1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 10

sp. nov., isolated from farmland soil Free

Abstract

A novel Gram-stain-positive bacterium, designated djl-8, was isolated from farmland soil in Nanjing, Jiangsu province, PR China. Cells of strain djl-8 were aerobic, non-motile, non-spore-forming and rod-shaped. The organism grew at 25–37 °C, pH 5.5–8.0 and 0.5–4.0 % NaCl (w/v). The DNA G+C content was 69.3 mol%. The diagnostic diamino acid in the cell-wall peptidoglycan was -2, 6-diaminopimelic acid. The major fatty acids (>5 %) were iso-C, anteiso-C, iso-C, 10-Me C and Cω8. The respiratory quinone was MK-8 (H) and the major polar lipids were phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and unknown phospholipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain djl-8 is a member of the genus and shared the highest similarity with SYP-A7303 (97.1 %), followed by mbc-2 (96.9 %), OS4 (96.6 %) and RP-B30 (96.6 %). Strain djl-8 exhibited low DNA–DNA relatedness with SYP-A7303 (26.9±2.1 %). On the basis of the morphological, physiological, biochemical and chemotaxonomic characteristics presented in this study, strain djl-8 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is djl-8 (=KCTC 39844=CCTCC AB 2017058).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): farmland soil , Gram-staining-positive and Nocardioides agrisoli sp. nov.
© 2017 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002158
2017-10-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/10/3722.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002158&mimeType=html&fmt=ahah

References

  1. Prauser H. Nocardioides, a New Genus of the order Actinomycetales . Int J Syst Bacteriol 1976; 26:58–65 [View Article]
     [Google Scholar]
  2. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  3. Lim JM, Kim SJ, Hamada M, Ahn JH, Weon HY et al. Nocardioides daecheongensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:4109–4114 [View Article][PubMed]
     [Google Scholar]
  4. Lee SD, Seong CN. Nocardioides opuntiae sp. nov., isolated from soil of a cactus. Int J Syst Evol Microbiol 2014; 64:2094–2099 [View Article][PubMed]
     [Google Scholar]
  5. Fan X, Qiao Y, Gao X, Zhang XH. Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment. Int J Syst Evol Microbiol 2014; 64:2217–2222 [View Article][PubMed]
     [Google Scholar]
  6. Lee SD, Lee DW. Nocardioides rubroscoriae sp. nov., isolated from volcanic ash. Antonie van Leeuwenhoek 2014; 105:1017–1023 [View Article][PubMed]
     [Google Scholar]
  7. Sun LN, Zhang J, Gong FF, Wang X, Hu G et al. Nocardioides soli sp. nov., a carbendazim-degrading bacterium isolated from soil under the long-term application of carbendazim. Int J Syst Evol Microbiol 2014; 64:2047–2052 [View Article][PubMed]
     [Google Scholar]
  8. Glaeser SP, Mcinroy JA, Busse HJ, Kämpfer P. Nocardioides zeae sp. nov., isolated from the stem of Zea mays. Int J Syst Evol Microbiol 2014; 64:2491–2496 [View Article][PubMed]
     [Google Scholar]
  9. Srinivasan S, Lee SS, Lee JJ, Kim MK. Nocardioides soli sp. nov., a bacterium isolated from a mountain soil. Antonie van Leeuwenhoek 2014; 106:271–278 [View Article][PubMed]
     [Google Scholar]
  10. Deng S, Chang X, Zhang Y, Ren L, Jiang F et al. Nocardioides antarcticus sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2015; 65:2615–2621 [View Article][PubMed]
     [Google Scholar]
  11. Tuo L, Dong YP, Habden X, Liu JM, Guo L et al. Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2015; 65:1604–1610 [View Article][PubMed]
     [Google Scholar]
  12. Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH et al. Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla). Int J Syst Evol Microbiol 2015; 65:1953–1958 [View Article][PubMed]
     [Google Scholar]
  13. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Nocardioides glacieisoli sp. nov., isolated from a glacier. Int J Syst Evol Microbiol 2015; 65:4845–4849 [View Article][PubMed]
     [Google Scholar]
  14. Sultanpuram VR, Mothe T, Mohammed F. Nocardioides solisilvae sp. nov., isolated from a forest soil. Antonie van Leeuwenhoek 2015; 107:1599–1606 [View Article][PubMed]
     [Google Scholar]
  15. Zhao Y, Liu Q, Kang MS, Jin F, Yu H et al. Nocardioides ungokensis sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2015; 65:4857–4862 [View Article][PubMed]
     [Google Scholar]
  16. Singh H, Du J, Trinh H, Won K, Yang JE et al. Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil. Int J Syst Evol Microbiol 2016; 66:371–378 [View Article][PubMed]
     [Google Scholar]
  17. Xu H, Zhang S, Cheng J, Asem MD, Zhang MY et al. Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L. Int J Syst Evol Microbiol 2016; 66:2013–2018 [View Article][PubMed]
     [Google Scholar]
  18. Wang L, Li J, Zhang G. Nocardioides rotundus sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2016; 66:1932–1936 [View Article][PubMed]
     [Google Scholar]
  19. Kämpfer P, Glaeser SP, Mcinroy JA, Busse HJ. Nocardioides zeicaulis sp. nov., an endophyte actinobacterium of maize. Int J Syst Evol Microbiol 2016; 66:1869–1874 [View Article][PubMed]
     [Google Scholar]
  20. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Short Protocols in Molecular Biology: a Compendium of Methods from Current Protocols in Molecular Biology, 3rd ed. New York: Wiley; 1995
     [Google Scholar]
  21. Lane DL. 16S/23S rRNA sequencing. In Stackebrandt ER, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, United Kingdom: Wiley; 1991 pp. 115–175
     [Google Scholar]
  22. Kim OS, Cho YJ, Lee K, Yoon SH, 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder RL. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 19–33
     [Google Scholar]
  30. Suzuki M, Nakagawa Y, Harayama S, Yamamoto S. Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov. with Tenacibaculum maritimum comb. nov. and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol 2001; 51:1639–1652 [View Article][PubMed]
     [Google Scholar]
  31. Ebersole LL. Acid-fast stain procedures. In Isenberg HD. (editor) Clinical Microbiology Procedures Handbook Washington, DC: American Society for Microbiology; 1992 pp. 3.5.1–3.5.3
     [Google Scholar]
  32. Breznak JA, Costilow RN. Physicochemical factors in growth. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 137–154
     [Google Scholar]
  33. Zhang H, Cheng MG, Sun B, Guo SH, Song M et al. Flavobacterium suzhouense sp. nov., isolated from farmland river sludge. Int J Syst Evol Microbiol 2015; 65:370–374 [View Article][PubMed]
     [Google Scholar]
  34. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  35. 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]
  36. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  37. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article][PubMed]
     [Google Scholar]
  38. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [Crossref]
     [Google Scholar]
  39. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newslett 1990; 20:1–6
     [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. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][PubMed]
     [Google Scholar]
  42. 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]
  43. Yoon JH, Kang SJ, Park S, Kim W, Oh TK. Nocardioides caeni sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 2009; 59:2794–2797 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002158
Loading
Nocardioides agrisoli sp. nov., isolated from farmland soil
Int J Syst Evol Microbiol 67, 3722 (2017); https://doi.org/10.1099/ijsem.0.002158
/content/journal/ijsem/10.1099/ijsem.0.002158
/content/journal/ijsem/10.1099/ijsem.0.002158
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