 9:3100–3108
     [Google Scholar]
  23. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014; 42:D490–D495 [View Article]
     [Google Scholar]
  24. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  25. Lee I, Kim YO, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103
     [Google Scholar]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–73 [View Article] [PubMed]
     [Google Scholar]
  27. Rodríguez RLM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118
     [Google Scholar]
  28. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
     [Google Scholar]
  29. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182–2191 [View Article] [PubMed]
     [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  31. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  32. Kang JW, Yang HG, Choi S, Kim YJ, Lee SD. Seongchinamella unica gen. nov.,sp. nov., isolated from a tidal mudflat of beach, and transfer of Halioglobus sediminis to Seongchinamella sediminis comb. nov. and Halioglobus lutimaris to Pseudohalioglobus gen. nov. as Pseudohalioglobus lutimaris comb. nov. Int J Syst Evol Microbiol 2020; 70:2194–2203 [View Article] [PubMed]
     [Google Scholar]
  33. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article] [PubMed]
     [Google Scholar]
  34. Murray TS, Ledizet M, Kazmierczak BI. Swarming motility, secretion of type 3 effectors and biofilm formation phenotypes exhibited within a large cohort of Pseudomonas aeruginosa clinical isolates. J Med Microbiol 2010; 59:511–520 [View Article] [PubMed]
     [Google Scholar]
  35. Dong X, Cai M. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  36. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  37. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  38. Ruan JS. A rapid determination method for phosphate lipids. Microbiol China 2006; 37:190–193
     [Google Scholar]
  39. Komagata K, Suzuki KI. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  40. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
     [Google Scholar]
  41. Bai X, Lai Q, Dong C, Li F, Shao Z. Marinomonas profundimaris sp. nov., isolated from deep-sea sediment sample of the Arctic Ocean. Antonie van Leeuwenhoek 2014; 106:449–455 [View Article] [PubMed]
     [Google Scholar]
  42. Dimitriu PA, Shukla SK, Conradt J, Márquez MC, Ventosa A et al. Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake. Int J Syst Evol Microbiol 2005; 55:2273–2278 [View Article]
     [Google Scholar]
  43. Phurbu D, Pema Y, Ma C, Lu H, Li H et al. Nitrincola tibetensis sp. nov., isolated from Lake XuguoCo on the Tibetan Plateau. Int J Syst Evol Microbiol 2019; 69:123–128
     [Google Scholar]
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Maribrevibacterium harenarium gen. nov., sp. nov., represented by a marine strain of the family Oceanospirillaceae
Int J Syst Evol Microbiol 71, 004872 (2021); https://doi.org/10.1099/ijsem.0.004872
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