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Abstract

A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27, was isolated from a shoot of collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10–40 °C (optimum, 30 °C), at pH 6.0–9.0 (optimum, pH 7.0) and with 0–14.0 % NaCl (optimum, 5.0–8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27 clustered with BH30097, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with BH30097 and any other type strain. Strain HU2P27 contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C and iso-C, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain HU2P27 with BH30097 were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27 from its phylogenetic relatives. The name sp. nov. is therefore proposed. The type strain is strain HU2P27 (=CGMCC 1.18646=KCTC 43248). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Lee . 2012 as a later heterotypic synonym of Kim . 2011.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31960020)
    • Principle Award Recipient: Ji-QuanSun
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2021-10-07
2024-03-29
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References

  1. Amoozegar MA, Bagheri M, Didari M, Mehrshad M, Schumann P et al. Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov. Int J Syst Evol Microbiol 2014; 64:3616–3623 [View Article] [PubMed]
    [Google Scholar]
  2. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic Names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  3. Zhang WY, Hu J, Zhang XQ, Zhu XF, Wu M. Aquibacillus salifodinae sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China. Antonie Van Leeuwenhoek 2015; 107:367–374 [View Article] [PubMed]
    [Google Scholar]
  4. Lee JC, Whang KS. Aquibacillus sediminis sp. nov., a moderately halophilic bacterium isolated from saltern soil. Int J Syst Evol Microbiol 2019; 69:3121–3127 [View Article] [PubMed]
    [Google Scholar]
  5. Lee J-S, Lim J-M, Lee KC, Lee J-C, Park Y-H et al. Virgibacillus koreensis sp. nov., a novel bacterium from a salt field, and transfer of Virgibacillus picturae to the genus Oceanobacillus as Oceanobacillus picturae comb. nov. with emended descriptions. Int J Syst Evol Microbiol 2006; 56:251–257 [View Article] [PubMed]
    [Google Scholar]
  6. Zhang Y-J, Zhou Y, Ja M, Shi R, Chun-Yu W-X et al. Virgibacillus albus sp. nov., a novel moderately halophilic bacterium isolated from Lop Nur salt lake in Xinjiang province, China. Antonie van Leeuwenhoek 2012; 102:553–560 [View Article] [PubMed]
    [Google Scholar]
  7. Khan AL, Halo BA, Elyassi A, Ali S, Al-Hosni K et al. Indole acetic acid and ACC deaminase from endophytic bacteria improves the growth of Solanum lycopersicum. Electronic Journal of Biotechnology 2016; 21:58–64 [View Article]
    [Google Scholar]
  8. Bargaz A, Lyamlouli K, Chtouki M, Zeroual Y, Dhiba D. Soil microbial resources for improving fertilizers efficiency in an integrated plant nutrient management system. Front Microbiol 2018; 9:1606 [View Article] [PubMed]
    [Google Scholar]
  9. Ei MM, Liu BH, Ma JJ, Shi LM, Jiang MG et al. Evaluation of Bacillus velezensis NKG-2 for bio-control activities against fungal diseases and potential plant growth promotion. Biol Control 2019; 134:23–31
    [Google Scholar]
  10. Kumar A, Singh S, Gaurav AK, Srivastava S, Verma JP. Plant Growth-promoting bacteria: Biological tools for the mitigation of salinity stress in plants. Front Microbiol 2020; 11:1216 [View Article] [PubMed]
    [Google Scholar]
  11. Sun J-Q, Xu L, Liu M, Wang X-Y, Wu X-L. Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata. Int J Syst Evol Microbiol 2016; 66:1943–1949 [View Article] [PubMed]
    [Google Scholar]
  12. Cherif-Silini H, Silini A, Yahiaoui B, Ouzari I, Boudabous A. Phylogenetic and plant-growth-promoting characteristics of Bacillus isolated from the wheat rhizosphere. Ann Microbiol 2016; 66:1087–1097 [View Article]
    [Google Scholar]
  13. Ma J-P, Wang Z, Lu P, Wang H-J, Ali SW et al. Biodegradation of the sulfonylurea herbicide chlorimuron-ethyl by the strain Pseudomonas sp. LW3. FEMS Microbiol Lett 2010; 296:203–209
    [Google Scholar]
  14. 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]
  15. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  16. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  17. Sun JQ, Xu L, Wang LJ, Wu XL. Draft genome sequence of a Rhodococcus strain isolated from tannery wastewater treatment sludge. Microbiol Resour Announc 2015; 3:e01463
    [Google Scholar]
  18. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
  19. Emms DM, Kelly S. Orthofinder: Phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
    [Google Scholar]
  20. Emms DM, Kelly S. Orthofinder: Solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:157 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Rodriguez-R LM, Konstantinidis KT. The Enveomics collection: A toolbox for specialized analyses of microbial genomes and metagenomes. PEER J 2016e1900
    [Google Scholar]
  23. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  24. Kim J, Jung M-J, Roh SW, Nam Y-D, Shin K-S et al. Virgibacillus alimentarius sp. nov., isolated from a traditional Korean food. Int J Syst Evol Microbiol 2011; 61:2851–2855 [View Article] [PubMed]
    [Google Scholar]
  25. Lee S-Y, Kang C-H, Oh T-K, Yoon J-H. Virgibacillus campisalis sp. nov., from a marine solar saltern. Int J Syst Evol Microbiol 2012; 62:347–351 [View Article] [PubMed]
    [Google Scholar]
  26. Seck E, Rathored J, Khelaifia S, Croce O, Robert C et al. Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut. New Microbes New Infect 2015; 8:116–126 [View Article] [PubMed]
    [Google Scholar]
  27. Hanlon DW, Ordal GW. Cloning and characterization of genes encoding methyl-accepting chemotaxis proteins in bacillus subtilis. J Biol Chem 1994; 269:14038–14046 [View Article] [PubMed]
    [Google Scholar]
  28. Bol DK, Yasbin RE. The isolation, cloning and identification of a vegetative catalase gene from Bacillus subtilis. Gene 1991; 109:31–37 [View Article] [PubMed]
    [Google Scholar]
  29. Kappes RM, Kempf B, Kneip S, Boch J, Gade J et al. Two evolutionarily closely related ABC transporters mediate the uptake of choline for synthesis of the osmoprotectant glycine betaine in Bacillus subtilis. Mol Microbiol 1999; 32:203–216 [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. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986
    [Google Scholar]
  32. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  33. Fred R, Aharon O. 5-peptidoglycan structure. Methods Microbiol 2011; 38:101–129
    [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  35. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  36. Kim B-C, Jeong W-J, Kim DY, Oh H-W, Kim H et al. Paenibacillus pueri sp. nov., isolated from Pu’er tea. Int J Syst Evol Microbiol 2009; 59:1002–1006 [View Article] [PubMed]
    [Google Scholar]
  37. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741 [View Article] [PubMed]
    [Google Scholar]
  38. Emms DM, Kelly S. STRIDE: Species Tree Root Inference from Gene Duplication Events. Mol Biol Evol 2017; 34:3267–3278 [View Article] [PubMed]
    [Google Scholar]
  39. Emms DM, Kelly S. STAG: species tree inference from all genes. BioRxiv 2018
    [Google Scholar]
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