1887

Abstract

An isolate, designated CFH 74404, was recovered from a hot spring in Tengchong, Yunnan province, PR China. Phylogenetic analysis indicated that the isolate belongs to the family and showed the highest 16S rRNA gene sequence similarity to KI4 (93.6 %), WKT50.2 (93.1 %), DSM 5159 (92.0 %) and KI3 (91.7 %). The average amino acid identity and average nucleotide identity values between strain CFH 74404 and the closest relatives were 42.0–75.9 % and 67.0–77.3 %, respectively. Cells of strain CFH 74404 stained Gram-positive and were aerobic, non-motile and short rod-shaped. Growth occurred at 20–65 °C (optimum, 55 °C), pH 6.0–8.0 (optimum, pH 7.0) and with up to 2.0 % (w/v) NaCl (optimum 0–1.0 %, w/v). The predominant respiratory quinone was MK-8. The major fatty acids (>10 %) were C (50.8 %) and C (16.8 %). The polar lipid profile of strain CFH 74404 included diphosphatidylglycerol, four unidentified phosphoglycolipids, phosphatidylinositol and three unidentified glycolipids. The G+C content of the genomic DNA was determined to be 67.1 mol% based on the draft genome sequence. On the basis of phenotypic, phylogenetic and genotypic analyses, it is concluded that strain CFH 74404 represents a new species of a novel genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain is CFH 74404 (=KCTC 62930=CGMCC 1.61585).

Funding
This study was supported by the:
  • Doctor Scientific Research Fund of Xinxiang Medical University (Award XYBSKYZZ201625)
    • Principle Award Recipient: HongMing
  • Key Technologies R&D Program of Henan Province (Award 202102110107)
    • Principle Award Recipient: HongMing
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: Jian-YuJiao
  • National Natural Science Foundation of China (Award 91951205 and 92251302)
    • Principle Award Recipient: Wen-JunLi
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005891
2023-05-19
2024-09-18
Loading full text...

Full text loading...

