1887

Abstract

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated as strain TK19130, was isolated from the Lonqi hydrothermal zone in the Southwest Indian Ridge. Growth occurred with 1–12 % (w/v) NaCl (optimum, 2–4 %), at 10–40 °C (optimum, 30–35 °C) and at pH 6.0–9.0 (optimum, pH 7.0–8.0). The genome of strain TK19130 was 3.15 Mb, with a DNA G+C content of 41.35 %. Based on the results of 16S rRNA gene sequence analysis, strain TK19130 was affiliated with the family , in which the highest similarity was 90.54 % to A6D-50, under the genus demarcation boundary (94.50 %). Average nucleotide identity values between strain TK19130 and adjacent strains were 67.17–72.00 %, lower than the recommended threshold of 73.98 % for genus delineation. The predominant respiratory quinone of strain TK19130 was menaquinone 6. Major polar lipids were phosphatidylethanolamine, three aminolipids and one unidentified polar lipid. Major fatty acids were detected as iso-C G, iso-C and iso-C 3-OH. Based on the polyphasic taxonomic evidence presented above, strain TK19130 formed an independent branch representing a new species of a novel genus within the family , for which the name gen. nov., sp. nov. is proposed. The type strain is TK19130 (=CGMCC 1.18993=JCM 35842=MCCC M28200).

Funding
This study was supported by the:
  • XMU Training Program of Innovation and Entrepreneurship for Undergraduates (Award 2022X0968)
    • Principle Award Recipient: BeihanChen
  • XMU Undergraduate Innovation and Entrepreneurship Training Programs (Award KFJJ-202218)
    • Principle Award Recipient: BeihanChen
  • International Science Partnership Programme of the Chinese Academy of Sciences (Award 121311KYSB20190029)
    • Principle Award Recipient: KaiTang
  • National Natural Science Foundation of China (Award 42276120)
    • Principle Award Recipient: KaiTang
  • National Natural Science Foundation of China (Award 42076160)
    • Principle Award Recipient: KaiTang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006166
2023-11-15
2024-07-22
Loading full text...

Full text loading...

References

  1. Reichenbach H. eds The Order Cytophagales, in The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, A. Balows New York, NY: Springer; 1992 pp 3631–3675
    [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  3. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
    [Google Scholar]
  4. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:2083 [View Article] [PubMed]
    [Google Scholar]
  5. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  6. Kirchman DL. The ecology of cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 2002; 39:91–100 [View Article] [PubMed]
    [Google Scholar]
  7. Chen Y, Zhang Z, Fu Y, Wang Y, Wang Y et al. Altuibacter lentus gen. nov., sp. nov., a novel member of family Flavobacteriaceae isolated from deep seawater of the South China Sea. Antonie van Leeuwenhoek 2013; 104:1151–1157 [View Article] [PubMed]
    [Google Scholar]
  8. Wu Y-H, Xamxidin M, Meng F-X, Zhang X-Q, Wang C-S et al. Marinirhabdus gelatinilytica gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:3095–3101 [View Article] [PubMed]
    [Google Scholar]
  9. Khan ST, Nakagawa Y, Harayama S. Galbibacter mesophilus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2007; 57:969–973 [View Article] [PubMed]
    [Google Scholar]
  10. Waśkiewicz A, Irzykowska L. Flavobacterium spp. – characteristics, occurrence, and toxicity. In Encyclopedia of Food Microbiology Academic Press; 2014 pp 938–942
    [Google Scholar]
  11. Buchan A, LeCleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol 2014; 12:686–698 [View Article] [PubMed]
    [Google Scholar]
  12. He Y, Zeng X, Xiong J, Lai Q, Li J et al. Wocania indica gen. nov., sp. nov., isolated from deep sea hydrothermal sulfide in the northwest Indian Ocean, and proposal to reclassify Flaviramulus ichthyoenteri as Wocania ichthyoenteri comb. nov. Int J Syst Evol Microbiol 2020; 70:5488–5496 [View Article] [PubMed]
    [Google Scholar]
  13. Li M, Jain S, Dick GJ. Genomic and transcriptomic resolution of organic matter utilization among deep-sea bacteria in guaymas basin hydrothermal plumes. Front Microbiol 2016; 7:1125 [View Article]
    [Google Scholar]
  14. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  17. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [Google Scholar]
  18. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article] [PubMed]
    [Google Scholar]
  19. Zerbino DR, McEwen GK, Margulies EH, Birney E. Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One 2009; 4:e8407 [View Article] [PubMed]
    [Google Scholar]
  20. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 2011; 27:578–579 [View Article] [PubMed]
    [Google Scholar]
  21. Hunt M, Newbold C, Berriman M, Otto TD. A comprehensive evaluation of assembly scaffolding tools. Genome Biol 2014; 15:R42 [View Article] [PubMed]
    [Google Scholar]
  22. Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol 2012; 13:R56 [View Article] [PubMed]
    [Google Scholar]
  23. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  24. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
    [Google Scholar]
  25. 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]
  26. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
    [Google Scholar]
  27. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11:e02475–19
    [Google Scholar]
  28. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  29. Huang Z, Du Y, Lai Q, Shao Z. Nonlabens xiamenensis sp. nov., isolated from coastal seawater. Antonie van Leeuwenhoek 2019; 112:1263–1271 [View Article] [PubMed]
    [Google Scholar]
  30. Liu J-J, Zhang X-Q, Pan J, Sun C, Zhang Y et al. Aequorivita viscosa sp. nov., isolated from an intertidal zone, and emended descriptions of Aequorivita antarctica and Aequorivita capsosiphonis. Int J Syst Evol Microbiol 2013; 63:3192–3196 [View Article] [PubMed]
    [Google Scholar]
  31. Sato K, Naya M, Hatano Y, Kondo Y, Sato M et al. Colony spreading of the gliding bacterium Flavobacterium johnsoniae in the absence of the motility adhesin SprB. Sci Rep 2021; 11:967 [View Article] [PubMed]
    [Google Scholar]
  32. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1988; 161:207
    [Google Scholar]
  33. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article] [PubMed]
    [Google Scholar]
  34. Fischer T, Schorb M, Reintjes G, Kolovou A, Santarella-Mellwig R et al. Biopearling of interconnected outer membrane vesicle chains by a marine flavobacterium. Appl Environ Microbiol 2019; 85:e00829-19 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006166
Loading
/content/journal/ijsem/10.1099/ijsem.0.006166
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error