1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 10

gen. nov., sp. nov., a member of the family isolated from marine sediment Free

Abstract

Three novel actinobacterial strains, designated as TPS16, TPS81 and TPS83, were isolated from a sample of marine sediment collected from Tioman Island, Malaysia. The strains formed abundant branched substrate mycelia without fragmentation along with production of blue spores and blue diffusible pigment on soybean meal agar. The strains could grow at pH ranging from pH 6 to 12 and in 0–8 % (w/v) NaCl. Cell-wall hydrolysis showed the presence of -diaminopimelic acid. The strains were closely related to SCSIO 00652 (97.60 %) and YIM 690053 (96.87 %) based on phylogenetic analysis of 16S rRNA gene sequences. Multilocus sequence analysis including , and genes further confirmed that strain TPS16 represented a distinct branch within the family . The predominant menaquinones were MK-11(H), MK-10(H), MK-11(H) and MK-10(H), while the major fatty acids were found to be iso-C, anteiso-C, iso-C and Cω9. Genome sequencing revealed genome sizes of approximately 6 Mb and G+C contents of 73.8 mol%. A new genus, gen. nov., is proposed within the family based on polyphasic data and the type species is gen. nov., sp. nov. The type strain is TPS16 (=DSM 46825=TBRC 5138).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinobacteria , genome and Malaysia
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003587
2019-10-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/10/3031.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003587&mimeType=html&fmt=ahah

