1887

Abstract

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2 was a member of the genus and most closely related to R-6514 (98.9 % similarity), RA9 (98.0 %) and R-7190 (97.7 %). A draft genome sequence determined for strain 3-2-2 revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2 and the closely related species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2 were iso-C, anteiso-C, iso-C and iso-C. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2 represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is 3-2-2 (=CGMCC 1.13685=LMG 30839).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 41601332 and 41401275)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003271
2019-02-12
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/4/1075.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003271&mimeType=html&fmt=ahah

References

  1. Cohn F. Untersuchungen über Bakterien. Beiträge zur Biologie der Pflanzen 1872; 1:127–224
    [Google Scholar]
  2. Ma K, Yin Q, Chen L, Lai Q, Xu Y. Bacillus acanthi sp. nov., isolated from the rhizosphere soil of a mangrove plant Acanthus ilicifolius . Int J Syst Evol Microbiol 2018; 68:3047–3051 [View Article][PubMed]
    [Google Scholar]
  3. Kumar S, Singh H, Kaur M, Kaur L, Tanuku NRS et al. Bacillus shivajii sp. nov., isolated from a water sample of Sambhar salt lake, India. Int J Syst Evol Microbiol
    [Google Scholar]
  4. Logan NA, de Vos P. Genus I. Bacillus . In De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009 pp. 21–128
    [Google Scholar]
  5. Liu B, Liu GH, Wang XY, Wang JP, Zhu YJ et al. Bacillus populi sp. nov. isolated from Populus euphratica rhizosphere soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 68:155–159 [View Article][PubMed]
    [Google Scholar]
  6. Poudel P, Miyamoto H, Miyamoto H, Okugawa Y, Tashiro Y et al. Thermotolerant Bacillus kokeshiiformis sp. nov. isolated from marine animal resources compost. Int J Syst Evol Microbiol 2014; 64:2668–2674 [View Article][PubMed]
    [Google Scholar]
  7. Feng L, Liu D, Sun X, Wang G, Li M. Bacillus cavernae sp. nov. isolated from cave soil. Int J Syst Evol Microbiol 2016; 66:801–806 [View Article][PubMed]
    [Google Scholar]
  8. Nguyen NL, Kim YJ, Hoang VA, Min JW, Liang ZQ et al. Bacillus ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2013; 63:855–860 [View Article][PubMed]
    [Google Scholar]
  9. Liu B, Liu GH, Cetin S, Schumann P, Pan ZZ et al. Bacillus gobiensis sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2016; 66:379–384 [View Article][PubMed]
    [Google Scholar]
  10. Nguyen TM, Kim J. Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method. Int J Syst Evol Microbiol 2015; 65:704–709 [View Article][PubMed]
    [Google Scholar]
  11. Liu B, Liu GH, Sengonca C, Schumann P, Wang JP et al. Bacillus praedii sp. nov., isolated from purplish paddy soil. Int J Syst Evol Microbiol 2017; 67:2823–2828 [View Article][PubMed]
    [Google Scholar]
  12. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article][PubMed]
    [Google Scholar]
  13. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. (editors) Methods for General and Molecular Microbiology Washington, DC: ASM Press; 2007 pp. 330–393
    [Google Scholar]
  14. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
    [Google Scholar]
  15. Dong XZ, Cai MY. Determination of biochemical properties. In Dong XZ, Cai MY. (editors) Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001 pp. 370–398
    [Google Scholar]
  16. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, United Kingdom: John Wiley & Sons Press; 1991 pp. 115–175
    [Google Scholar]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  22. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  25. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  26. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [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. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  30. 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]
  31. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  32. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  33. Kämpfer P, Rosselló-Mora R, Falsen E, Busse HJ, Tindall BJ. Cohnella thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 2006; 56:781–786 [View Article][PubMed]
    [Google Scholar]
  34. Choi JH, Cha CJ. Bacillus panacisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2014; 64:901–906 [View Article][PubMed]
    [Google Scholar]
  35. Díez-Méndez A, Rivas R, Mateos PF, Martínez-Molina E, Santín PJ et al. Bacillus terrae sp. nov. isolated from Cistus ladanifer rhizosphere soil. Int J Syst Evol Microbiol 2017; 67:1478–1481 [View Article][PubMed]
    [Google Scholar]
  36. Shivani Y, Subhash Y, Dave Bharti P, Sasikala C, Ramana C. Bacillus crescens sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:2531–2536 [View Article][PubMed]
    [Google Scholar]
  37. Lee GH, Rhee MS, Chang DH, Kwon KK, Bae KS et al. Bacillus solimangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 2014; 64:1622–1628 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003271
Loading
/content/journal/ijsem/10.1099/ijsem.0.003271
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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