Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Sphingomonas abietis sp. nov., an Endophytic Bacterium Isolated from Korean Fir

  • Lingmin Jiang (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Hanna Choe (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Yuxin Peng (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Doeun Jeon (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Donghyun Cho (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Yue Jiang (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Ju Huck Lee (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Cha Young Kim (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Jiyoung Lee (Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology)
  • Received : 2023.03.14
  • Accepted : 2023.07.06
  • Published : 2023.10.28
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Abstract

PAMB 00755T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755T was most closely related to Sphingomonas chungangi MAH-6T (97.7%) and Sphingomonas polyaromaticivorans B2-7T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C18:1ω7c and/or C18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755T as the type strain (= KCTC 92781T = GDMCC 1.3779T).

Keywords

Acknowledgement

We thank Dr. Gwang Joong Kim of Korea Basic Science Institute (KBI, Chuncheon Center) for kindly providing the FE-SEM image. Additionally, we would like to thank Dr. Aharon Oren from the Hebrew University of Jerusalem for his valuable comments and recommendations concerning nomenclature. This work was funded by a grant from the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative (KGM5282331), and a grant from the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2020R111A2072308).

References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T, Yamamoto H. 1990. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol. Immunol. 34: 99-119. https://doi.org/10.1111/j.1348-0421.1990.tb00996.x
  2. Takeuchi M, Hamana K, Hiraishi A. 2001. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51: 1405-1417. https://doi.org/10.1099/00207713-51-4-1405
  3. Dong L, Li S, Lian WH, Wei QC, Mohamad OAA, Hozzein WN, Ahmed I, Li WJ. 2022. Sphingomonas arenae sp. nov., isolated from desert soil. Int. J. Syst. Evol. Microbiol. 72. doi: 10.1099/ijsem.0.005195.
  4. Kim H, Chhetri G, Seo T. 2021. Sphingomonas xanthus sp. nov., isolated from beach soil. Curr. Microbiol. 78: 403-410. https://doi.org/10.1007/s00284-020-02273-z
  5. Shen L, Liu P, An M, Liang R, He X, Zhao G. 2022. Sphingomonas quercus sp. nov., isolated from Rhizosphere soil of Quercus mongolica. Curr. Microbiol. 79: 122.
  6. Kang M, Chhetri G, Kim J, Kim I, Seo T. 2021. Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand. Int. J. Syst. Evol. Microbiol. 71. doi: 10.1099/ijsem.0.004896.
  7. Sheu SY, Yang CC, Sheu DS, Tsai JM, Chen WM. 2020. Sphingomonas lacunae sp. nov., isolated from a freshwater pond. Int. J. Syst. Evol. Microbiol. 70: 5899-5910. https://doi.org/10.1099/ijsem.0.004491
  8. Kim I, Chhetri G, So Y, Jung Y, Park S, Seo T. 2022. Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots. Arch. Microbiol. 205: 16.
  9. Madhaiyan M, Saravanan VS, Wirth JS, Alex THH, Kim SJ, Weon HY, et al. 2020. Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants. Antonie Van Leeuwenhoek 113: 1617-1632. https://doi.org/10.1007/s10482-020-01468-5
  10. Jiang L, Seo J, Peng Y, Jeon D, Lee JH, Kim CY, et al. 2023. A nostoxanthin-producing bacterium, Sphingomonas nostoxanthinifaciens sp. nov., alleviates the salt stress of Arabidopsis seedlings by scavenging of reactive oxygen species. Front. Microbiol. 14: 1101150.
  11. Zhang DF, Cui XW, Zhao Z, Zhang AH, Huang JK, Li WJ. 2020. Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie Van Leeuwenhoek 113: 1523-1530. https://doi.org/10.1007/s10482-020-01460-z
  12. Xue H, Piao CG, Wang XZ, Lin CL, Guo MW, Li Y. 2018. Sphingomonas aeria sp. nov., isolated from air. Int. J. Syst. Evol. Microbiol. 68: 2866-2871. https://doi.org/10.1099/ijsem.0.002910
