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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 8

gen. nov., sp. nov., isolated from activated sludge No Access

Abstract

A bacterial strain designated as LB-31 was isolated from activated sludge. Strain LB-31 was Gram-stain-negative, non-spore-forming and rod-shaped with a single polar flagellum. The isolate grew at 15–37 °C, pH 5.5–8.5 and 0.5–8.5 % (w/v) NaCl. Genome sequencing revealed a genome size of 3.55 Mb, a G+C content of 61.1 mol% and 3222 protein-coding genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LB-31 formed a phyletic lineage that was distinct from the three known genus within the family . The 16S rRNA gene sequence similarity of strain LB-31 to all recognized bacterial species was no more than 94 %. Average nucleotide identity and digital DNA–DNA hybridization values between strain LB-31 and its phylogenetic neighbours were below 72 and 22 %, respectively. The average amino acid identity values for strain LB-31 and its closed phylogenetic neighbours and were below 63%, supporting that strain LB-31 was a member of a novel genus. The predominant respiratory quinone is Q-10, the fatty acid profile predominantly consisted of iso-C 9, iso-C, iso-C and summed feature 3 (comprising iso-C2-OH/C 7), and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The combined genotypic and phenotypic data show that strain LB-31 represents a novel species of a novel genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is LB-31 (=GDMCC 1.3625=KCTC 92687).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Pseudokordiimonas caeni and taxonomy
Funding
This study was supported by the:
  • High-qualified Talents Scientific Research Startup Foundation of Nanyang Normal University (Award 2019ZX013)
    • Principle Award Recipient: NaLi
  • Major Scientific and Technological Special Project of Guizhou Province (Award BM2022019)
    • Principle Award Recipient: JianHe
  • Postdoctoral Research Foundation of China (Award 2021M701735)
    • Principle Award Recipient: NaLi
  • National Natural Science Foundation of China (Award 31900082)
    • Principle Award Recipient: NaLi
© 2023 The Authors
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References

  1. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:5056 [View Article]
     [Google Scholar]
  2. Garrity GM, Brenner DJ, Krieg NR, Staley JT. Bergey’s Manual of Systematic Bacteriology. 2nd edn New York: Springer; 2005
     [Google Scholar]
  3. Kersters K, De Vos P, Gillis M, Swings J, Vandamme P et al. Introduction to the Proteobacteria. In the Prokaryotes. A Handbook on the Biology of Bacteria, Part 1 New York, NY: Springer; 2006 pp 3–37 [View Article]
     [Google Scholar]
  4. Paramasivam N, Ben-Dov E, Arotsker L, Kramarsky-Winter E, Zvuloni A et al. Bacterial consortium of Millepora dichotoma exhibiting unusual multifocal lesion event in the Gulf of Eilat, Red Sea. Microb Ecol 2013; 65:50–59 [View Article] [PubMed]
     [Google Scholar]
  5. Kwon KK, Lee HS, Yang SH, Kim SJ. Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the “Alphaproteobacteria.”. Int J Syst Evol Microbiol 2005; 55:2033–2037 [View Article] [PubMed]
     [Google Scholar]
  6. Ju Z, Zhang R, Hou X-J, Han S-B, Li Y et al. Kordiimonas pumila sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2018; 68:1743–1748 [View Article] [PubMed]
     [Google Scholar]
  7. Teramoto M, Nishijima M. Temperatibacter marinus gen. nov., sp. nov., a mesophilic bacterium isolated from surface seawater and description of Temperatibacteraceae fam. nov. in the class Alphaproteobacteria. Int J Syst Evol Microbiol 2014; 64:3075–3080 [View Article] [PubMed]
     [Google Scholar]
  8. Paramasivam N, Ben-Dov E, Arotsker L, Kushmaro A. Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma. Int J Syst Evol Microbiol 2013; 63:1880–1884 [View Article] [PubMed]
     [Google Scholar]
  9. Wu Y-H, Jian S-L, Meng F-X, Tohty D et al. Kordiimonas lipolytica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:2198–2204 [View Article]
     [Google Scholar]
  10. Beveridge TG, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, 3rd edn. American Society of Microbiology; 2007 pp 19–33
     [Google Scholar]
  11. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. eds Methods for General and Molecular Bacteriology vol 3 Washington, DC: American Society for Microbiology Press; 2007 pp 309–329
     [Google Scholar]
  12. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
     [Google Scholar]
  13. Zhang J, Chen S-A, Zheng J-W, Cai S, Hang B-J et al. Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium. Int J Syst Evol Microbiol 2012; 62:495–499 [View Article]
     [Google Scholar]
  14. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Woods WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology Press; 1994 pp 607–654
     [Google Scholar]
  15. Dong XZ, Cai MY. General Bacterial Identification System Handbook Beijing: Scientific Press (in Chinese); 2001 pp 377–385
     [Google Scholar]
  16. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  17. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 663:199–202 [View Article]
     [Google Scholar]
  18. Xie CH, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  22. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1 [View Article]
     [Google Scholar]
  23. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Sambrook J, Russell DW. Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2001
     [Google Scholar]
  28. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaSci 2012; 1:18 [View Article]
     [Google Scholar]
  29. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
     [Google Scholar]
  30. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  31. Liu B, Yang X, Sheng M, Yang Z, Qiu J et al. Sphingobacterium olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2020; 70:1931–1939 [View Article] [PubMed]
     [Google Scholar]
  32. 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; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Hua Z-S, Qu Y-N, Zhu Q, Zhou E-M, Qi Y-L et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018; 9:2832 [View Article] [PubMed]
     [Google Scholar]
  35. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
     [Google Scholar]
  36. Xu X-W, Huo Y-Y, Bai X-D, Wang C-S, Oren A et al. Kordiimonas lacus sp. nov., isolated from a ballast water tank, and emended description of the genus Kordiimonas. Int J Syst Evol Microbiol 2011; 61:422–426 [View Article] [PubMed]
     [Google Scholar]
  37. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
     [Google Scholar]
  38. Yang S-H, Kim M-R, Seo H-S, Lee SH, Lee J-H et al. Description of Kordiimonas aquimaris sp. nov., isolated from seawater, and emended descriptions of the genus Kordiimonas Kwon et al. 2005 emend. Xu et al. 2011 and of its existing species. Int J Syst Evol Microbiol 2013; 63:298–302 [View Article] [PubMed]
     [Google Scholar]
  39. Math RK, Jeong SH, Jin HM, Park MS, Kim JM et al. Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2012; 62:3049–3054 [View Article] [PubMed]
     [Google Scholar]
  40. Zhang HX, Zhao JX, Chen GJ, Du ZJ. Kordiimonas sediminis sp. nov., isolated from a sea cucumber culture pond. Antonie van Leeuwenhoek 2016; 109:705–711 [View Article] [PubMed]
     [Google Scholar]
  41. Lee I, Ouk Kim Y, Park SC, 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]
  42. 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 [View Article] [PubMed]
     [Google Scholar]
  43. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  44. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
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Pseudokordiimonas caeni gen. nov., sp. nov., isolated from activated sludge
Int J Syst Evol Microbiol 73, 006007 (2023); https://doi.org/10.1099/ijsem.0.006007
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