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Volume 71, Issue 7

sp. nov., isolated from rainbow trout and water No Access

Abstract

Cells of strains P66, V1 and W15Feb18 are Gram-stain-negative short rods and motile by one polar flagellum. Strain P66 was isolated from rainbow trout () cultivated at a fish farm in Turkey. Strain V1 was isolated from sand of an intertidal shore on the Galicia coast in Spain and strain W15Feb18 was isolated from water collected at the Woluwe River in Belgium. Based on 16S rRNA sequence similarity values, the strains were grouped under the genus and the phylogenetic group of species. The DNA G+C content ranged from 58.5 to 58.9 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. The absence of the hydrolysis of gelatin and the assimilation of arabinose, mannose and mannitol differentiated these strains from the closest species, . The major fatty acid components were C (29.91–31.68 %) and summed feature 3 (36.44–37.55 %). Multilocus sequence analysis with four and 83 housekeeping gene sequences and a core proteome analysis showed that these strains formed a phylogenetic cluster in the group of species. Genome comparisons by the average nucleotide identity based on and the Genome-to-Genome Distance Calculator demonstrated that the three strains belonged to the same genomic species and were distant from any known species, with similarity values lower than the thresholds established for species in the genus . These data permitted us to conclude that strains P66, V1 and W15Feb18 belong to a novel species in the genus , for which the name sp. nov. is proposed. The type strain is P66 (=CECT 30176=CCUG 74872). The other strains have been deposited in the CECT with the corresponding collection numbers: V1 (=CECT 30356) and W15Feb18 (=CECT 30355).

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  • Accepted:
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Keyword(s): genome analysis , multilocus analysis , Pseudomonas and rainbow trout
Funding
This study was supported by the:
  • TUBITAK (Award 118O420)
    • Principle Award Recipient: MuhammedDuman
© 2021 The Authors
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2021-07-09
2024-04-26
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References

