Acidovorax monticola sp. nov., isolated from soil

Original Paper

Abstract

A novel strain K-4-16T was isolated from forest soil of Namsan Mountain, Seoul, South Korea, and was taxonomically characterized by a polyphasic approach. Strain K-4-16T was observed to be a Gram-staining negative, grayish white-coloured, motile with peritrichous flagella, and rod shaped bacterium. It was able to grow at 15–45 °C, at pH 4.5–10.5, and at 0–4% (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strain K-4-16T belongs to the genus Acidovorax and is closely related to Acidovorax anthurii CFBP 3232T (98.3% sequence identity), Acidovorax konjaci K2T (97.9% sequence identity), Acidovorax valerianellae CFBP 4730T (97.8% sequence identity), and Acidovorax caeni R-24608T (97.8% sequence identity). The only respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The predominant fatty acids of strain K-4-16T were summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0, and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The genomic DNA G+C content of this novel strain was 64.7 mol%. The DNA–DNA relatedness between strain K-4-16T and its reference strains were below the threshold value of 70%. The morphological, physiological, chemotaxonomic, and phylogenetic analyses clearly distinguished this strain from its close phylogenetic neighbors. Thus, strain K-4-16T represents a novel species of the genus Acidovorax, for which the name Acidovorax monticola sp. nov. is proposed. The type strain is K-4-16T (= KEMB 9005-570T = KACC 19171T = NBRC 113141T).

Keywords

Acidovorax monticola Mountain soi Comamonadaceae Proteobacteria Novel species 

Notes

Acknowledgements

This work was supported by a Kyonggi University Research Grant (2017-011).

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Ethical approval

This study does not describe any experimental work related to humans.

Supplementary material

10482_2018_1083_MOESM1_ESM.docx (243 kb)
Supplementary material 1 (DOCX 242 kb)

References

  1. Beveridge TJ, Lawrence JR, Murray RGE (2007) Sampling and staining for light microscopy. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology, 3rd edn. American Society for Microbiology, Washington, DC, pp 19–33Google Scholar
  2. Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology, 3rd edn. American Society for Microbiology, Washington, DC, pp 309–329Google Scholar
  3. Chaudhary DK, Kim J (2016) Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 66:3170–3176CrossRefPubMedGoogle Scholar
  4. Chaudhary DK, Kim J (2017) Chryseobacterium nepalense sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 67:646–652CrossRefPubMedGoogle Scholar
  5. Choi JH, Kim MS, Roh SW, Bae JW (2010) Acidovorax soli sp. nov., isolated from landfill soil. Int J Syst Evol Microbiol 60:2715–2718CrossRefPubMedGoogle Scholar
  6. Chun SJ, Cui Y, Ko SR, Lee HG, Srivastava A, Oh HM, Ahn CY (2017) Acidovorax lacteus sp. nov., isolated from a culture of a bloom-forming cyanobacterium (Microcystis sp.). Antonie Van Leeuwenhoek.  https://doi.org/10.1007/s10482-017-0892-9 Google Scholar
  7. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354PubMedPubMedCentralGoogle Scholar
  8. Ezaki T, Hashimoto Y, Yabuuchi E (1989) 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 39:224–229CrossRefGoogle Scholar
  9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefPubMedGoogle Scholar
  11. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  12. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA gene. Appl Environ Microbiol 74:2461–2470CrossRefPubMedPubMedCentralGoogle Scholar
  13. Gardan L, Dauga C, Prior P, Gillis M, Saddler GS (2000) Acidovorax anthurii sp. nov., a new phytopathogenic bacterium which causes bacterial leaf-spot of anthurium. Int J Syst Evol Microbiol 50:235–246CrossRefPubMedGoogle Scholar
  14. Gardan L, Stead DE, Dauga C, Gillis M (2003) Acidovorax valerianellae sp. nov., a novel pathogen of lamb’s lettuce [valerianella locusta (L.) Latterr.]. Int J Syst Evol Microbiol 53:795–800CrossRefPubMedGoogle Scholar
  15. Hairaishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469CrossRefGoogle Scholar
  16. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  17. Hemraj V, Diksha S, Avneet G (2013) A review on commonly used biochemical test for bacteria. Innovare J Life Sci 1:1–7Google Scholar
  18. Heylen K, Liesbeth L, Vos PD (2008) Acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge. Int J Syst Evol Microbiol 58:73–77CrossRefPubMedGoogle Scholar
  19. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  20. Komagata K, Suzuki K (1987) Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–203CrossRefGoogle Scholar
  21. Li D, Rothballer M, Schmid M, Esperschütz J, Hartmann A (2011) Acidovorax radicis sp. nov., a wheat-root colonizing bacterium. Int J Syst Evol Microbiol 61:2589–2594CrossRefPubMedGoogle Scholar
  22. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218CrossRefGoogle Scholar
  23. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  24. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  25. Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining Gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758PubMedPubMedCentralGoogle Scholar
  26. Rossi-Tamisier M, Benamar S, Raoult D, Fournier PE (2015) Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species. Int J Syst Evol Microbiol 65:1929–1934CrossRefPubMedGoogle Scholar
  27. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  28. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., NewarkGoogle Scholar
  29. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654Google Scholar
  30. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  31. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  32. Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology, 3rd edn. American Society for Microbiology, Washington, DC, pp 330–393Google Scholar
  33. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  34. Willems A, Falsen E, Pot B, Jantzen E, Hoste B, Vandamme P, Gillis M, Kersters K, De Ley J (1990) Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int J Syst Evol Microbiol 40:384–398Google Scholar
  35. Willems A, Goor M, Thielemans S, Gillis M, Kersters K, De Ley J (1992) Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci. Int J Syst Evol Microbiol 42:107–119Google Scholar
  36. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R (2008) The All-Species Living Tree project: a 16S rRNA based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250CrossRefPubMedGoogle Scholar
  37. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Life Science, College of Natural SciencesKyonggi UniversitySuwonSouth Korea

Personalised recommendations