1887

Abstract

Twelve Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and motile strains (CY7W, CY18W, CY22W, FT31W, FT137W, FT147W, BYS50W, BYS107W, LFS511W, LX15W, LX22W and NL8W) were isolated from streams in China. Comparisons based on 16S rRNA gene sequences indicated that these strains take species of genus as close neighbours. The reconstructed phylogenetic and phylogenomic trees also showed that these strains cluster with species of genus together. The genome G+C contents of these strains were in the range of 45.3 to 53.3 mol%. The calculated pairwise OrthoANIu values and digital DNA–DNA hybridization values among these strains and related strains were in the range of 70.4 to 94.1% and 19.3 to 55.3% except that the values between strains CY7W and BYS50W were 99.0 and 91.8 %, respectively. Q-8 was their predominant respiratory quinone. C c and C were their major fatty acids. Their polar lipids profiles were similar, including phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and two kinds of unidentified aminolipids. Combining polyphasic taxonomic characteristics and phylogenetic relationships, twelve strains should represent eleven independent novel species of genus , for which the names sp. nov. (type strain BYS107W=GDMCC 1.2453=KCTC 82653), sp. nov. (type strain CY22W=GDMCC 1.1906=KACC 21951), sp. nov. (type strain FT137W=GDMCC 1.2456=KCTC 82656), sp. nov. (type strain LX15W=GDMCC 1.1910=JCM 34286), sp. nov. (type strain FT31W=GDMCC 1.1908=KACC 21953), sp. nov. (type strain CY18W=GDMCC 1.1904=KACC 21949), sp. nov. (type strain LFS511W=GDMCC 1.2458=KCTC 82658), sp. nov. (type strain LX22W=GDMCC 1.1912=KACC 21957), sp. nov. (type strain FT147W=GDMCC 1.2457=KCTC 82657), sp. nov. (type strain CY7W=GDMCC 1.1903=KACC 21961) and sp. nov. (type strain NL8W=GDMCC 1.1915=KACC 21960) are proposed.

Keyword(s): stream and Undibacterium
Funding
This study was supported by the:
  • gdas’ special project of science and technology development (Award 2020GDASYL-20200103016; 2020GDASYL-20200402001)
    • Principle Award Recipient: MeiyingXu
  • zhaoqing science and technology project (Award 2020G1019)
    • Principle Award Recipient: MeiyingXu
  • guangdong provincial programs for science and technology development (Award 2020B0202080005; 2019B110205004)
    • Principle Award Recipient: MeiyingXu
  • guangdong technological innovation strategy of special funds (Award Key Areas of Research and Development Program (2018B020205003))
    • Principle Award Recipient: MeiyingXu
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2021-10-22
2024-12-13
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References

