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Volume 69, Issue 12

gen. nov., sp. nov., a new member of the family from a karstic cavern Free

Abstract

A novel actinobacterium, designated strain CFH 30434, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province, PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive, non-motile and coccoid or short rods. The strain was found to be oxidase-positive and weakly catalase-positive. Strain CFH 30434 grew optimally at 28 °C, pH 7.0–9.0 and in the presence of up to 0–1.5 % NaCl (w/v). The whole-cell sugars were glucose, mannose and rhamnose. The major isoprenoid quinone was MK-9(H) and the major fatty acids (>10 % of the total fatty acids compositions) were anteiso-C, iso-C and iso-C. The polar lipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The genomic DNA G+C content was determined to be 72.3 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that CFH 30434 clustered within the family , and closely with the type strains of DSM 12657, DSM 17134 and CCTCC AA 208046 (97.3 %, 96.2 and 95.9 % sequence similarities, respectively). Phylogenetic analysis showed that strain CFH 30434 formed a separate evolutionary branch, and was parallel to other related genera of . Its phylogenetic distinctiveness and distinguishing phenotypic characteristics supported that strain CFH 30434 represents a novel genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain is CFH 30434 (=CGMCC 1.13856=KCTC 49093).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Antribacter gilvus gen. nov., sp. nov., , Karst cave and Polyphasic taxonomy
© 2019 Sun Yat-Sen University, P.R. China
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2019-12-01
2022-05-20
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References

  1. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  2. Zhi XY, Li WJ, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589–608 [View Article][PubMed]
     [Google Scholar]
  3. Schumann P, Weiss N, Stackebrandt E. Reclassification of Cellulomonas cellulans (Stackebrandt and Keddie 1986) as Cellulosimicrobium cellulans gen. nov., comb. nov. Int J Syst Evol Microbiol 2001 2001; 51:1007–1010 [View Article][PubMed]
     [Google Scholar]
  4. Stackebrandt E, Schumann P, Cui XL. Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov. Int J Syst Evol Microbiol 2004; 54:685–688 [View Article][PubMed]
     [Google Scholar]
  5. Nishijima M, Tazato N, Handa Y, Umekawa N, Kigawa R et al. Krasilnikoviella muralis gen. nov., sp. nov., a member of the family Promicromonosporaceae, isolated from the Takamatsuzuka Tumulus stone chamber interior and reclassification of Promicromonospora flava as Krasilnikoviella flava comb. nov. Int J Syst Evol Microbiol 2017; 67:294–300 [View Article][PubMed]
     [Google Scholar]
  6. Cui X, Schumann P, Stackebrandt E, Kroppenstedt RM, Pukall R et al. Myceligenerans xiligouense gen. nov., sp. nov., a novel hyphae-forming member of the family Promicromonosporaceae . Int J Syst Evol Microbiol 2004; 54:1287–1293 [View Article][PubMed]
     [Google Scholar]
  7. Rivas R, Sánchez M, Trujillo ME, Zurdo-Piñeiro JL, Mateos PF et al. Xylanimonas cellulosilytica gen. nov., sp. nov., a xylanolytic bacterium isolated from a decayed tree (Ulmus nigra). Int J Syst Evol Microbiol 2003; 53:99–103 [View Article][PubMed]
     [Google Scholar]
  8. Rivas R, Trujillo ME, Schumann P, Kroppenstedt RM, Sánchez M et al. Xylanibacterium ulmi gen. nov., sp. nov., a novel xylanolytic member of the family Promicromonosporaceae . Int J Syst Evol Microbiol 2004; 54:557–561 [View Article][PubMed]
     [Google Scholar]
  9. Stackebrandt E, Schumann P. Reclassification of Promicromonospora pachnodae Cazemier et al. 2004 as Xylanimicrobium pachnodae gen. nov., comb. nov. Int J Syst Evol Microbiol 2004; 54:1383–1386 [View Article][PubMed]
     [Google Scholar]
  10. Krasilnikov NA, Kalakoutskii LV, Kirillova NF. A new genus of Actinomycetales, Promicromonospora, gen. nov. Bull Acad Sci USSR Ser Biol 1961; 1:107–112
     [Google Scholar]
  11. Kaewkla O, Franco CMM. Promicromonospora callitridis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized root of an Australian native pine tree. Int J Syst Evol Microbiol 2017; 67:3559–3563 [View Article][PubMed]
     [Google Scholar]
  12. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  13. Ming H, Yin YR, Li S, Nie GX, Yu TT 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]
  14. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
     [Google Scholar]
  15. Atlas RM. In Parks LC. (editor) Handbook of Microbiological Media, 4th ed. Boca Raton, FL: CRC Press; 2010 pp. 719
     [Google Scholar]
  16. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ 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]
  17. 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]
  18. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  19. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL . In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 4 Baltimore: Williams & Willkins; 1989 pp. 2453–2492
     [Google Scholar]
  20. Tang SK, Wang Y, Chen Y, Lou K, Cao LL et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 2009; 59:2025–2032 [View Article][PubMed]
     [Google Scholar]
  21. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477[PubMed]
     [Google Scholar]
  22. 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]
  23. 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]
  24. 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]
  25. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123:31–36 [View Article][PubMed]
     [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
     [Google Scholar]
  27. 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 [View Article]
     [Google Scholar]
  28. 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]
  29. Li WJ, Xu P, Schumann P, Zhang YQ, 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]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  35. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  36. 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]
  37. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press; 1985
     [Google Scholar]
  38. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  39. Harrison P, Strulo B. SPADES - a process algebra for discrete event simulation. J Logic Comput 2000; 10:3–42 [View Article]
     [Google Scholar]
  40. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
     [Google Scholar]
  41. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article][PubMed]
     [Google Scholar]
  42. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44:D279–D285 [View Article][PubMed]
     [Google Scholar]
  43. 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]
  44. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article][PubMed]
     [Google Scholar]
  45. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  46. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
     [Google Scholar]
  47. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article][PubMed]
     [Google Scholar]
  48. Schumann P, Stackebrandt E. Family XII. Promicromonosporaceae Rainey, Ward-Rainey and Stackebrandt 1997, 484VP emend. Zhi, Li and Stackebrandt 2009, 598. In Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology Part A, 2nd ed. vol. 5 New York: Springer; 2012 pp. 995–1017
     [Google Scholar]
  49. Yoon JH, Kang SJ, Schumann P, Oh TK, Tk O. Cellulosimicrobium terreum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2007; 57:2493–2497 [View Article][PubMed]
     [Google Scholar]
  50. Brown JM, Steigerwalt AG, Morey RE, Daneshvar MI, Romero LJ et al. Characterization of clinical isolates previously identified as Oerskovia turbata: proposal of Cellulosimicrobium funkei sp. nov. and emended description of the genus Cellulosimicrobium . Int J Syst Evol Microbiol 2006; 56:801–804 [View Article][PubMed]
     [Google Scholar]
  51. Groth I, Schumann P, Schütze B, Gonzalez JM, Laiz L et al. Myceligenerans crystallogenes sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 2006; 56:283–287 [View Article][PubMed]
     [Google Scholar]
  52. Wang Y, Tang SK, Li Z, Lou K, Mao PH et al. Myceligenerans halotolerans sp. nov., an actinomycete isolated from a salt lake, and emended description of the genus Myceligenerans . Int J Syst Evol Microbiol 2011; 61:974–978 [View Article][PubMed]
     [Google Scholar]
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Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern
Int J Syst Evol Microbiol 69, 3792 (2019); https://doi.org/10.1099/ijsem.0.003682
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