1887

Abstract

A novel Gram-stain-positive, rod-shaped, endospore-forming, motile, aerobic bacterium, designated as P2, was isolated from a hot spring water sample collected from Ilica-Erzurum, Turkey. Phylogenetic analyses based on 16S rRNA gene sequence comparisons affiliated strain P2 with the genus , and the strain showed the highest sequence identity to NBRC 15712 (96.7 %). However, the pairwise sequence comparisons of the 16S rRNA genes revealed that strain P2 shared only 94.7 % sequence identity with subsp. NCIB 3610, indicating that strain P2 might not be a member of the genus . The digital DNA–DNA hybridization and average nucleotide identity values between strain P2 and NBRC 15712 were 19.8 and 74.2 %, respectively. The cell-wall peptidoglycan of strain P2 contained -diaminopimelic acid. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminophospholipid, five unidentified phospholipids and two unidentified lipids while the predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C and iso-C. The draft genome of strain P2 was composed of 82 contigs and found to be 3.5 Mb with 36.1 mol% G+C content. The results of phylogenomic and phenotypic analyses revealed that strain P2 represents a novel genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is P2 (=CECT 9886=DSM 107530=NCCB 100675). Based on the results of the present study, it is also suggested that and should be transferred to this novel genus as comb. nov. and comb. nov., respectively.

Funding
This study was supported by the:
  • Atatürk Üniversitesi
    • Principle Award Recipient: Not Applicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004549
2020-11-09
2024-12-07
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6418.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004549&mimeType=html&fmt=ahah

