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Abstract

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterium, capable of producing poly-β-hydroxyalkanoate, designated DP3N28-2, was isolated from the sediment collected from Daya Bay, Guangdong, PR China. Optimal growth occurred at 37–40 °C, pH 6.0 and in the presence of 4 % NaCl. The 16S rRNA gene sequences analysis revealed that DP3N28-2 showed highest similarities with DSM 23384 (98.3 %), 13–2-B6 (97.2 %), s El-219 (96.8 %), MM-10 (96.7 %), CL-GR66 (96.4 %) and L1 8-17 (96.1 %). The predominant fatty acids (>10 %) were summed feature 8 (Cω6 and/or Cω7; 72.1 %) and C (11.0 %). The polar lipids contain phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, one aminophosphlipid, one phospholipid and three unidentified lipids. The respiratory quinone was Q-10. The DNA G+C content was 63.0 mol% (data from the genome sequence). The estimated genome size was 5.12 Mb. The average nucleotide identity values between the DP3N28-2 genome and the genome of was 81.1 %, while the digital DNA–DNA hybridization value was 23.4 %. The phenotypic, genotypic and chemotaxonomic differences between DP3N28-2 and its phylogenetic relatives indicates that DP3N28-2 should be regarded as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is DP3N28-2 (=MCCC 1K06218=KCTC 82804).

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2022-03-09
2022-05-18
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References

  1. Zheng Q, Chen C, Yan X-J, Wang Y-N, Zeng Y-H et al. Mameliella alba gen. nov., sp. nov., a marine bacterium of the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol 2010; 60:953–957 [View Article]
    [Google Scholar]
  2. Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the “Roseobacter Clade” Into a novel family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12:1–24 [View Article] [PubMed]
    [Google Scholar]
  3. Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2021; 71:1–9 [View Article] [PubMed]
    [Google Scholar]
  4. Chen Z, Zhang J, Lei X, Lai Q, Yang L et al. Mameliella phaeodactyli sp. nov., a member of the family Rhodobacteraceae isolated from the marine algae Phaeodactylum tricornutum. Int J Syst Evol Microbiol 2015; 65:1617–1621 [View Article] [PubMed]
    [Google Scholar]
  5. Xu H, Jiang L, Li S, Zeng X, Shao Z. Mameliella atlantica sp. nov., a marine bacterium of the Roseobacter clade isolated from deep-sea sediment of the South Atlantic Ocean. Int J Syst Evol Microbiol 2015; 65:2255–2259 [View Article] [PubMed]
    [Google Scholar]
  6. Yang Y, Sun J, Tang K, Lin D, Li C et al. Ponticoccus lacteus sp. nov. of the family Rhodobacteraceae, isolated from surface seawater. Int J Syst Evol Microbiol 2015; 65:1247–1250 [View Article] [PubMed]
    [Google Scholar]
  7. Zhang G, Yang Y, Wang S, Sun Z, Jiao K. Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae. Int J Syst Evol Microbiol 2015; 65:2453–2458 [View Article]
    [Google Scholar]
  8. Liu Y, Zhang X, Lai Q, Shao Z. Reclassification of Mameliella phaeodactyli, Mameliella atlantica, Ponticoccus lacteus and Alkalimicrobium pacificum as later heterotypic synonyms of Mameliella alba and an emended description of Mameliella alba. Int J Syst Evol Microbiol 2018; 68:1047–1051 [View Article] [PubMed]
    [Google Scholar]
  9. Martínez-Gutiérrez CA, Latisnere-Barragán H, García-Maldonado JQ, López-Cortés A. Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. PeerJ 2018; 6:e4780 [View Article] [PubMed]
    [Google Scholar]
  10. Hiraishi A. Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 1992; 15:210–213 [View Article] [PubMed]
    [Google Scholar]
  11. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
    [Google Scholar]
  12. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  16. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:455–477 [View Article] [PubMed]
    [Google Scholar]
  19. 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 [View Article] [PubMed]
    [Google Scholar]
  20. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  21. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  22. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. Dong X, Cai M. Determinative Manual for Routine bacteriology Peking: Scientific Press; 2001
    [Google Scholar]
  25. Juengert JR, Bresan S, Jendrossek D. Determination of polyhydroxybutyrate (PHB) content in Ralstonia eutropha using gas chromatography and Nile red staining. Bio Protoc 2018; 8:e2748 [View Article] [PubMed]
    [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI; 1990
    [Google Scholar]
  27. Hanif M, Atsuta Y, Fujie K, Daimon H. Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples. Molecules 2012; 17:2628–2642 [View Article] [PubMed]
    [Google Scholar]
  28. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article] [PubMed]
    [Google Scholar]
  29. Vaskovsky VE, Kostetsky EY, Vasendin IM. A universal reagent for phospholipid analysis. J Chromatogr 1975; 114:129–141 [View Article] [PubMed]
    [Google Scholar]
  30. Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Methods Microbiol 2011; 38:165–181
    [Google Scholar]
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