1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 10

gen. nov., sp. nov., a new member of the family isolated from forest soil in a geothermal area Free

Abstract

Six mycelium-forming actinomycete strains were isolated from forest soil near the Cisolok geysers in West Java, Indonesia. The 16S rRNA gene sequences of these strains showed high similarity to members of genera in the family with values less than 96.0 %, and most closely related to the genus AG2-7(94.6–95.2 % similarity). The type strain, designated SL3-2-4, was aerobic, thermophilic, Gram-stain-positive that formed branched, non-fragmented substrate mycelia and unbranched aerial mycelia with long-chain, oval-shaped spores on International Project (ISP) 3 medium. It produced light-orange substrate mycelia and light-orange diffusible pigments on ISP 3 medium with 2 % gellan gum, grown at 30–55 °C, with optimum growth at 45 °C. The pH range for growth was 4.0–8.0, with optimum growth at pH 7.0. Strain SL3-2-4 was able to hydrolyze casein, esculin, gelatin, guanine, hypoxanthine, starch, L-tyrosine, and xanthine, but not adenine, carboxymethyl-cellulose, cellulose, chitin, Tween 20, or xylan. The major fatty acid was -C, and the major menaquinone was MK-8 (H). The detected polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyl--methylethanolamine, unidentified aminophospholipids, unidentified glycolipids, and unidentified phospholipids. The cell wall hydrolysate of SL3-2-4 contained -2,4-diaminopimelic acid. The whole cell sugars were arabinose and galactose. The DNA G+C content was 71.6 mol%. Phenotypic features and phylogenetic data differentiated SL3-2-4 from members of the family Therefore, the strain SL3-2-4 is proposed as a representative of a novel species in a novel genus, gen. nov., sp. nov. The type strain is SL3-2-4 (=UICC B-83=NRRL B-67478=InaCC A981).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): forest soil , geysers , polyphasic taxonomy and thermophilic actinomycete
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003594
2019-10-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/10/3080.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003594&mimeType=html&fmt=ahah

References

  1. Labeda DP, Goodfellow M, Chun J, Zhi XY, Li WJ. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2011; 61:1259–1264 [View Article][PubMed]
     [Google Scholar]
  2. Labeda DP, Goodfellow M. Pseudonocardiales ord. nov. Bergey’s Manual of Systematics of Archaea and Bacteria Bergey’s Manual Trust: John Wiley & Sons, Inc; 2015
     [Google Scholar]
  3. Wu H, Lian Y, Liu B, Ren Y, Qin P et al. Thermotunica guangxiensis gen. nov., sp. nov., isolated from mushroom residue compost. Int J Syst Evol Microbiol 2014; 64:1593–1599 [View Article][PubMed]
     [Google Scholar]
  4. Labeda DP, Kroppenstedt RM. Goodfellowia gen. nov., a new genus of the Pseudonocardineae related to Actinoalloteichus, containing Goodfellowia coeruleoviolacea gen. nov., comb. nov. Int J Syst Evol Microbiol 2006; 56:1203–1207 [View Article][PubMed]
     [Google Scholar]
  5. Labeda DP, Kroppenstedt RM, Euzéby JP, Tindall BJ. Proposal of Goodfellowiella gen. nov. to replace the illegitimate genus name Goodfellowia Labeda and Kroppenstedt 2006. Int J Syst Evol Microbiol 2008; 58:1047–1048 [View Article][PubMed]
     [Google Scholar]
  6. Tamura T, Zhiheng L, Yamei Z, Hatano K. Actinoalloteichus cyanogriseus gen. nov., sp. nov. Int J Syst Evol Microbiol 2000; 50:1435–1440 [View Article][PubMed]
     [Google Scholar]
  7. Tamura T, Ishida Y, Otoguro M, Hatano K, Suzuki K. Classification of 'Streptomyces tenebrarius' Higgins and Kastner as Streptoalloteichus tenebrarius nom. rev., comb. nov., and emended description of the genus Streptoalloteichus . Int J Syst Evol Microbiol 2008; 58:688–691 [View Article][PubMed]
     [Google Scholar]
  8. Labeda DP. Crossiella gen. nov., a new genus related to Streptoalloteichus . Int J Syst Evol Microbiol 2001; 51:1575–1579 [View Article][PubMed]
     [Google Scholar]
  9. Suriyachadkun C, Ngaemthao W, Chunhametha S, Tamura T, Sanglier JJ. Kutzneria buriramensis sp. nov., isolated from soil, and emended description of the genus Kutzneria . Int J Syst Evol Microbiol 2013; 63:47–52 [View Article][PubMed]
     [Google Scholar]
  10. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  11. Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A. Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost and description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria . Int J Syst Evol Microbiol 2010; 60:1794–1801
     [Google Scholar]
  12. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145[PubMed]
     [Google Scholar]
  13. Stott MB, Crowe MA, Mountain BW, Smirnova AV, Hou S et al. Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 2008; 10:2030–2041 [View Article][PubMed]
     [Google Scholar]
  14. Mordarska H, Mordarski M, Goodfellow M. Chemotaxonomic characters and classification of some nocardioform bacteria. J Gen Microbiol 1972; 71:77–86 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. Magee CM, Rodeheaver G, Edgerton MT, Edlich RF. A more reliable gram staining technic for diagnosis of surgical infections. Am J Surg 1975; 130:341–346 [View Article][PubMed]
     [Google Scholar]
  17. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
     [Google Scholar]
  18. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  19. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477[PubMed]
     [Google Scholar]
  20. 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]
  21. Harper JJ, Davis GHG. Two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol 1979; 29:56–58 [View Article]
     [Google Scholar]
  22. 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]
  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. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
     [Google Scholar]
  25. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  26. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  27. Lechevalier MP, Prauser H, Labeda DP, Ruan J-S. Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 1986; 36:29–37 [View Article]
     [Google Scholar]
  28. Warwick S, Bowen T, McVeigh H, Embley TM. A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia . Int J Syst Bacteriol 1994; 44:293–299 [View Article][PubMed]
     [Google Scholar]
  29. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  34. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  35. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [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. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article][PubMed]
     [Google Scholar]
  38. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 2017; 45:W36–W41 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003594
Loading
Gandjariella thermophila gen. nov., sp. nov., a new member of the family Pseudonocardiaceae, isolated from forest soil in a geothermal area
Int J Syst Evol Microbiol 69, 3080 (2019); https://doi.org/10.1099/ijsem.0.003594
/content/journal/ijsem/10.1099/ijsem.0.003594
/content/journal/ijsem/10.1099/ijsem.0.003594
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

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