1887

Abstract

A polyphasic taxonomic study was undertaken to clarify the exact position of the type strain cai42 of the species Pan . 2015. The results of the 16S rRNA gene sequence analysis indicated that the two sequences from cai42 shared 99.6 and 99.7 % similarity to that of the type strain SP32 of the species and formed a coherent clade in the phylogenetic tree. Whole genomic comparison between cai42 and SP32 yielded a digital DNA–DNA hybridization estimate of 36.3 %, an average nucleotide identity of 88.8 % and an average amino acid identity of 89.8 %, clearly indicating that the two strains should belong to two genospecies of the same genus. The close relationship between the two strains was underpinned by the results of genome-based phylogenetic analysis. Although cai42 and SP32 shared similar physiological and biochemical properties, some striking differences, such as mobility, the temperature range for growth and the polar lipid components, could distinguish them as separate species. Therefore, the comparative phenotypic and genotypic analyses supported the incorporation of into the genus as nom. nov. with the type strain cai42 (=CGMCC 1.12518=LMG 27406).

Funding
This study was supported by the:
  • Yang Liu , The Science and Technology Plan Project of Guangdong Province , (Award 2019B030316017)
  • Yang Liu , The GDAS' Special Project of Science and Technology Development , (Award 2020GDASYL-20200302002)
  • Yang Liu , The Key-Area Research and Development Program of Guangdong Province , (Award 2018B020205003)
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2020-05-07
2020-06-04
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References

  1. Foesel BU, Drake HL, Schramm A. Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. Syst Appl Microbiol 2011; 34:498–502 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  2. Jean E. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2013; 63:1–5
    [Google Scholar]
  3. Jiang L, Xu H, Shao Z, Long M. Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment. Int J Syst Evol Microbiol 2014; 64:2084–2088 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  4. Zhang S, Sun C, Xie J, Wei H, Hu Z et al. Defluviimonas pyrenivorans sp. nov., a novel bacterium capable of degrading polycyclic aromatic hydrocarbons. Int J Syst Evol Microbiol 2018; 68:957–961 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  5. Ren H, Ma H, Li H, Huang L, Luo Y. Acidimangrovimonas sediminis gen. nov., sp. nov., isolated from mangrove sediment and reclassification of Defluviimonas indica as Acidimangrovimonas indica comb. nov. and Defluviimonas pyrenivorans as Acidimangrovimonas pyrenivorans comb. nov. Int J Syst Evol Microbiol 2019; 69:2445–2451 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Math RK, Jin HM, Jeong SH, Jeon CO. Defluviimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat, and emended description of the genus Defluviimonas Foesel et al. 2011. Int J Syst Evol Microbiol 2013; 63:2895–2900 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Jung Y-T, Park S, Lee J-S, Yoon J-H. Defluviimonas aquaemixtae sp. nov., isolated from the junction between a freshwater spring and the ocean. Int J Syst Evol Microbiol 2014; 64:4191–4197 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  8. Pan X-C, Geng S, Lv X-L, Mei R, Jiangyang J-H et al. Defluviimonas alba sp. nov., isolated from an oilfield. Int J Syst Evol Microbiol 2015; 65:1805–1811 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Liu Y, Lai Q, Wang W, Shao Z. Defluviimonas nitratireducens sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:2752–2757 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Li A-H, Zhou Y-G. Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water. Int J Syst Evol Microbiol 2015; 65:1199–1206 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. 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]
  12. Zhao J-Y, Geng S, Xu L, Hu B, Sun J-Q et al. Complete genome sequence of Defluviimonas alba cai42T, a microbial exopolysaccharides producer. J Biotechnol 2016; 239:9–12 [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. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. Moore RL, Weiner RM, Gebers R. Notes: Genus Hyphomonas Pongratz 1957 nom. rev. emend., Hyphomonas polymorpha Pongratz 1957 nom. rev. emend., and Hyphomonas neptunium (Leifson 1964) comb. nov. emend. (Hyphomicrobium neptunium). Int J Syst Bacteriol 1984; 34:71–73 [CrossRef]
    [Google Scholar]
  18. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  19. 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]
  20. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  21. 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]
  22. 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][PubMed]
    [Google Scholar]
  23. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [CrossRef]
    [Google Scholar]
  24. 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:e02475–02419 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R et al. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res 2020; 48:D606–D612 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  26. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  27. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Jamestown, ND: 1990
    [Google Scholar]
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