1887

Abstract

A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium with monopolar flagella, designated as MC042, was isolated from the profound head ulcers of farmed Murray cod sampled from Zhejiang Province, China. Analysis of its 16S rRNA gene sequence and multilocus sequence analysis phylogeny showed that strain MC042 belonged to the genus , showing the highest 16S rRNA gene sequence similarity to BML3 (98.9 %), and less than 98.8 % similarity to other species with validly published names. Whole-genome sequencing and phylogenetic reconstruction based on a core set of 1563 genes further indicated that strain MC042 was most closely related to the clade formed by CHA0 and DSM 975 and distantly related to any of the validly published species of the genus . Furthermore, strain MC042 could be distinguished from its closely related species of the genus by its ability to assimilate maltose, -xylose and melibiose, but not -mannitol. The principal fatty acids were C, summed feature 3 (iso-C 2-OH and/or Cω) and summed feature 8 (C 7 and/or C 6). The respiratory quinone was Q-9. Polar lipids of strain MC042 comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified glycolipids, an unidentified lipid, an unknown glycolipid and aminolipid. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain MC042 is considered to represent a novel species, for which the name sp. nov. is proposed. The type strain is MC042 (=KCTC 72033=MCCC 1K03575).

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2020-03-26
2020-04-04
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References

  1. Migula W. Über ein neues system Der Bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–238
    [Google Scholar]
  2. Anwar N, Rozahon M, Zayadan B, Mamtimin H, Abdurahman M et al. Pseudomonas tarimensis sp. nov., an endophytic bacteria isolated from Populus euphratica. Int J Syst Evol Microbiol 2017; 67:4372–4378 [CrossRef][PubMed]
    [Google Scholar]
  3. Magi GE, Lopez-Romalde S, Magariños B, Lamas J, Toranzo AE et al. Experimental Pseudomonas anguilliseptica infection in turbot Psetta maxima (L.): a histopathological and immunohistochemical study. Eur J Histochem 2009; 53:9–79 [CrossRef][PubMed]
    [Google Scholar]
  4. Huang L, Zhao L, Liu W, Xu X, Su Y et al. Dual RNA-Seq Unveils Pseudomonas plecoglossicida htpG Gene Functions During Host-Pathogen Interactions With Epinephelus coioides. Front Immunol 2019; 10:984 [CrossRef][PubMed]
    [Google Scholar]
  5. Beaton A, Lood C, Cunningham-Oakes E, MacFadyen A, Mullins AJ et al. Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies. FEMS Microbiol Lett 2018; 365: [CrossRef][PubMed]
    [Google Scholar]
  6. Peix A, Ramírez-Bahena M-H, Velázquez E. The current status on the taxonomy of Pseudomonas revisited: an update. Infect Genet Evol 2018; 57:106–116 [CrossRef][PubMed]
    [Google Scholar]
  7. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 2005; 102:2567–2572 [CrossRef][PubMed]
    [Google Scholar]
  8. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef]
    [Google Scholar]
  9. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas. Front Microbiol 2015; 6:214 [CrossRef][PubMed]
    [Google Scholar]
  10. Chen WP, Kuo TT. A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res 1993; 21:2260 [CrossRef][PubMed]
    [Google Scholar]
  11. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [CrossRef][PubMed]
    [Google Scholar]
  12. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [CrossRef][PubMed]
    [Google Scholar]
  13. Liu Y, Rao Q, Tu J, Zhang J, Huang M et al. Acinetobacter piscicola sp. nov., isolated from diseased farmed Murray cod (Maccullochella peelii peelii). Int J Syst Evol Microbiol 2018; 68:905–910 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. Mulet M, Gomila M, Scotta C, Sánchez D, Lalucat J et al. Concordance between whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry and multilocus sequence analysis approaches in species discrimination within the genus Pseudomonas. Syst Appl Microbiol 2012; 35:455–464 [CrossRef][PubMed]
    [Google Scholar]
  16. Rao Q, Liu Y, Chen C, Lin Q, Ren L et al. Pseudomonas ovata sp. nov., Isolated from the Skin of the Tail of Farmed Murray cod (Maccullochella peelii peelii) with a Profound Ulceration. Curr Microbiol 2019; 76:1168–1174 [CrossRef][PubMed]
    [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  20. 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [CrossRef][PubMed]
    [Google Scholar]
  22. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016; 44:W22–W28 [CrossRef][PubMed]
    [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Palleroni NJ. Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology 2, 2nd ed. New York: Springer; 2005 pp 323–379
    [Google Scholar]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  27. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [CrossRef]
    [Google Scholar]
  28. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [CrossRef][PubMed]
    [Google Scholar]
  29. Vasconcellos RLF, Santos SN, Zucchi TD, Silva FSP, Souza DT et al. Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments. Arch Microbiol 2017; 199:1223–1229 [CrossRef][PubMed]
    [Google Scholar]
  30. Chen C, Su Y, Tao T, Fu G, Zhang C et al. Maripseudobacter aurantiacus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a sedimentation Basin. Int J Syst Evol Microbiol 2017; 67:778–783 [CrossRef][PubMed]
    [Google Scholar]
  31. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
    [Google Scholar]
  32. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial Systematics. Method Microbiol 1987; 19:161–207
    [Google Scholar]
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