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Abstract

A Gram-stain-negative bacterium, designated as YN2, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2 were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2 grew at 10–40 °C (optimum, 30 °C), pH 5.0–8.0 (pH 7.0) and with 0–1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2 belongs to the genus and shares the highest pairwise identity with 7c (98.6 %) and 301 (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C, C cyclo 8 and C ω7 as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA–DNA hybridization estimate values between strain YN2 and 7c, 301 and TagT2C (the only three species of with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YN2 (=CGMCC 1.19031=JCM 34666).

Funding
This study was supported by the:
  • Heilongjiang Provincial Science and Technology Department (Award GY2020YF0018)
    • Principle Award Recipient: FangMa
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/content/journal/ijsem/10.1099/ijsem.0.005139
2021-12-09
2024-04-19
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References

  1. Wiegel J, Wilke D, Baumgarten J, Opitz R, Schlegel HG. Transfer of the nitrogen-fixing hydrogen bacterium Corynebacterium autotrophicum Baumgarten et al. to Xanthobacter gen. nov. Int J Syst Bacteriol 1978; 28:573–581 [View Article]
    [Google Scholar]
  2. Malik KA, Claus D. Xanthobacter flavus, a new species of nitrogen-fixing hydrogen bacteria. Int J Syst Bacteriol 1979; 29:283–287 [View Article]
    [Google Scholar]
  3. Jenni B, Aragno M. Xanthobacter agilis sp. nov., a motile, dinitrogen-fixing, hydrogen-oxidizing bacterium. Syst Appl Microbiol 1987; 9:254–257 [View Article]
    [Google Scholar]
  4. Padden AN, Rainey FA, Kelly DP, Wood AP. Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes. Int J Syst Bacteriol 1997; 47:394–401 [View Article]
    [Google Scholar]
  5. Doronina NV, Trotsenko YA. Reclassification of “Blastobacter viscosus” 7d and “Blastobacter aminooxidans” 14a as Xanthobacter viscosus sp. nov. and Xanthobacter aminoxidans sp. nov. Int J Syst Evol Microbiol 2003; 53:179–182 [View Article] [PubMed]
    [Google Scholar]
  6. Hirano S, Kitauchi F, Haruki M, Imanaka T, Morikawa M et al. Isolation and characterization of Xanthobacter polyaromaticivorans sp. nov. 127W that degrades polycyclic and heterocyclic aromatic compounds under extremely low oxygen conditions. Biosci Biotechnol Biochem 2014; 68:557–564 [View Article]
    [Google Scholar]
  7. Doronina N, Trotsenko YA, Krauzova V, Suzina N. New methylotrophic isolates of the genus Xanthobacter. Microbiology 1996; 65:217–224
    [Google Scholar]
  8. Zaichikova MV, Berestovskaya YuYu, Akimov VN, Kizilova AK, Vasilieva LV et al. Xanthobacter xylophilus sp. nov., a member of the xylotrophic mycobacterial community of low-mineral oligotrophic waters. Microbiology 2010; 79:83–88 [View Article]
    [Google Scholar]
  9. Wiegel J. The genus Xanthobacter. The Prokaryotes: Volume 5: Proteobacteria. Alpha and Beta Subclasses 2006290–314 [View Article]
    [Google Scholar]
  10. Ma F, Wang Y, Yang J, Guo H, Su D et al. Degradation of 1,4-dioxane by Xanthobacter sp. YN2. Curr Microbiol 2021; 78:992–1005 [View Article] [PubMed]
    [Google Scholar]
  11. Parales RE, Adamus JE, White N, May HD. Degradation of 1,4-dioxane by an actinomycete in pure culture. Appl Environ Microbiol 1994; 60:4527–4530 [View Article] [PubMed]
    [Google Scholar]
  12. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
    [Google Scholar]
  13. Slobodkina GB, Panteleeva AN, Kostrikina NA, Kopitsyn DS, Bonch-Osmolovskaya EA et al. Tepidibacillus fermentans gen. nov., sp. nov.: a moderately thermophilic anaerobic and microaerophilic bacterium from an underground gas storage. Extremophiles 2013; 17:833–839 [View Article] [PubMed]
    [Google Scholar]
  14. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
    [Google Scholar]
  15. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
    [Google Scholar]
  16. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  17. Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ et al. Domain enhanced lookup time accelerated BLAST. Biol Direct 2012; 7:12. [View Article] [PubMed]
    [Google Scholar]
  18. 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 [View Article]
    [Google Scholar]
  19. 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]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology 1971; 20:406–416 [View Article]
    [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. 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]
  23. Jin XJ, Chen DZ, Zhu RY, Chen J, Chen JM. Characteristics of 1,4-dioxane degradation by Xanthobacter flavus DT8. Environ Sci 2012; 33:1657–1662
    [Google Scholar]
  24. 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]
  25. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M et al. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  26. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  27. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  28. Yoon S-H, Ha S, 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]
    [Google Scholar]
  29. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238. [View Article] [PubMed]
    [Google Scholar]
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  31. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
    [Google Scholar]
  32. Loginova NV, Iua T. Blastobacter viscosus, a new species of methanol-utilizing autotrophic bacteria. Microbiology 1980; 48:644–651
    [Google Scholar]
  33. Jenni B, Aragno M, Wiegel JKW. Numerical analysis and DNA-DNA hybridization studies on Xanthobacter and emendation of Xanthobacter flavus. Syst Appl Microbiol 1987; 9:247–253 [View Article]
    [Google Scholar]
  34. Doronina N, Govorukhina N, Trotsenko YA. Blastobacter aminooxidans, a new species of bacteria growing autotrophically on methylated amines. Microbiology 1983; 52:547–553
    [Google Scholar]
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