  13. Heidler von Heilborn D, Reinmuller J, Holzl G, Meier-Kolthoff JP, Woehle C, Marek M, et al. 2021. Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere. Int. J. Syst. Evol. Microbiol. 71. doi: 10.1099/ijsem.0.004973.
  14. Liu Y, Chen T, Cui X, Xu Y, Hu S, Zhao Y, et al. 2022. Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest. Int. J. Syst. Evol. Microbiol. 72. doi: 10.1099/ijsem.0.005312.
  15. Zhou XY, Zhang L, Su XJ, Hang P, Hu B, Jiang JD. 2019. Sphingomonas flavalba sp. nov., isolated from a procymidone-contaminated soil. Int. J. Syst. Evol. Microbiol. 69: 2936-2941. https://doi.org/10.1099/ijsem.0.003581
  16. Chen L, Chen WF, Xu ZL, Li W, Zhang XY, Li WJ, et al. 2018. Sphingomonas oleivorans sp. nov., isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol. 68: 3720-3725. https://doi.org/10.1099/ijsem.0.003014
  17. Feng GD, Wang YH, Zhang XJ, Chen WD, Zhang J, Xiong X, et al. 2019. Sphingomonas lenta sp. nov., a slowly growing bacterium isolated from an abandoned lead-zinc mine. Int. J. Syst. Evol. Microbiol. 69: 2214-2219. https://doi.org/10.1099/ijsem.0.003427
  18. Li Y, Bian DR, Chang JP, Guo LM, Yang XQ. 2020. Sphingomonas populi sp. nov., isolated from bark of Populus x euramericana. Int. J. Syst. Evol. Microbiol. 70: 897-901. https://doi.org/10.1099/ijsem.0.003841
  19. Thaller MC, D'Andrea MM, Marmo P, Civitareale C, Casu F, Migliore L. 2018. Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater. Int. J. Syst. Evol. Microbiol. 68: 2794-2799. https://doi.org/10.1099/ijsem.0.002896
  20. Zhang H, Xu L, Zhang JX, Sun JQ. 2020. Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa. Int. J. Syst. Evol. Microbiol. 70: 3816-3823. https://doi.org/10.1099/ijsem.0.004238
  21. Luo YR, Tian Y, Huang X, Kwon K, Yang SH, Seo HS, et al. 2012. Sphingomonas polyaromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from an oil port water sample. Int. J. Syst. Evol. Microbiol. 62: 1223-1227. https://doi.org/10.1099/ijs.0.033530-0
  22. Jiang L, Peng Y, Seo J, Jeon D, Jo MG, Lee JH, et al. 2022. Subtercola endophyticus sp. nov., a cold-adapted bacterium isolated from Abies koreana. Sci. Rep. 12: 12114.
  23. Jiang L, Pheng S, Lee KC, Kang SW, Jeong JC, Kim CY, et al. 2019. Cohnella abietis sp. nov., isolated from Korean fir (Abies koreana) rhizospheric soil of Halla mountain. J. Microbiol. 57: 953-958. https://doi.org/10.1007/s12275-019-9136-1
  24. Senthilraj R, Prasad GS, Janakiraman K. 2016. Sequence-based identification of microbial contaminants in non-parenteral products. Braz. J. Pharm. Sci. 52: 329-336. d https://doi.org/10.1590/S1984-82502016000200011
  25. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67: 1613-1617. https://doi.org/10.1099/ijsem.0.001755
  26. Tamura K, Stecher G, Kumar S. 2021. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38: 3022-3027. https://doi.org/10.1093/molbev/msab120
  27. Rodriguez RL, Gunturu S, Harvey WT, Rossello-Mora R, Tiedje JM, Cole JR, et al. 2018. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res. 46: W282-W288. https://doi.org/10.1093/nar/gky467
  28. Meier-Kolthoff JP, Auch AF, Klenk H-P, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
  29. Konstantinidis KT, Tiedje JM. 2005. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 187: 6258-6264. https://doi.org/10.1128/JB.187.18.6258-6264.2005
  30. Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J. 2018. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J. Microbiol. 56: 280-285. https://doi.org/10.1007/s12275-018-8014-6
  31. Sasser M. 2006. Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). MIDI Technical MIDI Technical Note #101 MIDI Inc, Newark, DE, USA.
  32. Collins M, Shah H, Minnikin D. 1980. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J. Appl. Bacteriol. 48: 277-282. https://doi.org/10.1111/j.1365-2672.1980.tb01227.x
  33. Lee SA, Kim Y, Sang MK, Song J, Kwon SW, Weon HY. 2019. Chryseolinea soli sp. nov., isolated from soil. J. Microbiol. 57: 122-126. https://doi.org/10.1007/s12275-019-8562-4
  34. Kim M, Oh HS, Park SC, Chun J. 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64: 346-351. https://doi.org/10.1099/ijs.0.059774-0
  35. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68: 461-466. https://doi.org/10.1099/ijsem.0.002516