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Abstract

A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30, was isolated from a root of collected in Inner Mongolia, northern China. Strain LD4P30 grew at pH 6.0–11.0 (optimum, pH 7.0), 10–40 °C (35 °C) and in the presence of 1–15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30 were iso-C, C 5 and anteiso-C; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30 clustered with TP2-8, YIM 91119 and BH312, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to TP2-8, YIM 91119, BH312 and all other current type strains, respectively. The digital DNA–DNA hybridization and average nucleotide identity based on values between strain LD4P30 and YIM 91119, TP2-8 and BH312 were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30 represents a novel species, for which the name is proposed. The type strain is LD4P30 (=CGMCC 1.17697=KCTC 82375).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31960020)
    • Principle Award Recipient: Ji-QuanSun
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/content/journal/ijsem/10.1099/ijsem.0.005140
2021-12-08
2022-01-28
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References

  1. Tindall BJ, Schumann P, Ingvorsen K, Waino M. Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillussalexigens comb. nov. Int J Syst Bacteriol 1999; 49:821–831 [View Article]
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  3. 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]
  4. Tang S-K, Wang Y, Lou K, Mao P-H, Jin X et al. Gracilibacillus saliphilus sp. nov., a moderately halophilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2009; 59:1620–1624 [View Article] [PubMed]
    [Google Scholar]
  5. Chamroensaksri N, Tanasupawat S, Akaracharanya A, Visessanguan W, Kudo T et al. Gracilibacillus thailandensis sp. nov., from fermented fish (pla-ra). Int J Syst Evol Microbiol 2010; 60:944–948 [View Article] [PubMed]
    [Google Scholar]
  6. Huang H, Wang Y, Yuan W, Xiao C, Ye J et al. Gracilibacillus marinus sp. nov., isolated from the northern South China Sea. Antonie Van Leeuwenhoek 2013; 104:695–701 [View Article] [PubMed]
    [Google Scholar]
  7. Chen Y-G, Cui X-L, Zhang Y-Q, Li W-J, Wang Y-X et al.. Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil. Int J Syst Evol Microbiol 2008; 58:2403–2408 [View Article] [PubMed]
    [Google Scholar]
  8. Chen Y-G, Cui X-L, Zhang Y-Q, Li W-J, Wang Y-X et al. Gracilibacillus quinghaiensis sp. nov., isolated from salt-lake sediment in the Qaidam Basin, north-west China. Syst Appl Microbiol 2008; 31:183–189 [View Article] [PubMed]
    [Google Scholar]
  9. Guan H-L, Zhang Y-J, Lu X-J, Jia M, Zhang Z-Y et al. Gracilibacillus eburneus sp.nov., a moderately halophilic bacterium isolated from Xinjiang province, China. Arch Microbiol 2018; 200:423–429 [View Article] [PubMed]
    [Google Scholar]
  10. Gao M, Liu Z-Z, Zhou Y-G, Liu H-C, Ma Y-C et al. Gracilibacillus kekensis sp. nov., a moderate halophile isolated from Keke Salt Lake. Int J Syst Evol Microbiol 2012; 62:1032–1036 [View Article] [PubMed]
    [Google Scholar]
  11. Jeon CO, Lim J-M, Jang HH, Park D-J, Xu L-H et al. Gracilibacillus lacisalsi sp. nov., a halophilic Gram-positive bacterium from a salt lake in China. Int J Syst Evol Microbiol 2008; 58:2282–2286 [View Article] [PubMed]
    [Google Scholar]
  12. Carrasco IJ, Márquez MC, Yanfen X, Ma Y, Cowan DA et al. Gracilibacillus orientalis sp. nov., a novel moderately halophilic bacterium isolated from a salt lake in Inner Mongolia, China. Int J Syst Evol Microbiol 2006; 56:599–604 [View Article] [PubMed]
    [Google Scholar]
  13. Huo Y-Y, Xu X-W, Cui H-L, Wu M. Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline-alkaline soil. Int J Syst Evol Microbiol 2010; 60:1383–1386 [View Article] [PubMed]
    [Google Scholar]
  14. Kim P, Lee J-C, Park D-J, Shin K-S, Kim J-Y et al. Gracilibacillus bigeumensis sp. nov., a moderately halophilic bacterium from solar saltern soil. Int J Syst Evol Microbiol 2012; 62:1857–1863 [View Article] [PubMed]
    [Google Scholar]
  15. He S-W, Wang X, Guo H-B, Han J-G, Thin KK et al. Gracilibacillus oryzae sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 2020; 70:5467–5472 [View Article] [PubMed]
    [Google Scholar]
  16. Oh YJ, Lee H-W, Lim SK, Kwon M-S, Lee J et al. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol 2016; 54:588–593 [View Article] [PubMed]
    [Google Scholar]
  17. Hirota K, Hanaoka Y, Nodasaka Y, Yumoto I. Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing. Int J Syst Evol Microbiol 2014; 64:3174–3180 [View Article] [PubMed]
    [Google Scholar]
