1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 1

sp. nov., isolated from farmland soil Free

Abstract

A bacterial strain designated YYJ7-1 was isolated from farmland soil in China and characterized using a polyphasic taxonomic approach. Cells of strain YYJ7-1 were Gram-staining-positive, aerobic or facultatively anaerobic, rod-shaped, motile and endospore-forming. Growth occurred at 18–42 °C (optimum at 35 °C), at pH 6.0–8.0 (optimum at pH 7.5) and with 0.0–4.0 % NaCl (optimum with 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus and showed high levels of sequence similarity with respect to 4401170 (98.6 %) and 5402403 (98.4 %), while lower 16S rRNA gene sequence similarities were observed with all other type strains (97.0 %). However, strain YYJ7-1 showed low DNA–DNA relatedness with 4401170 48.7±4.5 % (43.6±7.1 % in a reciprocal experiment), and 5402403 38.9±5.7 % (35.6±6.8 %). The major cellular fatty acids (>10.0 %) of strain YYJ7-1 were anteiso-C, iso-C and anteiso-C. The polar lipid profile consisted of phospholipids, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major isoprenoid quinone was MK-7. The DNA G+C content was 39.4 mol%. Based on these results, it is concluded that strain YYJ7-1 represents a novel species of the genus , for which the name sp. nov. is proposed, with YYJ7-1 (=ACCC 19965=KCTC 33849) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): farmland soil and Paenibacillus shunpengii sp. nov.
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002484
2018-01-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/1/211.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002484&mimeType=html&fmt=ahah

References

  1. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus . Antonie van Leeuwenhoek 1993; 64:253–260[PubMed] [Crossref]
     [Google Scholar]
  2. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus . Int J Syst Bacteriol 1997; 47:289–298 [View Article][PubMed]
     [Google Scholar]
  3. Huang XF, Wang FZ, Zhang W, Li J, Ling J et al. Paenibacillus abyssi sp. nov., isolated from an abyssal sediment sample from the Indian Ocean. Antonie van Leeuwenhoek 2014; 106:1089–1095 [View Article][PubMed]
     [Google Scholar]
  4. Dsouza M, Taylor MW, Ryan J, MacKenzie A, Lagutin K et al. Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil. Int J Syst Evol Microbiol 2014; 64:1406–1411 [View Article][PubMed]
     [Google Scholar]
  5. Zhu J, Wang W, Li SH, Song SQ, Xie YQ et al. Paenibacillus wulumuqiensis sp. nov. and Paenibacillus dauci sp. nov., two novel species of the genus Paenibacillus . Arch Microbiol 2015; 197:489–495 [View Article][PubMed]
     [Google Scholar]
  6. Roux V, Fenner L, Raoult D. Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine. Int J Syst Evol Microbiol 2008; 58:682–687 [View Article][PubMed]
     [Google Scholar]
  7. Guo GN, Zhou X, Chen ZL, Yang ZW, Li XD et al. Paenibacillus marchantiophytorum sp. nov., isolated from the liverwort Herbertus sendtneri . Int J Syst Evol Microbiol 2016; 66:755–761 [View Article][PubMed]
     [Google Scholar]
  8. Lim JM, Jeon CO, Park DJ, Xu LH, Jiang CL et al. Paenibacillus xinjiangensis sp. nov., isolated from Xinjiang province in China. Int J Syst Evol Microbiol 2006; 56:2579–2582 [View Article][PubMed]
     [Google Scholar]
  9. Zhou Y, Gao S, Wei DQ, Yang LL, Huang X et al. Paenibacillus thermophilus sp. nov., a novel bacterium isolated from a sediment of hot spring in Fujian province, China. Antonie van Leeuwenhoek 2012; 102:601–609 [View Article][PubMed]
     [Google Scholar]
  10. Zhang J, Ma XT, Gao JS, Zhang CW, Zhao JJ et al. Paenibacillus oryzisoli sp. nov., isolated from the rhizosphere of rice. Antonie Van Leeuwenhoek 2017; 110:69–75 [View Article][PubMed]
     [Google Scholar]
  11. Wang L, Baek SH, Cui Y, Lee HG, Lee ST. Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2012; 62:1284–1288 [View Article][PubMed]
     [Google Scholar]
  12. De Vos P, Ludwig WF, Schleifer KH, Whitman I. Family IV. Paenibacillaceae fam. nov. In Bergey's Manual of Systematic Bacteriology vol. 3 2011 pp. 269
     [Google Scholar]
  13. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor, NY: Cold Springer Harbor Laboratory; 2001
     [Google Scholar]
  14. Yoon JH, Lee ST, Park YH. Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 1998; 48:187–194 [View Article][PubMed]
     [Google Scholar]
  15. 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; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  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. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. da Mota FF, Gomes EA, Paiva E, Rosado AS, Seldin L. Use of rpoB gene analysis for identification of nitrogen-fixing Paenibacillus species as an alternative to the 16S rRNA gene. Lett Appl Microbiol 2004; 39:34–40 [View Article][PubMed]
     [Google Scholar]
  22. Adékambi T, Shinnick TM, Raoult D, Drancourt M. Complete rpoB gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Microbiol 2008; 58:1807–1814 [View Article][PubMed]
     [Google Scholar]
  23. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article][PubMed]
     [Google Scholar]
  24. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  25. Breznak JA, Costilow RN. Physicochemical factors in growth. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G. (editors) Methods for General and Molecular Bacteriology, 2nd ed. Washington, DC: American Society of Microbiology Press; 2007 pp. 309–329
     [Google Scholar]
  26. McCarthy AJ, Cross T. A taxonomic study of Thermomonospora and other monosporic actinomycetes. Microbiology 1984; 130:5–25 [View Article]
     [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  31. 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]
  32. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002484
Loading
Paenibacillus shunpengii sp. nov., isolated from farmland soil
Int J Syst Evol Microbiol 68, 211 (2018); https://doi.org/10.1099/ijsem.0.002484
/content/journal/ijsem/10.1099/ijsem.0.002484
/content/journal/ijsem/10.1099/ijsem.0.002484
Loading

Data & Media loading...

Supplements

Supplementary File 2

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