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Volume 68, Issue 12

Kyrpidia spormannii sp. nov., a thermophilic, hydrogen-oxidizing, facultative autotroph, isolated from hydrothermal systems at São Miguel Island, and emended description of the genus Kyrpidia Free

Abstract

A Gram-stain-positive, rod-shaped, non-motile, spore-forming bacterium, strain EA-1, was isolated from hydrothermal sediment samples from the Azores (São Miguel, Portugal). 16S rRNA gene sequence analysis of the isolated bacterium revealed a phylogenetic affiliation with the genus Kyrpidia . The sequence similarity of the five 16S rRNA gene copies to its closest relative, Kyrpidia tusciae , ranged from 97.79 to 97.85 %. The in silico estimate of DNA–DNA hybridization was 56.0 %. The dominant fatty acids of the novel isolate were anteiso-C17 : 0 (49.9 %), iso-C17 : 0 (23.0 %) and iso-C16 : 0 (13.3 %), while the quinone detected was menaquinone MK-7. Analysis of polar lipids identified phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and additional unidentified compounds comprising two glycolipids, two phospholipids and two lipids. The presence of meso-diaminopimelic acid in the peptidoglycan and mannose, arabinose and ribose in the cell wall of strain EA-1 were detected. The strain was able to grow heterotrophically as well as autotrophically with carbon dioxide as the sole carbon source and with hydrogen and oxygen as electron donor and acceptor, respectively. Based on its chemotaxonomic, physiological and genomic characteristics, the new strain is considered to represent a novel species within the genus Kyrpidia , for which the name Kyrpidia spormannii sp. nov. is proposed. The type strain is strain EA-1 (=DSM 106492=CCOS1194).

  • Received:
  • Accepted:
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Keyword(s): autotroph , Bacillus , Gram-positive , hydrogen oxidizer , Knallgas , Kyrpidia , spormannii , thermophilic and tusciae
© 2018 IUMS
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2018-09-20
2024-04-16
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References

  1. Klenk HP, 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][PubMed]
     [Google Scholar]
  2. Bonjour F, Aragno M. Bacillus tusciae, a new species of thermoacidophilic, facultatively chemolithoautotrophic hydrogen oxidizing sporeformer from a geothermal area. Arch Microbiol 1984; 139:397–401 [View Article]
     [Google Scholar]
  3. Sturm-Richter K, Golitsch F, Sturm G, Kipf E, Dittrich A et al. Unbalanced fermentation of glycerol in Escherichia coli via heterologous production of an electron transport chain and electrode interaction in microbial electrochemical cells. Bioresour Technol 2015; 186:89–96 [View Article][PubMed]
     [Google Scholar]
  4. Atlas RM. Handbook of microbiological media Boca Raton: CRC press; 2010
     [Google Scholar]
  5. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7[PubMed]
     [Google Scholar]
  6. Reiner JE, Lapp CJ, Bunk B, Spröer C, Overmann J et al. Complete genome sequence of Kyrpidia sp. strain EA-1, a thermophilic knallgas bacterium, isolated from the Azores. Genome Announc 2018; 6:e01505-17 [View Article][PubMed]
     [Google Scholar]
  7. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  8. 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]
  9. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  10. 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][PubMed]
     [Google Scholar]
  11. Saitou N, Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evo 1987; 4:406–425
     [Google Scholar]
  12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  13. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
     [Google Scholar]
  14. Mcilvaine TC. A buffer solution for colorimetric comparison. J Biol Chem 1921; 49:183–186
     [Google Scholar]
  15. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp. 21–41
     [Google Scholar]
  16. Chen W, Zhang C, Song L, Sommerfeld M, Hu Q. A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae. J Microbiol Methods 2009; 77:41–47 [View Article][PubMed]
     [Google Scholar]
  17. Koller M, Rodríguez-Contreras A. Techniques for tracing PHA-producing organisms and for qualitative and quantitative analysis of intra- and extracellular PHA. Eng Life Sci 2015; 15:558–581 [View Article]
     [Google Scholar]
  18. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  19. 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]
  20. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  21. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd ed. pp. 330–393
     [Google Scholar]
  22. Rhuland LE, Work E, Denman RF, Hoare DS. The behavior of the isomers of α,ε-diaminopimelic acid on paper chromatograms. J Am Chem Soc 1955; 77:4844–4846 [View Article]
     [Google Scholar]
  23. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  24. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44:D457–D462 [View Article][PubMed]
     [Google Scholar]
  25. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article][PubMed]
     [Google Scholar]
  26. The UniProt Consortium UniProt: the universal protein knowledgebase. Nucleic Acids Res 2017; 45:D158–D169 [View Article][PubMed]
     [Google Scholar]
  27. Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. Bergey’s Manual of Systematic Bacteriology vol. 3 The Firmicutes New York: Springer Science & Business Media; 2011
     [Google Scholar]
  28. Kankaanpää P, Yang B, Kallio H, Isolauri E, Salminen S. Effects of polyunsaturated fatty acids in growth medium on lipid composition and on physicochemical surface properties of lactobacilli. Appl Environ Microbiol 2004; 70:129–136 [View Article][PubMed]
     [Google Scholar]
  29. O'Leary WM. The fatty acids of bacteria. Bacteriol Rev 1962; 26:421–447[PubMed]
     [Google Scholar]
  30. Gallon JR. The oxygen sensitivity of nitrogenase: a problem for biochemists and micro-organisms. Trends Biochem Sci 1981; 6:19–23 [View Article]
     [Google Scholar]
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Kyrpidia spormannii sp. nov., a thermophilic, hydrogen-oxidizing, facultative autotroph, isolated from hydrothermal systems at São Miguel Island, and emended description of the genus Kyrpidia
Int J Syst Evol Microbiol 68, 3735 (2018); https://doi.org/10.1099/ijsem.0.003037
/content/journal/ijsem/10.1099/ijsem.0.003037
/content/journal/ijsem/10.1099/ijsem.0.003037
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