  18. Diop A, Seck EH, Dubourg G, Armstrong N, Blanc-Tailleur C et al. Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T, a moderate halophilic bacterium isolated from the human gut microflora. MicrobiologyOpen 2019; 8:e00638 [View Article] [PubMed]
    [Google Scholar]
  19. Ngom II, Hasni I, Senghor B, Lo CI, Armstrong N et al. Description of Gracilibacillus phocaeensis sp. nov., a new halophilic bacterium isolated from Senegalian human stool. New Microbes New Infect 2020; 38:100799 [View Article] [PubMed]
    [Google Scholar]
  20. Orhan F, Demirci A. Salt stress mitigating potential of halotolerant/halophilic plant growth promoting. Geomicrobiol J 2020; 37:663–669 [View Article]
    [Google Scholar]
  21. Podestá GS de, Freitas LG de, Dallemole-Giaretta R, Zooca RJF, Caixeta L de B et al. Meloidogyne javanica control by Pochonia chlamydosporia, Gracilibacillus dipsosauri and soil conditioner in tomato. Summa phytopathol 2013; 39:122–125 [View Article]
    [Google Scholar]
  22. Aslam F, Ali B. Halotolerant bacterial diversity associated with Suaeda fruticosa (L.) forssk. Improved growth of maize under salinity stress. Agronomy 2018; 8:131 [View Article]
    [Google Scholar]
  23. Wang S, Yang R, Xu L, Xing YT, Sun JQ. Qingshengfaniella alkalisoli gen. nov., sp. nov., a p-hydroxybenzoate-degrading strain isolated from saline soil. Int J Syst Evol Microbiol 2019; 71:004719 [View Article]
    [Google Scholar]
  24. Xing Y-T, Xu L, Wang H-T, Huang X-X, Wang S et al. Echinicola soli sp. nov., isolated from alkaline saline soil. Int J Syst Evol Microbiol 2020; 70:4139–4144 [View Article] [PubMed]
    [Google Scholar]
  25. Xu L, Huang XX, Fan DL, Sun JQ. Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2020; 70:1273–1281 [View Article] [PubMed]
    [Google Scholar]
  26. Zhang H, Xu L, Zhang JX, Sun JQ. Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa. Int J Syst Evol Microbiol 2020; 70:3816–3823 [View Article] [PubMed]
    [Google Scholar]
  27. Xu L, Wang H-T, Zhang J-X, Zhang H, Wang S et al.. Flavobacterium alkalisoli sp. nov., isolated from rhizosphere soil of Suaeda salsa. Int J Syst Evol Microbiol 2020; 70:3888–3898 [View Article] [PubMed]
    [Google Scholar]
  28. Xu L, Zhang H, Xing Y-T, Li N, Wang S et al. Complete genome sequence of Sphingobacterium psychroaquaticum strain SJ-25, an aerobic bacterium capable of suppressing fungal pathogens. Curr Microbiol 2020; 77:115–122 [View Article] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. Nutaratat P, Monprasit A, Srisuk N. High-yield production of indole-3-acetic acid by Enterobacter sp. DMKU-RP206, a rice phyllosphere bacterium that possesses plant growth-promoting traits. 3 Biotech 2017; 7:15 [View Article]
    [Google Scholar]
  32. Sun J-Q, Xu L, Guo Y, Li W-L, Shao Z-Q et al. Kribbella deserti sp. nov., isolated from rhizosphere soil of Ammopiptanthus mongolicus. Int J Syst Evol Microbiol 2017; 67:692–696 [View Article] [PubMed]
    [Google Scholar]
  33. Thompson JD, Gibson TJ, Plewniak F, Jeanpougin 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]
    [Google Scholar]
  34. 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]
  35. Edwards AWF, Larson A. The origin and early development of the method of minimum evolution for the reconstruction of phylogenetic trees. Syst Biol 1996; 45:79–91 [View Article]
    [Google Scholar]
  36. Dawyndt P, De Meyer H, De Baets B. UPGMA clustering revisited: A weight-driven approach to transitive approximation. Int J Approx Reason 2006; 42:174–191 [View Article]
    [Google Scholar]
  37. 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]
  38. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  39. Sun J-Q, Xu L, Wang L-J, Wu X-L. Draft genome sequence of a rhodococcus strain isolated from tannery wastewater treatment sludge. Genome Announc 2015; 3:e01463–14 [View Article]
    [Google Scholar]
  40. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  41. 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]
  42. 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]
  43. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238. [View Article] [PubMed]
    [Google Scholar]
  44. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182. [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  47. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  48. 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]
    [Google Scholar]
  49. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  50. Kates M. Techniques of Lipidology, 2nd edn. Amsterdam: Elsevier; 1986
    [Google Scholar]
  51. Komagata K, Suzuki K-I. Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1988; 19:161–207
    [Google Scholar]
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