References

  1. Garrity GM, Holt JG, Family I. Thermomicrobiaceae fam. nov. In Boone DR, Castenholz RW, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 1 New York: Springer; 2001 pp 447–450 [View Article]
    [Google Scholar]
  2. Demharter W, Hensel R, Smida J, Stackebrandt E. Sphaerobacter thermophilus gen. nov., sp. nov. A deeply rooting member of the Actinomycetes subdivision isolated from thermophilically treated sewage sludge. Syst Appl Microbiol 1989; 11:261–266 [View Article]
    [Google Scholar]
  3. Hugenholtz P, Stackebrandt E. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 2004; 54:2049–2051 [View Article] [PubMed]
    [Google Scholar]
  4. Sorokin DY, Vejmelkova D, Lücker S, Streshinskaya GM, Rijpstra WIC et al. Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi. Int J Syst Evol Microbiol 2014; 64:1859–1865 [View Article] [PubMed]
    [Google Scholar]
  5. Houghton KM, Morgan XC, Lagutin K, MacKenzie AD, Vyssotskii M et al. Thermorudis pharmacophila sp. nov., a novel member of the class Thermomicrobia isolated from geothermal soil, and emended descriptions of Thermomicrobium roseum, Thermomicrobium carboxidum, Thermorudis peleae and Sphaerobacter thermophilus. Int J Syst Evol Microbiol 2015; 65:4479–4487 [View Article] [PubMed]
    [Google Scholar]
  6. King CE, King GM. Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms. Int J Syst Evol Microbiol 2014; 64:2586–2592 [View Article] [PubMed]
    [Google Scholar]
  7. Jackson TJ, Ramaley RF, Meinschein WG. Thermomicrobium, a new genus of extremely thermophilic bacteria. Int J Syst Bacteriol 1973; 23:28–36 [View Article]
    [Google Scholar]
  8. Phillips WE, Perry JJ. Thermomicrobium fosteri sp. nov., a hydrocarbon-utilizing obligate thermophile. Int J Syst Bacteriol 1976; 26:220–225 [View Article]
    [Google Scholar]
  9. Wu D, Raymond J, Wu M, Chatterji S, Ren Q et al. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One 2009; 4:e4207 [View Article] [PubMed]
    [Google Scholar]
  10. Feng X-M, Mo Y-X, Han L, Nogi Y, Zhu Y-H et al. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2015; 65:3658–3665 [View Article] [PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. da Mota FF, Gomes EA, Paiva E, Rosado AS, Seldin L. 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 [View Article] [PubMed]
    [Google Scholar]
  14. Huang Y, Sun Y, Ma S, Chen L, Zhang H et al. Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity. FEMS Microbiol Lett 2013; 345:56–63 [View Article] [PubMed]
    [Google Scholar]
  15. Thomas P. Isolation of an ethanol-tolerant endospore-forming Gram-negative Brevibacillus sp. as a covert contaminant in grape tissue cultures. J Appl Microbiol 2006; 101:764–774 [View Article] [PubMed]
    [Google Scholar]
  16. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article] [PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  24. Liu Y-H, Guo J-W, Salam N, Li L, Zhang Y-G et al. Culturable endophytic bacteria associated with medicinal plant Ferula songorica: molecular phylogeny, distribution and screening for industrially important traits. 3 Biotech 2016; 6:209 [View Article] [PubMed]
    [Google Scholar]
  25. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  26. 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 [View Article] [PubMed]
    [Google Scholar]
  27. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
  30. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article] [PubMed]
    [Google Scholar]
  31. Salam N, Jiao JY, Zhang XT, Li WJ. Update on the classification of higher ranks in the phylum Actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
  34. 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] [PubMed]
    [Google Scholar]
  35. 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]
  36. 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]
  37. Bok JD, Yernool DA, Eveleigh DE. Purification, characterization, and molecular analysis of thermostable cellulases CelA and CelB from Thermotoga neapolitana. Appl Environ Microbiol 1998; 64:4774–4781 [View Article] [PubMed]
    [Google Scholar]
  38. 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]
  39. 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 [View Article] [PubMed]
    [Google Scholar]
  40. Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E 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 [View Article] [PubMed]
    [Google Scholar]
  41. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  42. Collins MD, Goodfellow M, Minnikin DE, Alderson G. Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 1985; 58:77–86 [View Article] [PubMed]
    [Google Scholar]
  43. 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]
  44. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  45. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  46. 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]
  47. Becraft ED, Dodsworth JA, Murugapiran SK, Ohlsson JI, Briggs BR et al. Single-cell-genomics-facilitated read binning of candidate phylum EM19 genomes from geothermal spring metagenomes. Appl Environ Microbiol 2016; 82:992–1003 [View Article] [PubMed]
    [Google Scholar]
  48. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013; 499:431–437 [View Article] [PubMed]
    [Google Scholar]
  49. King GM. Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity. Appl Environ Microbiol 2003; 69:7257–7265 [View Article] [PubMed]
    [Google Scholar]
  50. Schübel U, Kraut M, Mörsdorf G, Meyer O. Molecular characterization of the gene cluster coxMSL encoding the molybdenum-containing carbon monoxide dehydrogenase of Oligotropha carboxidovorans. J Bacteriol 1995; 177:2197–2203 [View Article] [PubMed]
    [Google Scholar]
  51. Hugendieck I, Meyer O. The structural genes encoding CO dehydrogenase subunits (cox L, M and S) in Pseudomonas carboxydovorans OM5 reside on plasmid pHCG3 and are, with the exception of Streptomyces thermoautotrophicus, conserved in carboxydotrophic bacteria. Arch Microbiol 1992; 157:301–304 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005891
Loading
/content/journal/ijsem/10.1099/ijsem.0.005891
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