1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 8

sp. nov., isolated from reclaimed grassland soil Free

Abstract

A light yellow-coloured, Gram-stain-negative, motile and rod-shaped bacterium, designated strain K-3-1, was isolated from reclaimed grassland soils of Belbari, Morang, Nepal. It was able to grow at 4–45 °C, at pH 5.0–10.0, and at 0–2 % (w/v) NaCl concentrations. This strain was taxonomically characterized by a polyphasic approach. Based on the 16S rRNA gene sequence analysis, strain K-3-1 belongs to the genus and is closely related to CCUG 58010 (98.3 % sequence similarity), TS3 (98.1 % sequence similarity), TSA1 (98.1 % sequence similarity), Y1243-1 (98.1 % sequence similarity), CCUG 38318 (98.0 % sequence similarity), CCUG 35299 (97.9 % sequence similarity), 5516 S-1 (97.6 % sequence similarity) and YIM 31775 (97.5 % sequence similarity). The predominant respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids of strain K-3-1 were summed feature 3 (Cω7 and/or Cω6), C, C, C 3-OH and summed feature 8 (Cω7 and/or Cω6). The genomic DNA G+C content of this novel strain was 66.8 mol%. The DNA–DNA relatedness between strain K-3-1 and its closest reference strains were significantly lower than the threshold value of 70 %. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-3-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is K-3-1 (=KEMB 9005-446=KACC 19000=JCM 31661).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Massilia agri sp. nov. , Oxalobacteraceae , Proteobacteria and reclaimed grassland soil
© 2017 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002002
2017-08-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/8/2696.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002002&mimeType=html&fmt=ahah

References

  1. La Scola B, Birtles RJ, Mallet MN, Raoult D. Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 1998; 36:2847–2852[PubMed]
     [Google Scholar]
  2. Shen L, Liu Y, Wang N, Yao T, Jiao N et al. Massilia yuzhufengensis sp. nov., isolated from an ice core. Int J Syst Evol Microbiol 2013; 63:1285–1290 [View Article][PubMed]
     [Google Scholar]
  3. Weon HY, Kim BY, Son JA, Jang HB, Hong SK et al. Massilia aerilata sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 2008; 58:1422–1425 [View Article][PubMed]
     [Google Scholar]
  4. Du Y, Yu X, Wang G. Massilia tieshanensis sp. nov., isolated from mining soil. Int J Syst Evol Microbiol 2012; 62:2356–2362 [View Article][PubMed]
     [Google Scholar]
  5. Gallego V, Sánchez-Porro C, García MT, Ventosa A. Massilia aurea sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2006; 56:2449–2453 [View Article][PubMed]
     [Google Scholar]
  6. Weon HY, Kim BY, Hong SB, Jeon YA, Koo BS et al. Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples. Int J Syst Evol Microbiol 2009; 59:1656–1660 [View Article][PubMed]
     [Google Scholar]
  7. Kämpfer P, Lodders N, Martin K, Falsen E. Massilia oculi sp. nov., isolated from a human clinical specimen. Int J Syst Evol Microbiol 2012; 62:364–369 [View Article][PubMed]
     [Google Scholar]
  8. Feng GD, Yang SZ, Li HP, Zhu HH. Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing. Int J Syst Evol Microbiol 2016; 66:50–55 [View Article][PubMed]
     [Google Scholar]
  9. Rodríguez-Díaz M, Cerrone F, Sánchez-Peinado M, Santacruz-Calvo L, Pozo C et al. Massilia umbonata sp. nov., able to accumulate poly-β-hydroxybutyrate, isolated from a sewage sludge compost-soil microcosm. Int J Syst Evol Microbiol 2014; 64:131–137 [View Article][PubMed]
     [Google Scholar]
  10. Kämpfer P, Falsen E, Busse HJ. Naxibacter varians sp. nov. and Naxibacter haematophilus sp. nov., and emended description of the genus Naxibacter. Int J Syst Evol Microbiol 2008; 58:1680–1684 [View Article][PubMed]
     [Google Scholar]
  11. 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]
  12. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218, IN1 [View Article]
     [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 SM, 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: [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. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  20. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  23. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article][PubMed]
     [Google Scholar]
  24. 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 Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  25. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. (editor) Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp. 21–33
     [Google Scholar]
  26. Powers EM. Efficacy of the ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758[PubMed]
     [Google Scholar]
  27. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
     [Google Scholar]
  28. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, D. C: American Society for Microbiology; 2007 pp. 309–329
     [Google Scholar]
  29. Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA et al. Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 2014; 64:594–598 [View Article][PubMed]
     [Google Scholar]
  30. Hemraj V, Diksha S, Avneet G. A review on commonly used biochemical test for bacteria. Innovare J Life Sci 2013; 1:1–7
     [Google Scholar]
  31. Chaudhary DK, Kim J. Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:4621–4627 [View Article][PubMed]
     [Google Scholar]
  32. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
     [Google Scholar]
  33. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  34. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  35. 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]
  36. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [CrossRef]
     [Google Scholar]
  37. 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]
  38. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354[PubMed]
     [Google Scholar]
  39. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI Inc; 1990. MIDI Technical Note 101
    [Google Scholar]
  40. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
  41. 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]
  42. Kämpfer P, Lodders N, Martin K, Falsen E. Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. Int J Syst Evol Microbiol 2011; 61:1528–1533 [View Article][PubMed]
     [Google Scholar]
  43. Kim J. Massilia kyonggiensis sp. nov., isolated from forest soil in Korea. J Microbiol 2014; 52:378–383 [View Article][PubMed]
     [Google Scholar]
  44. 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]
  45. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002002
Loading
Massilia agri sp. nov., isolated from reclaimed grassland soil
Int J Syst Evol Microbiol 67, 2696 (2017); https://doi.org/10.1099/ijsem.0.002002
/content/journal/ijsem/10.1099/ijsem.0.002002
/content/journal/ijsem/10.1099/ijsem.0.002002
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

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