1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 1

sp. nov., a novel endophytic bacterium isolated from root of (Pilger) Rehd Free

Abstract

A Gram-staining-positive, aerobic, rod-shaped, endospore-forming bacterium, designated strain M5HDSG1-1, was originally isolated from a surface-sterilized root of (Pilger) Rehd. in Guizhou, PR China. This bacterium was tested by a polyphasic approach to determine its taxonomic position. A 16S rRNA gene-based phylogenetic analysis revealed that M5HDSG1-1 had the greatest similarity to the type strain of DSM 15077 (99.1 %). The average nucleotide identity values between M5HDSG1-1 and DSM 15077 and NBRC 13626 were 73.3 and 72.8 %, respectively. The digital DNA–DNA hybridization values between M5HDSG1-1 and DSM 15077 and NBRC 13626 were 20.1 and 20.6 %, respectively, which were below the recommended thresholds. M5HDSG1-1 grew at a pH range of 6.0–12.0 (optimum, 7.0–8.0), at temperatures between 10 and 45 °C (optimum, 30 °C) and at 0–2 % (w/v) NaCl (optimum, 1 %). Neither substrate nor aerial mycelia was formed, and no diffusible pigments were observed on the media tested. The predominant isoprenoid quinone was menaquinone-7 (MK-7). The major fatty acids were -C, and -C. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified phospholipid. The DNA G+C content was 37.5 mol%. According to the phylogeneic, phenotypic and chemotaxonomic data, M5HDSG1-1 was clearly distinguishable from other species with validly published names in the genus and should therefore be classified as representing a novel species, and we suggest the name sp. nov. The type strain is M5HDSG1-1 (=JCM 33117=CGMCC 1.13668).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacillus , M5HDSG1-1 , novel species and taxonomic position
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 81960642)
    • Principle Award Recipient: Li Tuo
  • the Bidding Project of Zunyi Medical University (Award F-614)
    • Principle Award Recipient: Yun Liu
  • the PhD Start-up Fund of Zunyi Medical University (Award F-800)
    • Principle Award Recipient: Yun Liu
  • Youth Science and technology personnel growth project of Guizhou Provincial Education Department (Award Qian Jiao He KY Zi[2016]200))
    • Principle Award Recipient: Li Tuo
  • Science and Technology Foundation of Guizhou Province (Award Qian Ke He Jichu[2019]1347)
    • Principle Award Recipient: Li Tuo
  • National Natural Science Foundation of China (Award 81603079)
    • Principle Award Recipient: Li Tuo
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003776
2019-10-15
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/1/481.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003776&mimeType=html&fmt=ahah

References

  1. Cohn F. Untersuchungen über Bakterien. Beitrage zur Biologie der Pflanzen Heft 2 1872; 1:127–224
     [Google Scholar]
  2. Qiu F, Zhang X, Liu L, Sun L, Schumann P et al. Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root. Int J Syst Evol Microbiol 2009; 59:729–734 [View Article]
     [Google Scholar]
  3. Wang HF, Li QL, Zhang YG, Xiao M, Zhou XK et al. Bacillus capparidis sp. nov., an endophytic bacterium isolated from roots of Capparis spinosa L. Int J Syst Evol Microbiol 2017; 67:282–287 [View Article]
     [Google Scholar]
  4. Zhang YZ, Chen WF, Li M, Sui XH, Liu HC et al. Bacillus endoradicis sp. nov., an endophytic bacterium isolated from soybean root. Int J Syst Evol Microbiol 2012; 62:359–363 [View Article]
     [Google Scholar]
  5. Ma L, Xi JQ, Cao YH, Wang XY, Zheng SC et al. Bacillus endozanthoxylicus sp. nov., an endophytic bacterium isolated from Zanthoxylum bungeanum Maxim leaves. Int J Syst Evol Microbiol 2017; 67:3699–3705 [View Article]
     [Google Scholar]
  6. Lin SY, Hameed A, Liu YC, Wen CZ, Lai WA et al. Bacillus lycopersici sp. nov., isolated from a tomato plant (Solanum lycopersicum L.). Int J Syst Evol Microbiol 2015; 65:2085–2090 [View Article]
     [Google Scholar]
  7. Hong SW, Kwon SW, Kim SJ, Kim SY, Kim JJ et al. Bacillus oryzaecorticis sp. nov., a moderately halophilic bacterium isolated from rice husks. Int J Syst Evol Microbiol 2014; 64:2786–2791 [View Article]
     [Google Scholar]
  8. Qin S, Wang HB, Chen HH, Zhang YQ, Jiang CL et al. Glycomyces endophyticus sp. nov., an endophytic actinomycete isolated from the root of Carex baccans Nees. Int J Syst Evol Microbiol 2008; 58:2525–2528 [View Article]
     [Google Scholar]
  9. WJ L, 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
     [Google Scholar]
  10. 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]
     [Google Scholar]
  11. 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]
     [Google Scholar]
  12. 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]
     [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  15. 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]
  16. Tamura S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 2015
     [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  18. 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]
     [Google Scholar]
  19. 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]
     [Google Scholar]
  20. 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]
  21. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  22. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  23. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th edn. San Francisco: Benjamin Cummings Pearson Education; 2002
     [Google Scholar]
  24. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article]
     [Google Scholar]
  25. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477
     [Google Scholar]
  26. 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]
  27. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
     [Google Scholar]
  28. Guo L, Tuo L, Habden X, Zhang Y, Liu J et al. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 2015; 65:206–213 [View Article]
     [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI inc; 1990
     [Google Scholar]
  30. Tuo L, Yan XR, Li FN, Bao YX, Shi HC et al. Brachybacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from bark of Scutellaria baicalensis Georgi. Int J Syst Evol Microbiol 2018; 68:3563–3568 [View Article]
     [Google Scholar]
  31. Borsodi AK, Tóth E, Aszalós JM, Bárány Á, Schumann P et al. Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil. Int J Syst Evol Microbiol 2017; 67:3490–3495 [View Article]
     [Google Scholar]
  32. Zhao B, Lu W, Zhang S, Liu K, Yan Y et al. Reclassification of Bacillus saliphilus as Alkalicoccus saliphilus gen. nov., comb. nov., and description of Alkalicoccus halolimnae sp. nov., a moderately halophilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2017; 67:1557–1563 [View Article]
     [Google Scholar]
  33. Venkateswaran K, Kempf M, Chen F, Satomi M, Nicholson W et al. Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant. Int J Syst Evol Microbiol 2003; 53:165–172 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003776
Loading
Bacillus taxi sp. nov., a novel endophytic bacterium isolated from root of Taxus chinensis (Pilger) Rehd
Int J Syst Evol Microbiol 70, 481 (2020); https://doi.org/10.1099/ijsem.0.003776
/content/journal/ijsem/10.1099/ijsem.0.003776
/content/journal/ijsem/10.1099/ijsem.0.003776
Loading

Data & Media loading...

Supplements

Supplementary material 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