1887

Abstract

Two yellow-pigmented, non-motile, Gram-stain-negative, and rod-shaped bacteria, designated TW-4 and TNP-2 were obtained from oil-contaminated soil. Both strains degrade diesel oil, hydrolyse aesculin, DNA, Tween 40 and Tween 60. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain TW-4 formed a lineage within the family and clustered as members of the genus . The closest members of strain TW-4 were DSM 12447 (97.9 %, sequence similarity), KSS165-70 (97.8 %), T3-B9 (97.8 %), DSM 12444 (97.7 %), UCT-28 (97.7 %), and STM-24 (97.6 %). The sequence similarity for other members was ≤97.6 %. The genome of strain TW-4 was 4 683 467 bp long with 44 scaffolds and 4280 protein-coding genes. The sole respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (C 7 and/or C 6), summed feature 3 (C 7 and/or C 6), C and C 2-OH. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidyl--methylethanolamine (PME) and sphingoglycolipid (SGL). The DNA G+C content of the type strain was 65.0 %. The average nucleotide identity (ANIu) and DNA–DNA hybridization (dDDH) relatedness values between strain TW-4 and closest members were below the threshold value for species delineation. Based on polyphasic taxonomic analyses, strain TW-4 represents novel species in the genus , for which the name sp. nov. is proposed. The type strain is TW-4 (=KACC 21628=NBRC 114364) and strain TNP-2 (=KACC 21629=NBRC 114365) represents an additional strain. Based on new data obtained in this study, it is also proposed to reclassify as a later heterotypic synonym of .

Funding
This study was supported by the:
  • National Research Foundation (KR) (Award 2019R1F1A1058501)
    • Principle Award Recipient: JaisooKim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004628
2021-01-07
2024-11-12
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/2/ijsem004628.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004628&mimeType=html&fmt=ahah

References

  1. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article][PubMed]
    [Google Scholar]
  2. 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]
  3. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3170–3176 [View Article][PubMed]
    [Google Scholar]
  4. Sheu SY, Chen ZH, Chen WM. Novosphingobium piscinae sp. nov., isolated from a fish culture pond. Int J Syst Evol Microbiol 2016; 66:1539–1545 [View Article][PubMed]
    [Google Scholar]
  5. Nguyen TM, Myung SW, Jang H, Kim J. Description of Novosphingobium flavum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:3642–3650 [View Article][PubMed]
    [Google Scholar]
  6. Sheu SY, Liu LP, Chen WM. Novosphingobium bradum sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2016; 66:5083–5090 [View Article][PubMed]
    [Google Scholar]
  7. Xie F, Quan S, Liu D, He W, Wang Y et al. Novosphingobium kunmingense sp. nov., isolated from a phosphate mine. Int J Syst Evol Microbiol 2014; 64:2324–2329 [View Article][PubMed]
    [Google Scholar]
  8. Liu ZP, Wang BJ, Liu YH, Liu SJ. Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 2005; 55:1229–1232 [View Article][PubMed]
    [Google Scholar]
  9. Kämpfer P, Busse HJ, Glaeser SP. Novosphingobium lubricantis sp. nov., isolated from a coolant lubricant emulsion. Int J Syst Evol Microbiol 2018; 68:1560–1564 [View Article][PubMed]
    [Google Scholar]
  10. Gupta SK, Lal D, Lal R. Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59:156–161 [View Article][PubMed]
    [Google Scholar]
  11. Dahal RH, Kim J. Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil. Arch Microbiol 2018; 200:1067–1074 [View Article][PubMed]
    [Google Scholar]
  12. Dahal RH, Chaudhary DK, Kim J. Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968. Int J Syst Evol Microbiol 2018; 68:1955–1962 [View Article][PubMed]
    [Google Scholar]
  13. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  14. Yoon SH, 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][PubMed]
    [Google Scholar]
  15. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [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. Doetsch RN et al. Determinative methods of light microscopy. In Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. (editors) Manual of Methods for General Bacteriology Washington, DC. USA: American Society for Microbiology; 1981 pp 21–33
    [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  19. Dahal RH, Kim J. Flavobacterium ureilyticum sp. nov., a novel urea hydrolysing bacterium isolated from stream bank soil. Antonie van Leeuwenhoek 2018; 111:2131–2139 [View Article][PubMed]
    [Google Scholar]
  20. Chaudhary DK, Bajagain R, Jeong S-W, Kim J. Biodegradation of diesel oil and n-alkanes (C18, C20, and C22) by a novel strain Acinetobacter sp. K-6 in unsaturated soil. Environ Eng Res 2020; 25:290–298
    [Google Scholar]
  21. Sasser M. Bacterial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME); 1990
  22. 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. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  23. Komagata K, Suzuki KI. 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  24. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article][PubMed]
    [Google Scholar]
  27. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H, S-M H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. 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]
  30. 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][PubMed]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  32. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  33. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002; 4:770–773 [View Article][PubMed]
    [Google Scholar]
  34. 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; 56:281–285 [View Article][PubMed]
    [Google Scholar]
  35. Nie Y, Chi C-Q, Fang H, Liang J-L, Lu S-L et al. Diverse alkane hydroxylase genes in microorganisms and environments. Sci Rep 2014; 4:4968 [View Article][PubMed]
    [Google Scholar]
  36. 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]
  37. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  38. Balkwill DL, Drake GR, Reeves RH, Fredrickson JK, White DC et al. Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int J Syst Bacteriol 1997; 47:191–201 [View Article][PubMed]
    [Google Scholar]
  39. Editor L. Notification that new names and new combinations have appeared in volume 51, part 4, of the IJSEM. Int J Syst Evol Microbiol 2001; 51:1621–1623 [View Article][PubMed]
    [Google Scholar]
  40. Parker CT, Tindall BJ, Garrity GM. International code of nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article][PubMed]
    [Google Scholar]
  41. Kämpfer P, Witzenberger R, Denner EBM, Busse H-J, Neef A. Novosphingobium hassiacum sp. nov., a new species isolated from an aerated sewage pond. Syst Appl Microbiol 2002; 25:37–45 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004628
Loading
/content/journal/ijsem/10.1099/ijsem.0.004628
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error