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Volume 72, Issue 3

sp. nov., a novel endophytic bacterium isolated from bark of No Access

Abstract

A new endophytic bacterium, designated strain MQZ13P-4 was isolated from collected from Maowei sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, PR China. The 16S rRNA gene sequence similarity between strain MQZ13P-4 and its closest phylogenetic neighbour CBS5Q-3 was 97.9 %. Phylogenetic analyses using 16S rRNA gene sequences and whole-genome sequences showed that strain MQZ13P-4 formed a distinct lineage with CBS5Q-3, 40Bstr34 and JCM 30119. The draft genome of strain MQZ13P-4 was 5 153 243 bp in size and its DNA G+C content was 68.1 mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values among strain MQZ13P-4 and other related species were below the cut-off levels of 95, 70 and 95.5 %, respectively. The cell-wall peptidoglycan of strain MQZ13P-4 contained -diaminopimelic acid as the diagnostic diamino acid. The respiratory quinone was Q-10. The major cellular fatty acid was C 7. The polar lipids comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. Strain MQZ13P-4 had a typical chemical compositions of fatty acids, lipids, quinones and diagnostic diamino acid for species, but could be distinguished from known species of the genus . Based on polyphasic evidence, strain MQZ13P-4 represents novel species of the genus , for which the name sp. nov. is proposed. The type strain is MQZ13P-4 (=CGMCC 1.18727=JCM 34333).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genomics , Genus Jiella , Jiella sonneratiae and polyphasic taxonomy
Funding
This study was supported by the:
  • Zunyi Science and Technology Plan Project (Award [2019]19)
    • Principle Award Recipient: Hai-BoYi
  • Science and Technology Fund Project of Guizhou Provincial Health Commission (Award gzwjkj2019-1-042)
    • Principle Award Recipient: Hai-BoYi
  • Guizhou Provincial Science and Technology Foundation (Award Qian Ke He Jichu [2019]1347)
    • Principle Award Recipient: LiTuo
  • National Natural Science Foundation of China (Award 81960642)
    • Principle Award Recipient: LiTuo
© 2022 The Authors
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2022-03-30
2024-05-01
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References

  1. Liang J, Liu J, Zhang XH. Jiella aquimaris gen. nov., sp. nov., isolated from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:1127–1132 [View Article] [PubMed]
     [Google Scholar]
  2. Tuo L, Yan XR, Xiao JH. Jiella endophytica sp. nov., a novel endophytic bacterium isolated from root of Ficus microcarpa Linn. f. Antonie Van Leeuwenhoek 2019; 112:1457–1463 [View Article] [PubMed]
     [Google Scholar]
  3. Xue Z, Zhu S, Chen X, Chen T, Ren N et al. Jiella pacifica sp. nov., isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:4345–4350 [View Article] [PubMed]
     [Google Scholar]
  4. Liu J, Li F, Gao C-H, Han Y, Hao H et al. Nocardioides kandeliae sp. nov., an endophytic actinomycete isolated from leaves of Kandelia candel. Int J Syst Evol Microbiol 2017; 67:3888–3893 [View Article] [PubMed]
     [Google Scholar]
  5. Bai X, Xiong Y, Lu S, Jin D, Lai X et al. Streptococcuspantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2016; 66:3281–3286 [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  10. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  11. 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]
  12. 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]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  14. Lim HJ, Lee EH, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article] [PubMed]
     [Google Scholar]
  15. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  16. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article] [PubMed]
     [Google Scholar]
  17. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–80 [View Article] [PubMed]
     [Google Scholar]
  18. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–9 [View Article] [PubMed]
     [Google Scholar]
  19. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article]
     [Google Scholar]
  20. Afzal I, Shinwari ZK, Iqrar I. Selective isolation and characterization of agriculturally beneficial endophytic bacteria from wild hemp using canola (article). Pakistan Journal of Botany 2015; 47:1999–2008
     [Google Scholar]
  21. Vejan P, Abdullah R, Khadiran T, Ismail S, Nasrulhaq Boyce A et al. Role of plant growth promoting rhizobacteria in agricultural sustainability-a review. Molecules 2016; 21:573 [View Article] [PubMed]
     [Google Scholar]
  22. Lee SA, Kim T-W, Heo J, Sang M-K, Song J et al. Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum). J Microbiol 2020; 58:832–840 [View Article] [PubMed]
     [Google Scholar]
  23. Kang S-M, Asaf S, Khan AL, Khan A. Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions. Microorganisms 2020; 8:382 [View Article] [PubMed]
     [Google Scholar]
  24. Backer R, Rokem JS, Ilangumaran G, Lamont J, Praslickova D et al. Plant growth-promoting rhizobacteria: context, mechanisms of action, and roadmap to commercialization of biostimulants for sustainable agriculture. Front Plant Sci 2018; 9:1473 [View Article] [PubMed]
     [Google Scholar]
  25. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  26. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  27. Avram O, Rapoport D, Portugez S, Pupko T. M1CR0B1AL1Z3R-a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Res 2019; 47:W88–W92 [View Article] [PubMed]
     [Google Scholar]
  28. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color name Charts illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  29. 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]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical note 101 Newark, DE: MIDI inc; 1990
     [Google Scholar]
  31. Tuo L, Dong Y-P, Habden X, Liu J-M, Guo L et al. Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2015; 65:1604–1610 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. 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]
  34. 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]
     [Google Scholar]
  35. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
     [Google Scholar]
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Jiella sonneratiae sp. nov., a novel endophytic bacterium isolated from bark of Sonneratia apetala
Int J Syst Evol Microbiol 72, 005310 (2022); https://doi.org/10.1099/ijsem.0.005310
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