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Abstract

A novel endophytic bacterium, designated strain BGMRC 0089, was isolated from a surface-sterilized root of . Cells were observed to be Gram-negative, rod-shaped and motile with polar flagella. Strain BGMRC 0089 was found to grow optimally at 28–30 °C, pH 7.0–8.0 and in the presence of 1 % (w/v) NaCl. Strain BGMRC 0089 contained ubiquinone Q-10 and the predominant fatty acid was summed feature 8. The polar lipid profile of strain BGMRC 0089 was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine. Based on the results of 16S rRNA gene analysis, this isolate has the closest phylogenetic relationships with L6-16 (96.5 %) and N19 (96.4 %). Average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of the isolate with the type strains of the genera and were below 84.6, 73.9 and 22.1  %, respectively. Analysis the 4.55 Mb draft genome of strain BGMRC 0089 revealed several plant-associated genes, which may play important roles for the plant in the adaptation to the mangrove habitat. Based on its distinct phylogenetic, phenotypic and chemotaxonomic characteristics, strain BGMRC 0089 is proposed to represent a novel species, for which the name sp. nov. is proposed (type strain BGMRC 0089=DSM 100171=MCCC 1K04805).

Funding
This study was supported by the:
  • Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry (Award 17-259-74)
    • Principle Award Recipient: Shu-ShiHuang
  • This research was supported by the National Natural Science Foundation of China (Award 42066002)
    • Principle Award Recipient: Xian-LingQin
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2023-02-14
2024-12-14
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References

  1. De Lajudie P, Laurent-Fulele E, Willems A, Torek U, Coopman R et al. Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate neptunia natans in Senegal. Int J Syst Bacteriol 1998; 48:1277–1290
    [Google Scholar]
  2. Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K. Revised phylogeny of Rhizobiaceae: proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol 2015; 38:84–90 [View Article] [PubMed]
    [Google Scholar]
  3. Zhang GX, Ren SZ, Xu MY, Zeng GQ, Luo HD et al. Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge. Int J Syst Evol Microbiol 2011; 61:816–822 [View Article] [PubMed]
    [Google Scholar]
  4. Lin SY, Hameed A, Huang HI, Young CC. Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov. Int J Syst Evol Microbiol 2020; 70:397–405 [View Article]
    [Google Scholar]
  5. Peng GX, Yuan QH, Li HX, Zhang W, Tan ZY. Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta. Int J Syst Evol Microbiol 2008; 58:2158–2163 [View Article] [PubMed]
    [Google Scholar]
  6. Zhang X, Sun L, Ma X, Sui XH, Jiang R. Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice. Int J Syst Evol Microbiol 2011; 61:2425–2429 [View Article] [PubMed]
    [Google Scholar]
  7. Zhao J-J, Zhang J, Sun L, Zhang R-J, Zhang C-W et al. Rhizobium oryziradicis sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2017; 67:963–968 [View Article] [PubMed]
    [Google Scholar]
  8. Ophel K, Kerr A. Agrobacterium vitis sp. nov. for strains of agrobacterium biovar 3 from grapevines. Int J Syst Bacteriol 1990; 40:236–241 [View Article]
    [Google Scholar]
  9. Yao LJ, Shen YY, Zhan JP, Xu W, Cui GL et al. Rhizobium taibaishanense sp. nov., isolated from a root nodule of Kummerowia striata. Int J Syst Evol Microbiol 2012; 62:335–341 [View Article] [PubMed]
    [Google Scholar]
  10. Kittiwongwattana C, Thawai C. Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis). Int J Syst Evol Microbiol 2013; 63:3823–3828 [View Article] [PubMed]
    [Google Scholar]
  11. de Lamballerie X, Zandotti C, Vignoli C, Bollet C, de Micco P. A one-step microbial DNA extraction method using “Chelex 100” suitable for gene amplification. Res Microbiol 1992; 143:785–790 [View Article] [PubMed]
    [Google Scholar]
  12. Walsh PS, Metzger DA, Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 1991; 10:506–513 [PubMed]
    [Google Scholar]
  13. Li W-J, Xu P, Schumann P, Zhang Y-Q, 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]
  14. 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]
  15. Yoon SH, Ha SM, Lim J, Kwon S, 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. 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]
  17. 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]
    [Google Scholar]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  26. Speck JJ, James EK, Sugawara M, Sadowsky MJ, Gyaneshwara P. An alkane sulfonate monooxygenase is required for symbiotic nitrogen fixation by Bradyrhizobium diazoefficiens (syn. Bradyrhizobium japonicum) USDA110T. Appl Environ Microb 2019; 85:1–10
    [Google Scholar]
  27. Rajkumar M, Prasad MNV, Swaminathan S, Freitas H. Climate change driven plant-metal-microbe interactions. Environ Int 2013; 53:74–86 [View Article]
    [Google Scholar]
  28. Deakin WJ, Broughton WJ. Symbiotic use of pathogenic strategies: rhizobial protein secretion systems. Nat Rev Microbiol 2009; 7:312–320 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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
    [Google Scholar]
  31. Gordon RE, Barnett DA, Handerhan JE, Pang CN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  32. Graham PH, Parker CA. Diagnostic features in the characterisation of the root-nodule bacteria of legumes. Plant Soil 1964; 20:383–396 [View Article]
    [Google Scholar]
  33. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812
    [Google Scholar]
  34. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newslett 1990; 20:1–6
    [Google Scholar]
  35. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester:John Wiley &Sons; 1994 pp 345–401
    [Google Scholar]
  36. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  37. 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]
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