1887

Abstract

A Gram-stain-negative, aerobic, rod-shaped and motile bacterial strain, designated L53-10-65, was isolated from deep seawater of the South China Sea. Strain L53-10-65 was found to grow at 4–41 °C (optimum, 28 °C), at pH 5.0–9.0 (pH 7.0–8.0) and in 0–7 % (w/v) NaCl (2 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain L53-10-65 fell within the genus , with the highest similarity to IO390501 (98.4 %), followed by ‘’ L15 (97.7 %) and IFO 13584 (96.8 %). The digital DNA–DNA hybridization (dDDH) values between strain L53-10-65 and the three relatives above were 43.7, 21.5 and 20.9 %, respectively; the average nucleotide identity (ANI) values were 91.3, 78.4 and 76.8 %, respectively. These values were below the 70 % dDDH and 95–96 % ANI thresholds for bacterial species delineation. The major cellular fatty acids of strain L53-10-65 were summed feature 8 (C 7 and/or C 6), C 7 11-methyl and C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The respiratory quinone was identified as Q-10. The DNA G+C content of strain L53-10-65 was 61.3 mol%. Based on the results of phylogenetic analysis and distinctive phenotypic characteristics, strain L53-10-65 is concluded to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain of the species is L53-10-65 (=MCCC 1A05139=KCTC 72888). Moreover, we propose that is a later heterotypic synonym of based on the present results.

Funding
This study was supported by the:
  • Yang Liu , the Science and Technology Plan Project of Guangdong Province , (Award 2019B030316017)
  • Honghui Zhu , the GDAS' Special Project of Science and Technology Development , (Award 2020GDASYL-20200302002)
  • Honghui Zhu , the Key-Area Research and Development Program of Guangdong Province , (Award 2018B020205003)
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2020-04-28
2020-06-04
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References

  1. Nakagawa Y, Sakane T, Yokota A. Transfer of "Pseudomonas riboflavina" (Foster 1944), a gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int J Syst Bacteriol 1996; 46:16–22 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Yoon J-H, Kang S-J, Park S, Oh T-K. Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia . Int J Syst Evol Microbiol 2007; 57:1310–1314 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  3. Mohd Nor MN, Sabaratnam V, Tan GYA. Devosia elaeis sp. nov., isolated from oil palm rhizospheric soil. Int J Syst Evol Microbiol 2017; 67:851–855 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Bautista VV, Monsalud RG, Yokota A. Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi. Int J Syst Evol Microbiol 2010; 60:627–632 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Zhang D-C, Redzic M, Liu H-C, Zhou Y-G, Schinner F et al. Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia . Int J Syst Evol Microbiol 2012; 62:710–715 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Lee SD. Devosia subaequoris sp. nov., isolated from beach sediment. Int J Syst Evol Microbiol 2007; 57:2212–2215 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Jia Y-Y, Sun C, Pan J, Zhang W-Y, Zhang X-Q et al. Devosia pacifica sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:2637–2641 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Lin D, Huang Y, Chen Y, Zhu S, Yang J et al. Devosia indica sp. nov., isolated from surface seawater in the Indian Ocean. Int J Syst Evol Microbiol 2020; 70:340–345 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Wang G, Wang Y, Ji F, Xu L, Yu M et al. Biodegradation of deoxynivalenol and its derivatives by Devosia insulae A16. Food Chem 2019; 276:436–442 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Rivas R, Velázquez E, Willems A, Vizcaíno N, Subba-Rao NS et al. A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce. Appl Environ Microbiol 2002; 68:5217–5222 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Dua A, Malhotra J, Saxena A, Khan F, Lal R. Devosia lucknowensis sp. nov., a bacterium isolated from hexachlorocyclohexane (HCH) contaminated pond soil. J Microbiol 2013; 51:689–694 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. Lai Q, Liu Y, Yuan J, Du J, Wang L et al. Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments. PLoS One 2014; 9:e106353 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. 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][PubMed]
    [Google Scholar]
  14. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Czelusniak J, Goodman M, Moncrief ND, Kehoe SM. Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences. Methods Enzymol 1990; 183:601–615 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  19. Kim M, H-S O, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes; 2014; 64346–351
  20. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  21. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  22. 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][PubMed]
    [Google Scholar]
  23. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Brenner DJ, Grimont PAD 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]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:1912619131 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 2014; 42:D581–D591 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  26. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  27. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  28. Yoo S-H, Weon H-Y, Kim B-Y, Hong S-B, Kwon S-W et al. Devosia soli sp. nov., isolated from greenhouse soil in Korea. Int J Syst Evol Microbiol 2006; 56:2689–2692 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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