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Abstract

Two Gram-stain-negative, aerobic, rod-shaped, non-endospore-forming and motile bacterial strains, designated IT1137 and S025, were isolated from an intertidal sediment sample collected from the Fildes Peninsula (King George Island, Maritime Antarctica) and a soil sample under red snow in the Ny-Ålesund region (Svalbard, High Arctic), respectively. The 16S rRNA gene sequence similarity values grouped them in the genus . The two strains were characterized phenotypically using API 20E, API 20NE, API ZYM and Biolog GENIII tests and chemotaxonomically by their fatty acid contents, polar lipids and respiratory quinones. Multilocus sequence analysis (concatenated 16S rRNA, , and sequences), together with genome comparisons by average nucleotide identity and digital DNA–DNA hybridization, were performed. The results showed that the similarity values of the two isolates with the type strains of related species were below the recognized thresholds for species definition. Based on polyphasic taxonomy analysis, it can be concluded that strains IT1137 and S025 represent two novel species of the genus , for which the names sp. nov. (type strain IT1137=PMCC 100533=CCTCC AB 2023226=JCM 36637) and sp. nov. (type strain S025=PMCC 200367= CCTCC AB 2023225=JCM 36638) are proposed.

Funding
This study was supported by the:
  • Key Technologies Research and Development Program (Award 2022YFC2807501)
    • Principle Award Recipient: Yin-XinZeng
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2024-07-29
2025-04-19
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References

