1887

Abstract

Three closely related, facultative anaerobic, Gram-stain-negative, twitching motile, short rod-shaped, non-endospore-forming, moderately thermophilic bacteria, designated strains SYSU G05001, SYSU G05003 and SYSU G05004, were isolated from a hot spring microbial mat, collected from Rehai National Park, Tengchong, Yunnan Province, south-western China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that these three strains were closely related to SE-1 (97.97, 98.18, 97.90 % sequence similarity). Whole genome sequencing and polyphasic taxonomic approach were used to determine the genomic profile and taxonomic status of the novel strain SYSU G05001. Cell growth occurred at 37–80 °C (optimum, 55 °C), pH 6.0–8.0 (optimum, pH 7.0) and with 0–3.0 % (w/v) NaCl (optimum, 1%). Thiosulfate enhanced cell growth. MK-8 was the predominant menaquinone. The major cellular fatty acids included iso-C, iso-C and anteiso-C. The major polar lipids were consisted of aminophospholipid, glycolipid and phospholipids. The whole genome of strain SYSU G05001 consisted of 2.55 Mbp and the DNA G+C content was 64.94 mol%. The average nucleotide identity (≤94.95 %) and digital DNA–DNA hybridization (≤62.3 %) values between strain SYSU G05001 and other members of the genus were all lower than the threshold values recommended for distinguishing novel prokaryotic species. On the basis of the presented polyphasic evidence and genotypic data, it is proposed that strain SYSU G05001 (=KCTC 82627=MCCC 1K06118) represents a novel species of the genus , for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • China Postdoctoral Science Foundation (Award 2020M672948)
    • Principle Award Recipient: ShaTan
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: Jian-YuJiao
  • National Natural Science Foundation of China (Award 31970122)
    • Principle Award Recipient: En-MinZhou
  • National Natural Science Foundation of China (Award 32100042)
    • Principle Award Recipient: ShaTan
  • National Natural Science Foundation of China (Award 32170101)
    • Principle Award Recipient: Wen-DongXian
  • National Natural Science Foundation of China (Award 91951205)
    • Principle Award Recipient: Wen-JunLi
  • Guangdong Basic and Applied Basic Research Foundation (Award 2019A1515110227)
    • Principle Award Recipient: LanLiu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005265
2022-02-24
2024-11-05
Loading full text...

Full text loading...

References

  1. Egamberdieva D, Birkeland N-K, Panosyan H, Li W-J et al. Extremophiles in Eurasian ecosystems: ecology, diversity, and applications. In Diversity of Thermophiles in Terrestrial Hot Springs of Yunnan and Tibet, China Singapore: Springer; 2018 pp 57–59 [View Article]
    [Google Scholar]
  2. Brock TD, Freeze H. Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol 1969; 98:289–297 [View Article]
    [Google Scholar]
  3. 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 [View Article] [PubMed]
    [Google Scholar]
  4. 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 [View Article] [PubMed]
    [Google Scholar]
  5. Da Costa MS, Rainey FA, Nobre MF. The genus Thermus and relatives. In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E. eds The Prokaryotes New York, NY: Springer; 2006 pp 797–812
    [Google Scholar]
  6. Li M-M, Xian W-D, Zhang X-T, Yin Y-R, Zhou E-M et al. Thermus caldilimi sp. nov., a thermophilic bacterium isolated from a geothermal area. Antonie van Leeuwenhoek 2019; 112:1767–1774 [View Article] [PubMed]
    [Google Scholar]
  7. Ming H, Zhao Z-L, Ji W-L, Ding C-L, Cheng L-J et al. Thermus thermamylovorans sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2020; 70:1729–1737 [View Article] [PubMed]
    [Google Scholar]
  8. 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 [View Article] [PubMed]
    [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Biology 1971; 20:406–416 [View Article]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. Nei M, Kumar S. Molecular evolution and phylogenetics. Mol Phylogenet Evol 2002; 25:567–568 [View Article]
    [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. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  19. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
    [Google Scholar]
  20. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article] [PubMed]
    [Google Scholar]
  23. Lin S-H, Liao Y-C. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 2013; 8:e60843 [View Article] [PubMed]
    [Google Scholar]
  24. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  27. Jiao J-Y, Fu L, Hua Z-S, Liu L, Salam N et al. Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. ISME J 2021; 15:3005–3018 [View Article] [PubMed]
    [Google Scholar]
  28. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
    [Google Scholar]
  29. 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 [View Article] [PubMed]
    [Google Scholar]
  30. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. 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:W242–5 [View Article] [PubMed]
    [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  34. Zhou E-M, Xian W-D, Mefferd CC, Thomas SC, Adegboruwa AL et al. Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles 2018; 22:983–991 [View Article] [PubMed]
    [Google Scholar]
  35. Salzer R, Kern T, Joos F, Averhoff B. Environmental factors affecting the expression of type IV pilus genes as well as piliation of Thermus thermophilus. FEMS Microbiol Lett 2014; 357:56–62 [View Article] [PubMed]
    [Google Scholar]
  36. Hanada S, Takaichi S, Matsuura K, Nakamura K. Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 2002; 52:187–193 [View Article] [PubMed]
    [Google Scholar]
  37. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
    [Google Scholar]
  38. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
    [Google Scholar]
  39. Tambalo DD, Del Bel KL, Bustard DE, Greenwood PR, Steedman AE et al. Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade. Microbiology 2010; 156:1673–1685 [View Article] [PubMed]
    [Google Scholar]
  40. Odds F. Biochemical tests for identification of medical bacteria. J Clin Pathol 1981; 34:572 [View Article]
    [Google Scholar]
  41. 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 [View Article] [PubMed]
    [Google Scholar]
  42. Smibert R, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray TGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington, DC: ASM; 1994 pp 607–654
    [Google Scholar]
  43. 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 [View Article] [PubMed]
    [Google Scholar]
  44. Skirnisdottir S, Hreggvidsson GO, Holst O, Kristjansson JK. Isolation and characterization of a mixotrophic sulfur-oxidizing Thermus scotoductus. Extremophiles 2001; 5:45–51 [View Article] [PubMed]
    [Google Scholar]
  45. Kieft TL, Fredrickson JK, Onstott TC, Gorby YA, Kostandarithes HM et al. Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate. Appl Environ Microbiol 1999; 65:1214–1221 [View Article] [PubMed]
    [Google Scholar]
  46. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  47. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  48. 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]
  49. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  50. 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 [View Article]
    [Google Scholar]
  51. 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
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005265
Loading
/content/journal/ijsem/10.1099/ijsem.0.005265
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