1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 8

sp. nov., isolated from soil Free

Abstract

A novel Gram-stain-positive, strictly aerobic, motile, spore-forming and rod-shaped bacterial strain, designated R-3, was isolated from a soil sample obtained from the shore of Lake Panyang, Sichuan Province, PR China. Strain R-3 hydrolysed starch and casein. It could not assimilate -glucose as a carbon source, or produce acid from -glucose and -arabinose. Phylogenetic, phenotypic, chemotaxonomic and molecular studies were performed on the new isolate. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R-3 was a member of the genus , exhibiting the highest sequence similarity to TEGR-3 (98.4 %). The organism grew at 4–38 °C (optimum, 28–30 °C), at pH 6.0–10.0 (pH 7.0–7.5) and with 0–2.5 % (w/v) NaCl (1 %). The predominant menaquinone was MK-7. Anteiso-C (60.7 %) and C (15.5 %) were the major fatty acids. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. The DNA G+C content of strain R-3 was determined to be 47.0 mol%. The DNA–DNA relatedness between strain R-3 and TEGR-3 was 21.2 %. Based on the results obtained in this study, strain R-3 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is R-3 (=CGMCC 1.16135=KCTC 33912).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): New taxa , novel species and Paenibacillus
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003475
2019-08-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/8/2354.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003475&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]
     [Google Scholar]
  2. Zhuang J, Xin D, Zhang YQ, Guo J, Zhang J et al. Paenibacillus albidus sp. nov., isolated from grassland soil. Int J Syst Evol Microbiol 2017; 67:4685–4691 [View Article][PubMed]
     [Google Scholar]
  3. Simon L, Škraban J, Kyrpides NC, Woyke T, Shapiro N et al. Paenibacillus aquistagni sp. nov., isolated from an artificial lake accumulating industrial wastewater. Antonie van Leeuwenhoek 2017; 110:1189–1197 [View Article][PubMed]
     [Google Scholar]
  4. Chen C, Xin K, Li M, Li X, Cheng J et al. Paenibacillus sinopodophylli sp. nov., a siderophore-producing endophytic bacterium isolated from roots of Sinopodophyllum hexandrum (Royle) Ying. Int J Syst Evol Microbiol 2016; 66:4993–4999 [View Article][PubMed]
     [Google Scholar]
  5. Li P, Lin W, Liu X, Li S, Luo L et al. Paenibacillus aceti sp. nov., isolated from the traditional solid-state acetic acid fermentation culture of Chinese cereal vinegar. Int J Syst Evol Microbiol 2016; 66:3426–3431 [View Article][PubMed]
     [Google Scholar]
  6. 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]
  7. Priest FG. Paenibacillus. In William W. (editor) Bergey’s Manual of Systematics of Archaea and Bacteria Hoboken, UK: John Wiley & Sons, Ltd; 2015 pp. 1–40
     [Google Scholar]
  8. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
     [Google Scholar]
  9. 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]
  10. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
     [Google Scholar]
  11. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
     [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  14. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
     [Google Scholar]
  15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
     [Google Scholar]
  18. 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]
  19. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4:184–192 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology: report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
  22. Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  23. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Goldfine H, Bloch K. On the origin of unsaturated fatty acids in clostridia. J Biol Chem 1961; 236:2596–2601[PubMed]
     [Google Scholar]
  26. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  27. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  28. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M. (editor) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
     [Google Scholar]
  29. Carro L, Flores-Félix JD, Cerda-Castillo E, Ramírez-Bahena MH, Igual JM et al. Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum. Int J Syst Evol Microbiol 2013; 63:4433–4438 [View Article][PubMed]
     [Google Scholar]
  30. Valverde A, Peix A, Rivas R, Velázquez E, Salazar S et al. Paenibacillus castaneae sp. nov., isolated from the phyllosphere of Castanea sativa Miller. Int J Syst Evol Microbiol 2008; 58:2560–2564 [View Article][PubMed]
     [Google Scholar]
  31. Carro L, Flores-Félix JD, Ramírez-Bahena MH, García-Fraile P, Martínez-Hidalgo P et al. Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus . Int J Syst Evol Microbiol 2014; 64:3028–3033 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003475
Loading
Paenibacillus luteus sp. nov., isolated from soil
Int J Syst Evol Microbiol 69, 2354 (2019); https://doi.org/10.1099/ijsem.0.003475
/content/journal/ijsem/10.1099/ijsem.0.003475
/content/journal/ijsem/10.1099/ijsem.0.003475
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