References

  1. Kroppenstedt RM, Evtushenko LI. The family Nocardiopsaceae . In Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E et al. (editors) The Prokaryotes New York, NY, USA: Springer; 2014 pp. 754–795
     [Google Scholar]
  2. Nocardiopsis MJ. a new genus of the order Actinomycetales . Int J Syst Evol Microbiol 1976; 26:487–493
     [Google Scholar]
  3. Li J, Yang J, Zhu WY, He J, Tian XP et al. Nocardiopsis coralliicola sp. nov., isolated from the gorgonian coral, Menella praelonga . Int J Syst Evol Microbiol 2012; 62:1653–1658 [View Article][PubMed]
     [Google Scholar]
  4. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora . Int J Syst Bacteriol 1998; 48 Pt 2:411–422 [View Article][PubMed]
     [Google Scholar]
  5. Yang LL, Tang SK, Zhang YQ, Zhi XY, Wang D et al. Thermobifida halotolerans sp. nov., isolated from a salt mine sample, and emended description of the genus Thermobifida . Int J Syst Evol Microbiol 2008; 58:1821 [View Article][PubMed]
     [Google Scholar]
  6. Cai M, Zhi XY, Tang SK, Zhang YQ, Xu LH et al. Streptomonospora halophila sp. nov., a halophilic actinomycete isolated from a hypersaline soil. Int J Syst Evol Microbiol 2008; 58:1556–1560 [View Article][PubMed]
     [Google Scholar]
  7. Tang SK, Tian XP, Zhi XY, Cai M, Wu JY et al. Haloactinospora alba gen. nov., sp. nov., a halophilic filamentous actinomycete of the family Nocardiopsaceae . Int J Syst Evol Microbiol 2008; 58:2075–2080 [View Article][PubMed]
     [Google Scholar]
  8. Tian XP, Tang SK, Dong JD, Zhang YQ, Xu LH et al. Marinactinospora thermotolerans gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea. Int J Syst Evol Microbiol 2009; 59:948–952 [View Article][PubMed]
     [Google Scholar]
  9. Chang X, Liu W, Zhang XH. Spinactinospora alkalitolerans gen. nov., sp. nov., an actinomycete isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:2805–2810 [View Article][PubMed]
     [Google Scholar]
  10. Chang X, Liu W, Zhang XH. Salinactinospora qingdaonensis gen. nov., sp. nov., a halophilic actinomycete isolated from a salt pond. Int J Syst Evol Microbiol 2012; 62:954–959 [View Article][PubMed]
     [Google Scholar]
  11. Kämpfer P, Schäfer J, Lodders N, Martin K. Murinocardiopsis flavida gen. nov., sp. nov., an actinomycete isolated from indoor walls. Int J Syst Evol Microbiol 2010; 60:1729 [View Article][PubMed]
     [Google Scholar]
  12. Guo L, Tuo L, Habden X, Zhang Y, Liu J et al. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 2015; 65:206–213 [View Article][PubMed]
     [Google Scholar]
  13. Liu MJ, Zhu WY, Li J, Zhao GZ, Xiong Z et al. Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota . Int J Syst Evol Microbiol 2015; 65:2562–2568 [View Article][PubMed]
     [Google Scholar]
  14. Zhang YG, Lu XH, Ding YB, Wang SJ, Zhou XK et al. Lipingzhangella halophila gen. nov., sp. nov., a new member of the family Nocardiopsaceae . Int J Syst Evol Microbiol 2016; 66:4071–4076 [View Article][PubMed]
     [Google Scholar]
  15. Ng ZY, Tan GYA. Selective isolation and characterisation of novel members of the family Nocardiopsaceae and other actinobacteria from a marine sediment of Tioman Island. Antonie Van Leeuwenhoek 2018; 111:727–742 [View Article][PubMed]
     [Google Scholar]
  16. Vidgen ME, Hooper JN, Fuerst JA. Diversity and distribution of the bioactive actinobacterial genus Salinispora from sponges along the Great Barrier Reef. Antonie van Leeuwenhoek 2012; 101:603–618 [View Article][PubMed]
     [Google Scholar]
  17. Freel KC, Edlund A, Jensen PR. Microdiversity and evidence for high dispersal rates in the marine actinomycete 'Salinispora pacifica'. Environ Microbiol 2012; 14:480–493 [View Article][PubMed]
     [Google Scholar]
  18. Jensen MA, Webster JA, Straus N. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 1993; 59:945–952[PubMed]
     [Google Scholar]
  19. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Jones MP, Mccarthy AJ, Cross T. Taxonomic and serologic studies on Micropolyspora faeni and Micropolyspora strains from soil bearing the specific epithet rectivirgula . J Gen Microbiol 1979; 115:343–354 [View Article][PubMed]
     [Google Scholar]
  23. Gledhill WE, Casida LE. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia . Appl Microbiol 1969; 18:340–349[PubMed]
     [Google Scholar]
  24. Iwasaki A, Itoh H, Mori T. A new broad-spectrum aminoglycoside antibiotic complex, sporaricin. II. Taxonomic studies on the sporaricin producing strain Saccharopolyspora hirsuta subsp. Kobensis nov. subsp. J Antibiot 1979; 32:180–186 [View Article][PubMed]
     [Google Scholar]
  25. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  26. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  27. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  28. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  29. 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]
  30. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000; 17:1251–1258 [View Article][PubMed]
     [Google Scholar]
  31. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
     [Google Scholar]
  32. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  33. Nei M, Kumar S. Molecular Evolution and Phylogenetics Oxford, UK: Oxford University Press; 2000 pp. 147-–152
     [Google Scholar]
  34. Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012; 28:1420–1428 [View Article][PubMed]
     [Google Scholar]
  35. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
     [Google Scholar]
  36. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  37. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–14 [View Article][PubMed]
     [Google Scholar]
  38. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
     [Google Scholar]
  39. Li SH, Yu XY, Park DJ, Hozzein WN, Kim CJ et al. Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie van Leeuwenhoek 2015; 107:357–366 [View Article][PubMed]
     [Google Scholar]
  40. Weber T, Blin K, Duddela S, Krug D, Kim HU et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 2015; 43:W237–W243 [View Article][PubMed]
     [Google Scholar]
  41. Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J et al. Next-generation systematics: an innovative approach to resolve the structure of complex prokaryotic taxa. Sci Rep 2016; 6:38392 [View Article][PubMed]
     [Google Scholar]
  42. Boncompagni E, Osteras M, Poggi MC, le Rudulier D. Occurrence of choline and glycine betaine uptake and metabolism in the family Rhizobiaceae and their roles in osmoprotection. Appl Environ Microbiol 1999; 65:2072[PubMed]
     [Google Scholar]
  43. Kuhlmann AU, Hoffmann T, Bursy J, Jebbar M, Bremer E. Ectoine and hydroxyectoine as protectants against osmotic and cold stress: uptake through the SigB-controlled betaine-choline- carnitine transporter-type carrier EctT from Virgibacillus pantothenticus . J Bacteriol 2011; 193:4699–4708 [View Article][PubMed]
     [Google Scholar]
  44. Scholz A, Stahl J, De Berardinis V, Müller V, Averhoff B. Osmotic stress response in Acinetobacter baylyi: identification of a glycine-betaine biosynthesis pathway and regulation of osmoadaptive choline uptake and glycine-betaine synthesis through a choline-responsive BetI repressor. Environ Microbiol Rep 2016; 8:316–322 [View Article][PubMed]
     [Google Scholar]
  45. Rennella E, Sára T, Juen M, Wunderlich C, Imbert L et al. RNA binding and chaperone activity of the E. coli cold-shock protein CspA . Nucleic Acids Res 2017; 45:4255–4268 [View Article][PubMed]
     [Google Scholar]
  46. Zhang Y, Burkhardt DH, Rouskin S, Li GW, Weissman JS et al. A stress response that monitors and regulates mRNA structure is central to cold shock adaptation. Mol Cell 2018; 70:274–286 [View Article][PubMed]
     [Google Scholar]
  47. Schumann W. Regulation of bacterial heat shock stimulons. Cell Stress Chaperones 2016; 21:959–968 [View Article][PubMed]
     [Google Scholar]
  48. Frey AD, Kallio PT. Nitric oxide detoxification – a new era for bacterial globins in biotechnology?. Trends Biotechnol 2005; 23:69–73 [View Article]
     [Google Scholar]
  49. Johnson JE, Choksi K, Widger WR. NADH-Ubiquinone oxidoreductase: substrate-dependent oxygen turnover to superoxide anion as a function of flavin mononucleotide. Mitochondrion 2003; 3:97–110 [View Article][PubMed]
     [Google Scholar]
  50. Peng G, Meyer B, Sokolova L, Liu W, Bornemann S et al. Identification and characterization two isoforms of NADH:ubiquinone oxidoreductase from the hyperthermophilic eubacterium Aquifex aeolicus . Biochim Biophys Acta Bioenerg 2018; 1859:366–373 [View Article][PubMed]
     [Google Scholar]
  51. Binepal G, Gill K, Crowley P, Cordova M, Brady LJ et al. Trk2 Potassium transport system in Streptococcus mutans and its role in potassium homeostasis, biofilm formation, and stress tolerance. J Bacteriol 2016; 198:1087–1100 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003587
Loading
Marinitenerispora sediminis gen. nov., sp. nov., a member of the family Nocardiopsaceae isolated from marine sediment
Int J Syst Evol Microbiol 69, 3031 (2019); https://doi.org/10.1099/ijsem.0.003587
/content/journal/ijsem/10.1099/ijsem.0.003587
/content/journal/ijsem/10.1099/ijsem.0.003587
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