1887

Abstract

A novel moderately thermophilic aerobic bacterium, strain TP075, was isolated from soil collected from an athletic field in Japan. Strain TP075 is a rod-shaped, aerobic bacterium that forms terminal endospores. The KOH lysis test suggested that the cell wall of the isolate has a Gram-positive structure. For aerobic growth, the optimum pH and temperature were 4.0–5.0 and 47–50 °C, respectively. Draft genome sequencing showed that the G+C content of genomic DNA was 46.5 mol%. Branched-chain fatty acids (iso-C, anteiso-C and iso-C) were the major components of the cellular fatty acid profile. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain TP075 belongs to the family , with the highest similarity to CCUG53762 (92.6%) and CAU11108 (92.5%). Genome-based analyses indicated that strain TP075 and the most closely related strain, DSM 22757, share an average amino acid identity value of 62.57% and an average nucleotide identity value of 70.86 %. The results obtained in this study suggest that strain TP075 represents a novel species of a novel genus, for which we propose the name gen. nov., sp. nov. with type strain TP075 (= JCM 34430=TBRC 15189).

Funding
This study was supported by the:
  • MEXT (Award S1512004)
    • Principle Award Recipient: NorifumiShirasaka
  • Kindai University
    • Principle Award Recipient: ToruJojima
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005827
2023-05-09
2024-06-25
Loading full text...

Full text loading...

References

  1. Jojima T, Ioku Y, Fukuta Y, Shirasaka N, Matsumura YM. Supplemental material. Figshare; 2023 https://doi.org/10.6084/m9.figshare.20515062.v1
  2. da Costa MS, Rainey FA. Family II. Alicyclobacillaceae fam. nov. In Vos P, Garrity G, Jones D, Krieg N, Ludwig W et al. eds Bergey’s Manual of Systematic Bacteriology Volume 3: The Firmicutes New York: Springer; 2009 p 229
    [Google Scholar]
  3. Klenk H-P, Lapidus A, Chertkov O, Copeland A, Del Rio TG et al. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Stand Genomic Sci 2011; 5:121–134 [View Article]
    [Google Scholar]
  4. Watanabe M, Kojima H, Fukui M. Proposal of Effusibacillus lacus gen. nov., sp. nov., and reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae comb. nov. and Alicyclobacillus consociatus as Effusibacillus consociatus comb. nov. Int J Syst Evol Microbiol 2014; 64:2770–2774 [View Article]
    [Google Scholar]
  5. Steven B, Chen MQ, Greer CW, Whyte LG, Niederberger TD. Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost. Int J Syst Evol Microbiol 2008; 58:1497–1501 [View Article]
    [Google Scholar]
  6. Matsubara H, Goto K, Matsumura T, Mochida K, Iwaki M et al. Alicyclobacillus acidiphilus sp. nov., a novel thermo-acidophilic, omega-alicyclic fatty acid-containing bacterium isolated from acidic beverages. Int J Syst Evol Microbiol 2002; 52:1681–1685 [View Article] [PubMed]
    [Google Scholar]
  7. Deinhard G, Blanz P, Poralla K, Altan E. Bacillus acidoterrestris sp. nov., a new thermotolerant acidophile isolated from different soils. Syst Appl Microbiol 1987; 10:47–53 [View Article]
    [Google Scholar]
  8. Hussey MA, Zayaitz A. Endospore stain protocol. asm Pub2Web; 2007 https://asm.org/Protocols/Endospore-Stain-Protocol
  9. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758 [View Article] [PubMed]
    [Google Scholar]
  10. Nakano MM, Zuber P. Anaerobic growth of a “strict aerobe” (Bacillus subtilis). Annu Rev Microbiol 1998; 52:165–190 [View Article] [PubMed]
    [Google Scholar]
  11. Darland G, Brock TD. Bacillus acidocaldarius sp. nov., an acidophilic thermophilic spore-forming bacterium. J Gen Microbiol 1971; 67:9–15 [View Article]
    [Google Scholar]
  12. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  13. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [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. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [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. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article] [PubMed]
    [Google Scholar]
  18. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on A standard genome relatedness index. MBio 2020; 11: Epub ahead of print 25 February 2020 [View Article]
    [Google Scholar]
  19. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  20. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article]
    [Google Scholar]
  21. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
    [Google Scholar]
  22. Imperio T, Viti C, Marri L. Alicyclobacillus pohliae sp. nov., a thermophilic, endospore-forming bacterium isolated from geothermal soil of the north-west slope of Mount Melbourne (Antarctica). Int J Syst Evol Microbiol 2008; 58:221–225 [View Article] [PubMed]
    [Google Scholar]
  23. da Costa MS, Rainey FA, Albuquerque L. Alicyclobacillus. In Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P et al. eds Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc and Bergey’s Manual Trust; 2015 [View Article]
    [Google Scholar]
  24. Lee BD, Apel WA, DeVeaux LC, Sheridan PP. Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius. J Ind Microbiol Biotechnol 2017; 44:1443–1458 [View Article] [PubMed]
    [Google Scholar]
  25. Kim JH, Kim W. Tumebacillus soli sp. nov., isolated from non-rhizosphere soil. Int J Syst Evol Microbiol 2016; 66:2192–2197 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005827
Loading
/content/journal/ijsem/10.1099/ijsem.0.005827
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare
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