  1. Silby M, 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. Lalucat J, Mulet M, Gomila M, García-Valdés E. Genomics in bacterial taxonomy: Impact on the genus Pseudomonas. Genes (Basel) 2020; 11:139 [View Article]
     [Google Scholar]
  3. Palleroni NJ. Pseudomonas. Brenner D, Krieg N, Staley J. eds In Bergey’s Manual of Systematic Bacteriology, 2nd. ed Vol 2 New York: Springer; 2005 pp 323–379
     [Google Scholar]
  4. Duman M, Mulet M, Saticioglu IB, Altun S, Gomila M et al. Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey. Syst Appl Microbiol 2020; 43:126103 [View Article] [PubMed]
     [Google Scholar]
  5. Duman M, Mulet M, Altun S, Saticioglu IB, Ozdemir B et al. The diversity of Pseudomonas species isolated from fish farms in Turkey. Aquaculture 2021; 535:736369 [View Article]
     [Google Scholar]
  6. Duman M, Mulet M, Altun S, Saticioglu IB, Gomila M et al. Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov., Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout. Int J Syst Evol Microbiol 2021; 535:736369
     [Google Scholar]
  7. Mulet M, David Z, Nogales B, Bosch R, Lalucat J et al. Pseudomonas diversity in crude-oil-contaminated intertidal sand samples obtained after the Prestige oil spill. Appl Environ Microbiol 2011; 77:1076–1085 [View Article] [PubMed]
     [Google Scholar]
  8. Matthijs S, Coorevits A, Gebrekidan TT, Tricot C, Wauven CV et al. Evaluation of Opri and OPRL genes as molecular markers for the genus Pseudomonas and their use in studying the biodiversity of a small belgian river. Res Microbiol 2013; 164:254–261 [View Article] [PubMed]
     [Google Scholar]
  9. OIE Fish Diseases Commission Diagnostic Manual for Aquatic Animal Diseases; 2000
     [Google Scholar]
  10. Pirnay JP, Matthijs S, Colak H, Chablain P, Bilocq F et al. Global Pseudomonas aeruginosa biodiversity as reflected in a Belgian river. Environ Microbiol 2005; 7:969–980 [View Article] [PubMed]
     [Google Scholar]
  11. Mulet M, Gomila M, Ramírez A, Cardew S, Moore ERB et al. Uncommonly isolated clinical Pseudomonas: identification and phylogenetic assignation. Eur J Clin Microbiol Infect Dis 2017; 36:351–359 [View Article] [PubMed]
     [Google Scholar]
  12. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530 [View Article] [PubMed]
     [Google Scholar]
  13. Mulet M, Gomila M, Gruffaz C, Meyer J-M, Palleroni NJ et al. Phylogenetic analysis and siderotyping as useful tools in the taxonomy of pseudomonas stutzeri: description of a novel genomovar. Int J Syst Evol Microbiol 2008; 58:2309–2315 [View Article]
     [Google Scholar]
  14. Mulet M, Bennasar A, Lalucat J, García-Valdés E. An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cell Probes 2009; 23:140–147 [View Article] [PubMed]
     [Google Scholar]
  15. Jukes T, Cantor C. Evolution of protein molecules. Munro H. eds In Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21–132
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evolution 1981; 17:368–376 [View Article]
     [Google Scholar]
  17. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
     [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method. A new method for reconstructing phylogenetic trees. Biol and Evol 1987; 4:406–425
     [Google Scholar]
  19. Yoon SH, SM H, 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; 67:5–1613
     [Google Scholar]
  20. 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]
  21. Moore ERB, Mau M, Arnscheidt A, Böttger EC, Hutson RA et al. The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst Appl Microbiol 1996; 19:465–643
     [Google Scholar]
  22. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A et al. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000; 146:10
     [Google Scholar]
  23. Anzai Y, Kim H, Park J, Wakabayashi H, Oyaizu H. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 2000; 50:1563–1589 [View Article]
     [Google Scholar]
  24. Alanjary M, Steinke K, Ziemert N. Automlst: An automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Research 2019; 458:276–282 [View Article]
     [Google Scholar]
  25. Avram O, Rapoport D, Portugez S, Pupko T. M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res 2019; 47:W88–W92 [View Article]
     [Google Scholar]
  26. Richter M, Rosselló-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2019; 106:19126–19131
     [Google Scholar]
  27. 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 [View Article] [PubMed]
     [Google Scholar]
  28. Lalucat J. Analysis of refractile (R) bodies. Mayer E. eds In Methods in Microbiology –Electron Microscopy in Microbiology Vol 20 London: Academic Press; 1988 pp 79–90
     [Google Scholar]
  29. Sanchez D, Mulet M, Rodríguez AC, David Z, Lalucat J et al. Pseudomonas aestusnigri sp. nov., isolated from crude oil-contaminated intertidal sand samples after the Prestige oil spill. Syst Appl Microbiol 2014; 37:89–94 [View Article] [PubMed]
     [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  31. MIDI Sherlock Microbial Identification System Operating Manual, version 6 1 Newark, DE: MIDI Inc; 2008
     [Google Scholar]
  32. Frasson D, Opoku M, Picozzi T, Torossi T, Balada S et al. Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:2853–2861 [View Article]
     [Google Scholar]
  33. Mulet M, Sánchez D, Lalucat J, Lee K, García-Valdés E. Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol. Int J Syst Evol Microbiol 2015; 65:4013–4018 [View Article]
     [Google Scholar]
  34. Oh WT, Jun JW, Giri SS, Yun S, Kim HJ et al. Pseudomonas tructae sp. nov., novel species isolated from rainbow trout kidney. Int J Syst Evol Microbiol 2019; 69:3851–3856 [View Article]
     [Google Scholar]
  35. Xiang W, Chen S, Huang C, Gao T. Pseudomonas hutmensis sp. nov., a new fluorescent member of Pseudomonas putida group. Curr Microbiol 2019; 76:872–878 [View Article]
     [Google Scholar]
  36. Gao J, Xie G, Peng F, Zhixiong X et al. Pseudomonas donghuensis sp. nov., exhibiting high-yields of siderophore. Antonie van Leeuwenhoek 2015; 107:83–94 [View Article] [PubMed]
     [Google Scholar]
  37. WT O, Jun JW, Giri SS, Yun S, Kim HJ et al. Pseudomonas tructae sp. nov., novel species isolated from rainbow trout kidney. Int J Syst Evol Microbiol 2019; 69:3851–3856
     [Google Scholar]
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Pseudomonas arcuscaelestis sp. nov., isolated from rainbow trout and water
Int J Syst Evol Microbiol 71, 004860 (2021); https://doi.org/10.1099/ijsem.0.004860
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