1887

Abstract

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-71, was isolated from the soil of a rice field. The colonies were observed to be milky yellow-coloured, smooth, spherical and 0.1–0.4 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-71 was found to be able to grow at 15–37 °C, pH 5.0–10.0 and with 0–3.0 % NaCl (w/v). The strain was found to be positive for the catalase test, but negative for the oxidase test. The strain was positive for hydrolysis of aesculin and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus and to be closely related to MAH-6 (98.5 % sequence similarity), B2-7 (98.4 %) and SY-6 (96.6 %). Strain MAHUQ-71 has a draft genome size of 4 255 278 bp (10 contigs), annotated with 4098 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain MAHUQ-71 and the closest type strain MAH-6 were in the range of 85.6 and 30.6 %, respectively. The genomic DNA G+C content was determined to be 66.7 mol%. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as summed feature 8 (C 7 and/or C 6), C and C 2OH. The main polar lipids were phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and sphingoglycolipid. On the basis of dDDH and ANI values, as well as the results of genotypic, chemotaxonomic and physiological analyses, strain MAHUQ-71 represents a novel species within the genus , for which the name sp. nov. is proposed, with MAHUQ-71 (=KACC 22252=CGMCC 1.19065) as the type strain.

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2023-09-27
2024-12-12
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References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990; 34:99–119 [View Article] [PubMed]
    [Google Scholar]
  2. Luo Y-R, Tian Y, Huang X, Kwon K, Yang S-H et al. Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample. Int J Syst Evol Microbiol 2012; 62:1223–1227 [View Article] [PubMed]
    [Google Scholar]
  3. Han S-I, Lee J-C, Ohta H, Whang K-S. Sphingomonas oligoaromativorans sp. nov., an oligotrophic bacterium isolated from a forest soil. Int J Syst Evol Microbiol 2014; 64:1679–1684 [View Article] [PubMed]
    [Google Scholar]
  4. Liu Y, Yao S, Lee Y-J, Cao Y, Zhai L et al. Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch. Int J Syst Evol Microbiol 2015; 65:2817–2823 [View Article] [PubMed]
    [Google Scholar]
  5. Akter S, Huq MA. Sphingomonas chungangi sp. nov., a bacterium isolated from garden soil sample. Int J Syst Evol Microbiol 2020; 70:4151–4157 [View Article] [PubMed]
    [Google Scholar]
  6. Akter S, Lee S-Y, Moon S-K, Choi C, Balusamy SR et al. Sphingomonas horti sp. nov., a novel bacterial species isolated from soil of a tomato garden. Arch Microbiol 2021; 203:543–548 [View Article] [PubMed]
    [Google Scholar]
  7. Kim S-J, Moon J-Y, Lim J-M, Ahn J-H, Weon H-Y et al. Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively. Int J Syst Evol Microbiol 2014; 64:926–932 [View Article] [PubMed]
    [Google Scholar]
  8. Chen H, Jogler M, Rohde M, Klenk H-P, Busse H-J et al. Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov. Int J Syst Evol Microbiol 2013; 63:735–743 [View Article] [PubMed]
    [Google Scholar]
  9. Holmes B, Owen RJ, Evans A, Malnick H, Willcox WR. Pseudomonas paucimobilis, a new species isolated from human clinical specimens, the hospital environment, and other sources. Int J Syst Bacteriol 1977; 27:133–146 [View Article]
    [Google Scholar]
  10. Takeuchi M, Sakane T, Yanagi M, Yamasato K, Hamana K et al. Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int J Syst Bacteriol 1995; 45:334–341 [View Article] [PubMed]
    [Google Scholar]
  11. Kim H, Nishiyama M, Kunito T, Senoo K, Kawahara K et al. High population of Sphingomonas species on plant surface. J Appl Microbiol 1998; 85:731–736 [View Article]
    [Google Scholar]
  12. Chung EJ, Jo EJ, Yoon HS, Song GC, Jeon CO et al. Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2011; 61:2389–2394 [View Article] [PubMed]
    [Google Scholar]
  13. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematic New York: Wiley; 1991 pp 115–175
    [Google Scholar]
  14. 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]
  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. Hall TA. Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  17. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [View Article]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 1987; 4:406–425
    [Google Scholar]
  19. 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]
  20. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Yoon SH, Ha SM, Lim JM, Kwon SJ, 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]
  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. Shi W, Sun Q, Fan G, Hideaki S, Moriya O et al. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694–D705 [View Article] [PubMed]
    [Google Scholar]
  25. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article] [PubMed]
    [Google Scholar]
  26. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. 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]
  27. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849 [View Article]
    [Google Scholar]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  29. Huq MA. Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden. Arch Microbiol 2017; 200:581–587 [View Article] [PubMed]
    [Google Scholar]
  30. Cappuccino JG, Sherman N. Biochemical Activities of Microorganisms. In Microbiology, A Laboratory Manual Menlo Park, CA: The Benjamin/Cummings Publishing Co., Inc; 1992 pp 188–247
    [Google Scholar]
  31. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
    [Google Scholar]
  32. Huq MA. Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden. Arch Microbiol 2018; 200:343–348 [View Article] [PubMed]
    [Google Scholar]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc: 1990
    [Google Scholar]
  34. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  35. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
    [Google Scholar]
  36. Huq MdA, Lee S-Y, Moon B, Choi C, Moon S-K et al. Solitalea agri sp. nov., a new member of the genus Solitalea isolated from rhizospheric soil of a jujube tree. Int J Syst Evol Microbiol 2023; 73:005858 [View Article]
    [Google Scholar]
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