  1. Kämpfer P, Rosselló-Mora R, Hermansson M, Persson F, Huber B et al. Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2007; 57:1510–1515 [View Article] [PubMed]
    [Google Scholar]
  2. Eder W, Wanner G, Ludwig W, Busse H-J, Ziemke-Kägeler F et al. Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum. Int J Syst Evol Microbiol 2011; 61:384–391 [View Article] [PubMed]
    [Google Scholar]
  3. Sheu SY, Lin YS, Chen JC, Chen WM. Undibacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond. Int J Syst Evol Microbiol 2014; 64:1036–1042 [View Article] [PubMed]
    [Google Scholar]
  4. Sheu SY, Lin YS, Chen JC, Kwon SW, Chen WM. Undibacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond. Int J Syst Evol Microbiol 2014; 64:3459–3466 [View Article] [PubMed]
    [Google Scholar]
  5. Kim S-J, Moon J-Y, Weon H-Y, Hong S-B, Seok S-J et al. Undibacterium jejuense sp. nov. and Undibacterium seohonense sp. nov., isolated from soil and freshwater, respectively. Int J Syst Evol Microbiol 2014; 64:236–241 [View Article] [PubMed]
    [Google Scholar]
  6. Du J, Akter S, Won K, Singh H, Shik Yin C et al. Undibacterium aquatile sp. nov., isolated from a waterfall. Int J Syst Evol Microbiol 2015; 65:4128–4133 [View Article] [PubMed]
    [Google Scholar]
  7. Chen WM, Hsieh TY, Young CC, Sheu SY. Undibacterium amnicola sp. nov., isolated from a freshwater stream. Int J Syst Evol Microbiol 2017; 67:5094–5101 [View Article] [PubMed]
    [Google Scholar]
  8. Phurbu D, Liu Z-X, Liu H-C, Pema Y, Yungchen L et al. Undibacterium crateris sp. nov., isolated from water of crater lake. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  9. Li X, Chang X, Zhang Y, Liu Z, Da X et al. Undibacterium arcticum sp. nov., isolated from arctic alpine soil. Int J Syst Evol Microbiol 2016; 66:2797–2802 [View Article] [PubMed]
    [Google Scholar]
  10. Lee S-Y, Kang W, Kim PS, Kim HS, Sung H et al. Undibacterium piscinae sp. nov., isolated from Korean shiner intestine. Int J Syst Evol Microbiol 2019; 69:3148–3154 [View Article] [PubMed]
    [Google Scholar]
  11. Baldani JI, Rouws L, Cruz LM, Olivares FL, Schmid M. The family Oxalobacteraceae. Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds In The Prokaryotes Springer; 2014 pp 919–974
    [Google Scholar]
  12. Lane DJ. 16S/23S rrna sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic acid sequencing techniques in bacterial systematics New York, USA: Wiley; 1991 pp 115–175
    [Google Scholar]
  13. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing Ezbiocloud: A taxonomically united database of 16s rrna and whole genome assemblies. Int J Syst Evol Microbiol 2016; 67:1613–1617
    [Google Scholar]
  14. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Kimura M. The neutral theory of molecular evolution. Sci Am 1979; 241:102–108 [View Article]
    [Google Scholar]
  17. 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]
  18. Kluge AG, Farris JS. Quantitative phyletics and the evolution of Anurans. Systematic Zoology 1969; 18:1 [View Article]
    [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  23. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1–6 [View Article]
    [Google Scholar]
  24. 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]
    [Google Scholar]
  25. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  26. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article]
    [Google Scholar]
  27. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
    [Google Scholar]
  28. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article] [PubMed]
    [Google Scholar]
  29. Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M. New approach for understanding genome variations in KEGG. Nucleic Acids Res 2019; 47:D590–D595 [View Article]
    [Google Scholar]
  30. Zhu XF. Modern Experimental Technique of Microbiology Hangzhou, China: Zhejiang University Press; 2011
    [Google Scholar]
  31. Lu HB, Xing P, Phurbu D, Tang Q, Wu QL. Pelagibacterium montanilacus sp. nov., an alkaliphilic bacterium isolated from Lake Cuochuolong on the Tibetan Plateau. Int J Syst Evol Microbiol 2018; 68:2220–2225 [View Article] [PubMed]
    [Google Scholar]
  32. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic gram-negative rods. J Gen Microbiol 1982; 128:1959–1968 [View Article]
    [Google Scholar]
  33. Zhong Z-P, Liu Y, Wang F, Zhou Y-G, Liu H-C et al. Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:422–429 [View Article] [PubMed]
    [Google Scholar]
  34. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. International Journal of Systematic Bacteriology 1988; 38:358–361 [View Article]
    [Google Scholar]
  35. Sasser M. Identification of bacteria through fatty acid analysis. Klement Z, Rudolph K, Sands DC. eds In Methods in phytobacteriology Budapest, Hungary: Akademiai Kaido; 1990 pp 199–204
    [Google Scholar]
  36. 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. Journal of Microbiological Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  37. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  38. 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 [View Article] [PubMed]
    [Google Scholar]
  39. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the AD Hoc committee on Reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
    [Google Scholar]
  40. Broek AV, Vanderleyden J. The role of bacterial motility, chemotaxis, and attachment in bacteria-plant interactions. Mol Plant-Microbe Interact 1995; 8:800 [View Article]
    [Google Scholar]
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