1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 11

sp. nov., isolated from maize field, and emended description of Nakamura 2004 Free

Abstract

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT480, isolated from soil sampled in a maize field in Taiwan, ROC. Cells of strain CC-CFT480 were rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 3 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT480 associated with (97.2 % sequence identity), (95.7 %), (95.4 %) and (95.2 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain CC-CFT480 and were 74.2 and 20.1 %, respectively. Strain CC-CFT480 contained iso-C, C c alcohol and iso-C 10 as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown aminophospholipids, one uncharacterized aminophospholipid and two unknown phospholipids. The major polyamine was spermidine. The DNA G+C content was 34.8 mol% and the predominant quinone was menaquinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT480 is proposed to represent a novel species, for which the name sp. nov. (type strain CC-CFT480=BCRC 81216=JCM 33498).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): average nucleotide identity (ANI) , Cerasibacillus terrae , digital DNA–DNA hybridization (dDDH) and strain CC-CFT480T
Funding
This study was supported by the:
  • Ministry of Science and Technology, Taiwan (Award 109-2313-B-005-026)
    • Principle Award Recipient: Chiu-Chung Young
  • Ministry of Science and Technology, Taiwan (Award 109-2313-B-005-026)
    • Principle Award Recipient: Shih-Yao Lin
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004470
2020-09-17
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/11/5725.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004470&mimeType=html&fmt=ahah

References

  1. Nakamura K, Haruta S, Ueno S, Ishii M, Yokota A et al. Cerasibacillus quisquiliarum gen. nov., sp. nov., isolated from a semi-continuous decomposing system of kitchen refuse. Int J Syst Evol Microbiol 2004; 54:1063–1069 [View Article][PubMed]
     [Google Scholar]
  2. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  3. de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852–1863 [View Article][PubMed]
     [Google Scholar]
  4. Kämpfer P, Arun AB, Busse H-J, Langer S, Young C-C et al. Virgibacillus soli sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2011; 61:275–280 [View Article][PubMed]
     [Google Scholar]
  5. Yoon J-H, Kang S-J, Jung Y-T, Lee KC, Oh HW et al. Virgibacillus byunsanensis sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2010; 60:291–295 [View Article][PubMed]
     [Google Scholar]
  6. An S-Y, Asahara M, Goto K, Kasai H, Yokota A. Virgibacillus halophilus sp. nov., spore-forming bacteria isolated from soil in Japan. Int J Syst Evol Microbiol 2007; 57:1607–1611 [View Article][PubMed]
     [Google Scholar]
  7. Heyndrickx M, Lebbe L, Kersters K, De Vos P, Forsyth G et al. Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus. Int J Syst Bacteriol 1998; 48:99–106 [View Article]
     [Google Scholar]
  8. Heyndrickx M, Lebbe L, Kersters K, Hoste B, De Wachter R et al. Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998. Int J Syst Bacteriol 1999; 49 Pt 3:1083–1090 [View Article][PubMed]
     [Google Scholar]
  9. Murray RGE, Doetsch RN, Robinow CF. Determination and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 32–34
     [Google Scholar]
  10. Lin S-Y, Liu Y-C, Hameed A, Hsu Y-H, Lai W-A et al. Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter. Int J Syst Evol Microbiol 2013; 63:3762–3768 [View Article][PubMed]
     [Google Scholar]
  11. Hameed A, Shahina M, Lin S-Y, Lai W-A, Hsu Y-H et al. Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter. Int J Syst Evol Microbiol 2014; 64:138–145 [View Article][PubMed]
     [Google Scholar]
  12. Zhou J, Fries MR, Chee-Sanford JC, Tiedje JM. Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 1995; 45:500–506 [View Article][PubMed]
     [Google Scholar]
  13. Heiner CR, Hunkapiller KL, Chen SM, Glass JI, Chen EY. Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 1998; 8:557–561 [View Article][PubMed]
     [Google Scholar]
  14. Yoon S-H, Ha S-M, 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]
  15. 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]
  16. 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]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [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. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism 3 New York: Academic Press; 1969 pp 21–32
     [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  24. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  25. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
     [Google Scholar]
  26. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  27. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  28. Lin S-Y, Hameed A, Liu Y-C, Wen C-Z, Lai W-A 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][PubMed]
     [Google Scholar]
  29. Lin S-Y, Hameed A, Liu Y-C, Hsu Y-H, Lai W-A et al. Bacillus formosensis sp. nov., isolated from pesticide wastewater. Int J Syst Evol Microbiol 2015; 65:3800–3805 [View Article][PubMed]
     [Google Scholar]
  30. Rhuland LE, Work E, Denman RF, Hoare DS. The behavior of the isomers of diaminopimelic acid on paper chromatograms. J Am Chem Soc 1955; 77:4844–4846 [View Article]
     [Google Scholar]
  31. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article][PubMed]
     [Google Scholar]
  32. Paisley R. MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual Newark, DE: MIDI; 1996
     [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  34. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [View Article][PubMed]
     [Google Scholar]
  35. 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]
  36. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004470
Loading
Cerasibacillus terrae sp. nov., isolated from maize field, and emended description of Cerasibacillus quisquiliarum Nakamura et al. 2004
Int J Syst Evol Microbiol 70, 5725 (2020); https://doi.org/10.1099/ijsem.0.004470
/content/journal/ijsem/10.1099/ijsem.0.004470
/content/journal/ijsem/10.1099/ijsem.0.004470
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