1887

Abstract

A novel thermophilic bacterium, designated CFH 72773 was isolated from the enrichment of a Jinze hot spring sample which was collected from Dientan town, Tengchong county, Yunnan province, south-western PR China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and non-sporulating. The taxonomic position of the strain was investigated by using a polyphasic approach. Growth occurred at 37–75 °C, pH 6.0–8.0 and with 0–2.0 % (w/v) NaCl. Comparison of the 16S rRNA gene sequences indicated the strain represented a member of the genus and showed close relationships to the type strains YIM 77925 (96.3 % similarity) and RF-4 (96.2 % similarity). The whole genome of CFH 72773 consisted of 2.25 Mbp and the DNA G+C content was 69.5 mol%. A total of 2262 genes, including a variety of enzymes for chemolithotrophy and anerobic respiration, were predicted. The strain had a unique negative oxidase activity and could hydrolyze starch at high temperature. Furthermore, various genes related to methane, sulfur, fumarate and nitrate metabolism were found, all these indicated that it is worth studying the novel strain. The predominant menaquinone is MK-8. The predominant cellular fatty acids included iso-C, iso-C and iso-C. The major polar lipids were comprised of aminophospholipid, glycolipid and two phospholipids. On the basis of low ANI values, different phenotypic and chemotaxonomic characters and phylogenetic analysis, we made a proposal that strain CFH 72773 represents a novel member of the genus , for which the name sp. nov. is proposed. The type strain is CFH 72773 (=CCTCC AB2018244=KCTC 43129).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003965
2020-01-22
2020-02-28
Loading full text...

Full text loading...