References

  1. Cohn F. Untersuchungen uber Bakterien. Beitr Biol Pflanz 1872; 1:127–224
    [Google Scholar]
  2. Liu GH, Liu B, Liu QY, Wang JP, Che JM et al. Bacillus xiapuensis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2019; 69:1714–1719 [View Article][PubMed]
    [Google Scholar]
  3. Sun QL, Yu C, Luan ZD, Lian C, Hu YH et al. Description of Bacillus kexueae sp. nov. and Bacillus manusensis sp. nov., isolated from hydrothermal sediments. Int J Syst Evol Microbiol 2018; 68:829–834 [View Article][PubMed]
    [Google Scholar]
  4. Sun L, Chen Y, Tian W, Yao L, Chen Z et al. Bacillus acidinfaciens sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2019; 69:1075–1080 [View Article][PubMed]
    [Google Scholar]
  5. 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]
  6. Inan K, Canakci S, Belduz AO, Sahin F. Brevibacillus aydinogluensis sp. nov., a moderately thermophilic bacterium isolated from Karakoc hot spring. Int J Syst Evol Microbiol 2012; 62:849–855 [View Article][PubMed]
    [Google Scholar]
  7. Verma A, Pal Y, Ojha AK, Kumari M, Khatri I et al. Taxonomic insights into the phylogeny of Bacillus badius and proposal for its reclassification to the genus Pseudobacillus as Pseudobacillus badius comb. nov. and reclassification of Bacillus wudalianchiensis Liu et al., 2017 as Pseudobacillus wudalianchiensis comb. nov. Syst Appl Microbiol 2019; 42:360–372 [View Article][PubMed]
    [Google Scholar]
  8. Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article][PubMed]
    [Google Scholar]
  9. Jiang D, Jiang K, Ren J, Wu J, Li J. Resurrection of the genus Leptomantis, with description of a new genus to the family Rhacophoridae (Amphibia: Anura). Asian Herpetol Res 2019; 10:1–12
    [Google Scholar]
  10. Ay H, Saygin H, Sahin N. Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae . Int J Syst Evol Microbiol 2020; 70:2569–2579 [View Article]
    [Google Scholar]
  11. Saha T, Ranjan VK, Ganguli S, Thakur S, Chakraborty B et al. Pradoshia eiseniae gen. nov., sp. nov., a spore-forming member of the family Bacillaceae capable of assimilating 3-nitropropionic acid, isolated from the anterior gut of the earthworm Eisenia fetida . Int J Syst Evol Microbiol 2019; 69:1265–1273 [View Article][PubMed]
    [Google Scholar]
  12. Wang D, Xiang Y, Jiang C, Zhang J, Hua Z et al. Pueribacillus theae gen. nov., sp. nov., isolated from Pu’er tea. Int J Syst Evol Microbiol 2018; 68:2878–2882 [View Article]
    [Google Scholar]
  13. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. 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]
  18. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian Protein Metabolism 3 1969 p 132
    [Google Scholar]
  19. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article][PubMed]
    [Google Scholar]
  20. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
    [Google Scholar]
  24. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
    [Google Scholar]
  25. Swofford DL. Sinauer Associatesversion. 2002;4;b10 Sunderland, MA: PAUP*. Phylogenetic analysis using parsimony (*and other methods); 2002
  26. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  27. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article][PubMed]
    [Google Scholar]
  28. Mungan MD, Alanjary M, Blin K, Weber T, Medema MH et al. ARTS 2.0: feature updates and expansion of the antibiotic resistant target seeker for comparative genome mining. Nucleic Acids Res 2020; 48:W546–W552 [View Article][PubMed]
    [Google Scholar]
  29. Davis JJ, Gerdes S, Olsen GJ, Olson R, Pusch GD et al. PATtyFams: protein families for the microbial genomes in the PATRIC database. Front Microbiol 2016; 7:118 [View Article][PubMed]
    [Google Scholar]
  30. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ et al. Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics 2009; 25:1422–1423 [View Article][PubMed]
    [Google Scholar]
  31. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758–771 [View Article][PubMed]
    [Google Scholar]
  32. Wattam AR, Brettin T, Davis JJ, Gerdes S, Kenyon R et al. Assembly, annotation, and comparative genomics in PATRIC, the all bacterial bioinformatics resource center. Comparative Genomics New York, NY: Humana Press; 2018 pp 79–101
    [Google Scholar]
  33. 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]
  34. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
    [Google Scholar]
  35. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes (No. e1900v1). PeerJ Preprints 2016
    [Google Scholar]
  36. Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P. Phylogenomic re-assessment of the thermophilic genus Geobacillus . Syst Appl Microbiol 2016; 39:527–533 [View Article][PubMed]
    [Google Scholar]
  37. Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY. Phylogenomic analysis of the gammaproteobacterial methanotrophs (order Methylococcales) calls for the reclassification of members at the genus and species levels. Front Microbiol 2018; 9:3162 [View Article][PubMed]
    [Google Scholar]
  38. 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:e02475-19 [View Article][PubMed]
    [Google Scholar]
  39. 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]
  40. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  41. Schäffer C, Franck WL, Scheberl A, Kosma P, McDermott TR et al. Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov. Int J Syst Evol Microbiol 2004; 54:2361–2368 [View Article][PubMed]
    [Google Scholar]
  42. Liu X, Li G, Lai Q, Sun F, Du Y et al. Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea. Antonie van Leeuwenhoek 2015; 107:893–900 [View Article][PubMed]
    [Google Scholar]
  43. Habib N, Khan IU, Hussain F, Zhou EM, Xiao M et al. Meiothermus luteus sp. nov., a slightly thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2017; 67:2910–2914 [View Article][PubMed]
    [Google Scholar]
  44. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes . Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  45. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article][PubMed]
    [Google Scholar]
  46. 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]
  47. Kroppenstedt RM, Goodfellow M. The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillospora and Thermomonospora . Prokaryotes: A Handbook on the Biology of Bacteria 3, 3rd ed. 2006 pp 682–724
    [Google Scholar]
  48. Collins MD. Analysis of isoprenoid quinones. Methods Microbiol 1985; 18:329–366
    [Google Scholar]
  49. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Midi Inc; 1990
    [Google Scholar]
  50. Logan NA, Vos PD. Bacillus. Bergey’s Manual of Systematics of Archaea and Bacteria 17 2015 pp 1–63
    [Google Scholar]
  51. Bhandari V, Ahmod NZ, Shah HN, Gupta RS. Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus . Int J Syst Evol Microbiol 2013; 63:2712–2726 [View Article][PubMed]
    [Google Scholar]
  52. Parker CT, Tindall BJ, Garrity GM. International code of nomenclature of prokaryotes: Prokaryotic code (2008 revision). Int J Syst Evol Microbiol 2019; 69:S1–S111
    [Google Scholar]
  53. Pichinoty F, De Barjac H, Mandel M, Asselineau J. Description of Bacillus azotoformans sp. nov. Int J Syst Bacteriol 1983; 33:660–662 [View Article]
    [Google Scholar]
  54. Bao P, Xiao KQ, Wang HJ, Xu H, Xu PP et al. Characterization and potential applications of a selenium nanoparticle producing and nitrate reducing bacterium Bacillus oryziterrae sp. nov. Sci Rep 2016; 6:1–10 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004549
Loading
/content/journal/ijsem/10.1099/ijsem.0.004549
Loading

Data & Media loading...

Supplements

Supplementary material 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