  1. Silby MW, Winstanley C, Godfrey SAC, Levy SB, Jackson RW. Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 2011; 35:652–680 [View Article] [PubMed]
    [Google Scholar]
  2. Hesse C, Schulz F, Bull CT, Shaffer BT, Yan Q et al. Genome-based evolutionary history of Pseudomonas spp. Environ Microbiol 2018; 20:2142–2159 [View Article] [PubMed]
    [Google Scholar]
  3. Migula W. Über ein neues system der bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–328
    [Google Scholar]
  4. Carrión O, Miñana-Galbis D, Montes MJ, Mercadé E. Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic. Int J Syst Evol Microbiol 2011; 61:2401–2405 [View Article]
    [Google Scholar]
  5. Hu T, Zeng Y-X, Zhang Y-H, Du Y, Han W et al. Complete genome sequence of one novel marine Pseudomonas sp. BSw22131 growing with dimethylsulfoniopropionate (DMSP) as the sole carbon source. Mar Genom 2023; 68:101016 [View Article]
    [Google Scholar]
  6. Hu Y-Q, Zeng Y-X, Du Y, Zhao W, Li H-R et al. Comparative genomic analysis of two Arctic Pseudomonas strains reveals insights into the aerobic denitrification in cold environments. BMC Genom 2023; 24:534 [View Article] [PubMed]
    [Google Scholar]
  7. See-Too WS, Salazar S, Ee R, Convey P, Chan K-G et al. Pseudomonas versuta sp. nov., isolated from Antarctic soil. Syst Appl Microbiol 2017; 40:191–198 [View Article] [PubMed]
    [Google Scholar]
  8. Sorty AM, Zervas A, García de Salamone IE, Nelson LM, Stougaard P. Pseudomonas hormoni sp. nov., a plant hormone producing bacterium isolated from Arctic grass, Ellesmere Island, Canada. Int J Syst Evol Microbiol 2023; 73:10 [View Article] [PubMed]
    [Google Scholar]
  9. Kim HS, Suh MK, Kim J-S, Do HE, Eom MK et al. Pseudomonas aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2023; 73:12 [View Article]
    [Google Scholar]
  10. Kong D, Li Q, Zhou Y, Wang Y, Jiang X et al. Pseudomonas tumuqii sp. nov., isolated from greenhouse soil. Arch Microbiol 2022; 204:249 [View Article]
    [Google Scholar]
  11. Vanparys B, Heylen K, Lebbe L, De Vos P. Pseudomonas peli sp. nov. and Pseudomonas borbori sp. nov., isolated from a nitrifying inoculum.. Int J Syst Evol Microbiol 2006; 56:1875–1881
    [Google Scholar]
  12. Andersen SM, Johnsen K, Sørensen J, Nielsen P, Jacobsen CS. Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site. Int J Syst Evol Microbiol 2000; 50 Pt 6:1957–1964 [View Article] [PubMed]
    [Google Scholar]
  13. Verhille S, Baida N, Dabboussi F, Izard D, Leclerc H. Taxonomic study of bacteria isolated from natural mineral waters: proposal of Pseudomonas jessenii sp. nov. and Pseudomonas mandelii sp. nov. Syst Appl Microbiol 1999; 22:45–58 [View Article] [PubMed]
    [Google Scholar]
  14. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
    [Google Scholar]
  15. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  16. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
  17. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
    [Google Scholar]
  18. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article]
    [Google Scholar]
  19. Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021; 49:9077–9096 [View Article] [PubMed]
    [Google Scholar]
  20. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematic New York: Wiley; 1991 pp 115–175
    [Google Scholar]
  21. Zeng Y, Liu W, Li H, Yu Y, Chen B. Effect of restriction endonucleases on assessment of biodiversity of cultivable polar marine planktonic bacteria by amplified ribosomal DNA restriction analysis. Extremophiles 2007; 11:685–692 [View Article]
    [Google Scholar]
  22. 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]
  23. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994; 22:4673–4680 [View Article]
    [Google Scholar]
  24. 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]
  25. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  26. Nei M, Kumar S. Molecular Evolution and Phylogenetics USA: Oxford University Press; 2000 [View Article]
    [Google Scholar]
  27. Girard L, Lood C, Höfte M, Vandamme P, Rokni-Zadeh H et al. The ever-expanding Pseudomonas genus: description of 43 new species and partition of the Pseudomonas putida group. Microorganisms 2021; 9:1766 [View Article] [PubMed]
    [Google Scholar]
  28. 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 [View Article] [PubMed]
    [Google Scholar]
  29. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  31. Palleroni NJ. Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 2 New York: Springer; 2005 pp 323–379
    [Google Scholar]
  32. Liu D, Zhang Y, Fan G, Sun D, Zhang X et al. IPGA: a handy integrated prokaryotes genome and pan-genome analysis web service. imeta 2022; 1:e55 [View Article] [PubMed]
    [Google Scholar]
  33. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
    [Google Scholar]
  34. Lai Q, Shao Z. Pseudomonas xiamenensis sp. nov., a denitrifying bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2008; 58:1911–1915 [View Article] [PubMed]
    [Google Scholar]
  35. Cui H-L, Sun F-F, Gao X, Dong Y, Xu X-W et al. Haladaptatus litoreus sp. nov., an extremely halophilic archaeon from a marine solar saltern, and emended description of the genus Haladaptatus. Int J Syst Evol Microbiol 2010; 60:1085–1089 [View Article] [PubMed]
    [Google Scholar]
  36. Song H, Hu Y, Zhu H, Wang Q, Liu G et al. Three novel species of coccoid green algae within the Watanabea clade (Trebouxiophyceae, Chlorophyta). Int J Syst Evol Microbiol 2016; 66:5465–5477 [View Article] [PubMed]
    [Google Scholar]
  37. Smibert RM, Kreg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Washington, DC: American Society of Microbiology; 1994 pp 611–654
    [Google Scholar]
  38. Bowman JP, Nichols CM, Gibson JAE. Algoriphagus ratkowskyi gen. nov., sp. nov., Brumimicrobium glaciale gen. nov., sp. nov., Cryomorpha ignava gen. nov., sp. nov. and Crocinitomix catalasitica gen. nov., sp. nov., novel flavobacteria isolated from various polar habitats. Int J Syst Evol Microbiol 2003; 53:1343–1355 [View Article]
    [Google Scholar]
  39. King EO, Ward MK, Ranley DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301–307 [PubMed]
    [Google Scholar]
  40. Zhang Y-X, Yu Y, Luo W, Zeng Y-X, Du Z-J et al. Devosia beringensis sp. nov., isolated from surface sediment of the Bering Sea. Int J Syst Evol Microbiol 2021; 71:004995 [View Article] [PubMed]
    [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990
    [Google Scholar]
  42. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  43. Tindall B. Lipid composition of Halobacterium Lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  44. Kates M. Lipid Extraction Procedures. In Techniques of Lipidology Amsterdam: Elsevier; 1986 pp 100–111
    [Google Scholar]
  45. Lai Q, Liu X, Yuan J, Xie S, Shao Z. Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 2019; 69:932–936 [View Article] [PubMed]
    [Google Scholar]
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