References

  1. Brock TD, Freeze H. Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol 1969;98: 289– 297 [CrossRef]
    [Google Scholar]
  2. da Costa MS, Rainey FA. Thermaceae fam. nov In Boone DR, Castenholz RW. (editors) Bergey’s Manual of Systematic Bacteriology1, 2nd ed. Springer; 2001; pp 404– 414
    [Google Scholar]
  3. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018;68: 1825– 1829 [CrossRef]
    [Google Scholar]
  4. Yu T-T, Ming H, Yao J-C, Zhou E-M, Park D-J et al. Thermus amyloliquefaciens sp. nov., isolated from a hot spring sediment sample. Int J Syst Evol Microbiol 2015;65: 2491– 2495 [CrossRef]
    [Google Scholar]
  5. Zhang XQ, Ying Y, Ye Y, Xu XW, Zhu XF et al. Thermus arciformis sp. nov., a thermophilic species from a geothermal area. Int J Syst Evol Microbiol 2010;60: 834– 839 [CrossRef]
    [Google Scholar]
  6. Khan IU, Habib N, Hussain F, Xian W-D, Amin A et al. Thermus caldifontis sp. nov., a thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2017;67: 2868– 2872 [CrossRef]
    [Google Scholar]
  7. Ming H, Yin Y-R, Li S, Nie G-X, Yu T-T et al. Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 2014;64: 650– 656 [CrossRef]
    [Google Scholar]
  8. Chung AP, Rainey FA, Valente M, Nobre MF, da Costa MS. Thermus i gniterrae sp. nov. and Thermus antranikianii sp. nov., two new species from Iceland. Int J Syst Evol Microbiol 2000;50 Pt 1: 209– 217 [CrossRef]
    [Google Scholar]
  9. Bjornsdottir SH, Petursdottir SK, Hreggvidsson GO, Skirnisdottir S, Hjorleifsdottir S et al. Thermus islandicus sp. nov., a mixotrophic sulfur-oxidizing bacterium isolated from the torfajokull geothermal area. Int J Syst Evol Microbiol 2009;59: 2962– 2966 [CrossRef]
    [Google Scholar]
  10. Williams RA, Smith KE, Welch SG, Micallef J. Thermus oshimai sp. nov., isolated from hot springs in Portugal, Iceland, and the Azores, and comment on the concept of a limited geographical distribution of Thermus species. Int J Syst Bacteriol 1996;46: 403– 408 [CrossRef]
    [Google Scholar]
  11. Williams RA, Smith KE, Welch SG, Micallef J, Sharp RJ. DNA relatedness of Thermus strains, description of Thermus brockianus sp. nov., and proposal to reestablish Thermus thermophilus (Oshima and Imahori). Int J Syst Bacteriol 1995;45: 495– 499 [CrossRef]
    [Google Scholar]
  12. Hudson JA, Morgan HW, Daniel RM. Thermus filiformis sp. nov., a filamentous caldoactive bacterium. Int J Syst Bacteriol 1987;37: 431– 436 [CrossRef]
    [Google Scholar]
  13. Oshima T, IMAHORI K. Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 1974;24: 102– 112 [CrossRef]
    [Google Scholar]
  14. Kristjánsson JK, Hjörleifsdóttir S, Marteinsson VT, Alfredsson GA. Thermus scotoductus, sp. nov., a pigment-producing thermophilic bacterium from hot tap water in Iceland and including Thermus sp. X-1. Syst Appl Microbiol 1994;17: 44– 50 [CrossRef]
    [Google Scholar]
  15. Zhou E-M, Xian W-D, Jiao J-Y, Liu L, Li M-M et al. Physiological and genomic properties of Thermus tenuipuniceus sp. nov., a novel slight reddish color member isolated from a terrestrial geothermal spring. Syst Appl Microbiol 2018;41: 611– 618 [CrossRef]
    [Google Scholar]
  16. Vajna B, Kanizsai S, Kéki Z, Márialigeti K, Schumann P et al. Thermus composti sp. nov., isolated from oyster mushroom compost. Int J Syst Evol Microbiol 2012;62: 1486– 1490 [CrossRef]
    [Google Scholar]
  17. Yu T-T, Yao J-C, Ming H, Yin Y-R, Zhou E-M et al. Thermus tengchongensis sp. nov., isolated from a geothermally heated soil sample in Tengchong, Yunnan, south-west China. Antonie van Leeuwenhoek 2013;103: 513– 518 [CrossRef]
    [Google Scholar]
  18. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988;239: 487– 491 [CrossRef]
    [Google Scholar]
  19. Li W-J, Xu P, Schumann P, Zhang Y-Q, 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 [CrossRef]
    [Google Scholar]
  20. da Mota FF, Gomes EA, Paiva E, Rosado AS, Seldin L et al. Use of rpoB gene analysis for identification of nitrogen-fixing Paenibacillus species as an alternative to the 16S rRNA gene. Lett Appl Microbiol 2004;39: 34– 40 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. Pruesse E, Peplies J, Glöckner FO. Sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012;28: 1823– 1829 [CrossRef]
    [Google Scholar]
  23. 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 [CrossRef]
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425 [CrossRef]
    [Google Scholar]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  26. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20: 406– 416 [CrossRef]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  29. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012;1: 18 [CrossRef]
    [Google Scholar]
  30. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25: 955– 964 [CrossRef]
    [Google Scholar]
  31. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35: 3100– 3108 [CrossRef]
    [Google Scholar]
  32. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007;23: 673– 679 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  34. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012;28: 1033– 1034 [CrossRef]
    [Google Scholar]
  35. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32: 1792– 1797 [CrossRef]
    [Google Scholar]
  36. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000;17: 540– 552 [CrossRef]
    [Google Scholar]
  37. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015;32: 268– 274 [CrossRef]
    [Google Scholar]
  38. Letunic I, Bork P. Interactive tree of life (iTOL) V3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016;44: W242– W245 [CrossRef]
    [Google Scholar]
  39. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013;195: 413– 418 [CrossRef]
    [Google Scholar]
  40. Buck JD, Nonstaining BJD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982;44: 992– 993 [CrossRef]
    [Google Scholar]
  41. Leifson E. Atlas of bacterial flagellation. Q Rev Biol 1960; 242
    [Google Scholar]
  42. Nie G-X, Ming H, Li S, Zhou E-M, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012;62: 2650– 2656 [CrossRef]
    [Google Scholar]
  43. Groth I et al. Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 2004;54: 2121– 2129 [CrossRef]
    [Google Scholar]
  44. Nie G-X, Ming H, Li S, Zhou E-M, Cheng J et al. Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley. Antonie van Leeuwenhoek 2012;101: 811– 817 [CrossRef]
    [Google Scholar]
  45. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956;178: 703– 704 [CrossRef]
    [Google Scholar]
  46. 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 [CrossRef]
    [Google Scholar]
  47. Roberts FJ, MacFaddin JF. Biochemical tests for identification of medical bacteria, the Williams and Wilkins CO. Clin Biochem 1976;9: 178 [CrossRef]
    [Google Scholar]
  48. Uttley AHC, Collins CH. Cowan and Steel's Manual for the Identification of Medical Bacteria24, 3rd ed. J Hosp Infect; 1993; p 332
    [Google Scholar]
  49. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100: 221– 230 [CrossRef]
    [Google Scholar]
  50. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983;54: 31– 36 [CrossRef]
    [Google Scholar]
  51. 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 [CrossRef]
    [Google Scholar]
  52. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990;20: 16
    [Google Scholar]
  53. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980;48: 459– 470 [CrossRef]
    [Google Scholar]
  54. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979;47: 87– 95 [CrossRef]
    [Google Scholar]
  55. Nobre MF, Trüper HG, da Costa MS. Transfer of Thermus ruber (Loginova, et al. 1984), Thermus silvanus (Tenreiro, et al. 1995), and Thermus chliarophilus (Tenreiro, et al. 1995) to Meiothemus gen. nov. as Meiothermus ruber comb. nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus. Int J Syst Evol Microbiol 1996;46: 604– 606
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003965
Loading
/content/journal/ijsem/10.1099/ijsem.0.003965
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