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Volume 74, Issue 4

sp. nov., isolated from rhizospheric soil of eggplant and genome mining for the prediction of biosynthetic gene clusters Open Access

Abstract

A Gram-stain negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-54, was isolated from the rhizospheric soil of eggplant. The colonies were observed to be light pink coloured, smooth, spherical and 0.2–0.6 mm in diameter when grown on R2A agar medium for 2 days. MAHUQ-54 was able to grow at 15–40 °C, at pH 5.5–9.0 and in the presence of 0–0.5 % NaCl (w/v). The strain gave positive results for both catalase and oxidase tests. The strain was positive for hydrolysis of -tyrosine, urea, Tween 20 and Tween 80. On the basis of the results of 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus and is closely related to L10 (98.8 % sequence similarity) and Feox-1 (98.2 %). MAHUQ-54 has a draft genome size of 5 994 516 bp (60 contigs), annotated with 5348 protein-coding genes, 45 tRNA and 5 rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values between MAHUQ-54 and its closest phylogenetic neighbours were 75.8–83.3 and 20.8–25.3 %, respectively. genome mining revealed that MAHUQ-54 has a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 70.4 %. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as C, summed feature 3 (comprising Cω7 and/or Cω6) and summed feature 8 (comprising Cω7 and/or Cω6). On the basis of dDDH, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAHUQ-54 represents a novel species within the genus , for which the name sp. nov. is proposed, with MAHUQ-54 (=KACC 22001 = CGMCC 1.18515) as the type strain.

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  • Accepted:
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Keyword(s): Aquincola agrisoli , digital DNA–DNA hybridisation , genome sequence , in silico genome mining and secondary metabolites
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-05-15
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References

  1. Lechner U, Brodkorb D, Geyer R, Hause G, Härtig C et al. Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium. Int J Syst Evol Microbiol 2007; 57:1295–1303 [View Article] [PubMed]
     [Google Scholar]
  2. Garrity GM, Bell JA, Lilburn T, Order I. Burkholderiales ord. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol 2 New York: Springer; 2005 pp 575–763
     [Google Scholar]
  3. Piveteau P, Fayolle F, Vandecasteele JP, Monot F. Biodegradation of tert-butyl alcohol and related xenobiotics by a methylotrophic bacterial isolate. Appl Microbiol Biotechnol 2001; 55:369–373 [View Article] [PubMed]
     [Google Scholar]
  4. Chen WM, Chen YL, Li YS, Sheu SY. Aquincola amnicola sp. nov., isolated from a freshwater river. Arch Microbiol 2018; 200:811–817 [View Article] [PubMed]
     [Google Scholar]
  5. Sheu SY, Hsieh TY, Chen WM. Aquincola rivuli sp. nov., isolated from a freshwater stream. Int J Syst Evol Microbiol 2019; 69:2226–2232 [View Article] [PubMed]
     [Google Scholar]
  6. Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759 [View Article] [PubMed]
     [Google Scholar]
  7. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematic New York: Wiley; 1991 pp 115–175
     [Google Scholar]
  8. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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]
  9. 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]
  10. Hall TA. Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  11. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [View Article]
     [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 1987; 4:406–425
     [Google Scholar]
  13. 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]
  14. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  15. Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  16. 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 [View Article] [PubMed]
     [Google Scholar]
  17. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  18. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849 [View Article]
     [Google Scholar]
  19. 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]
     [Google Scholar]
  20. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article]
     [Google Scholar]
  21. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
     [Google Scholar]
  22. Shi W, Sun Q, Fan G, Hideaki S, Moriya O et al. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694–D705 [View Article] [PubMed]
     [Google Scholar]
  23. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
     [Google Scholar]
  24. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Research 2008; 36:W181–W184 [View Article]
     [Google Scholar]
  25. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  26. Huq MA. Chryseobacterium chungangensis sp. nov., a bacterium isolated from soil of sweet gourd garden. Arch Microbiol 2018; 200:581–587 [View Article] [PubMed]
     [Google Scholar]
  27. Cappuccino JG, Sherman N. Biochemical Activities of Microorganisms. In Microbiology, A Laboratory Manual Menlo Park, CA, USA: The Benjamin/Cummings Publishing Co., Inc; 1992 pp 188–247
     [Google Scholar]
  28. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  29. Huq MA. Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden. Arch Microbiol 2018; 200:343–348 [View Article] [PubMed]
     [Google Scholar]
  30. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  31. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  32. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
     [Google Scholar]
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Aquincola agrisoli sp. nov., isolated from rhizospheric soil of eggplant and in silico genome mining for the prediction of biosynthetic gene clusters
Int J Syst Evol Microbiol 74, 006355 (2024); https://doi.org/10.1099/ijsem.0.006355
/content/journal/ijsem/10.1099/ijsem.0.006355
/content/journal/ijsem/10.1099/ijsem.0.006355
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