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Mucilaginibacter endophyticus sp. nov., an endophytic polysaccharide-producing bacterium isolated from a stem of Miscanthus sinensis

  • Zhendong Zhang
  • Feng Sun
  • Yan Chen
  • Lunguang Yao
  • Zhaojin ChenEmail author
  • Wei TianEmail author
Original Paper
  • 14 Downloads

Abstract

In this study, a Gram-negative, rod-shaped, endophytic bacterial strain (RS1T) capable of producing large amounts of exopolysaccharides was isolated from a stem of Miscanthus sinensis. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RS1T is closely related to Mucilaginibacter kameinonensis NBRC 102645T (98.72%), followed by Mucilaginibacter gossypiicola Gh-48T (97.56%) and Mucilaginibacter oryzae DSM 19975T (97.36%). The DNA G + C content of strain RS1T was determined to be 42.80 mol%. ANIb and GGDC values from genomic comparison between the genomes of strain RS1T and the related reference species were less than 95% and 70%, respectively. The major cellular fatty acids (more than 10% of total fatty acids) were identified as iso-C15: 0, C16:0, iso-C17:0-3OH and summed feature 3 (C16: 1ω7c and/or iso-C15:02-OH). The only isoprenoid quinone detected was MK-7. Based on the physiological, genotypic and genomic characteristics, strain RS1T is concluded to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter endophyticus sp. nov. is proposed (type strain RS1T = KCTC 62785T = GDMCC 1.1414T).

Keywords

Mucilaginibacter endophyticus Endophytic bactium Molecular phylogeny Polyphasic taxonomy 

Notes

Acknowledgements

This research was supported by National Natural Science Foundation of China (Grant No. 41601332), the Key Research Project of Colleges and Universities of Henan Province Education Department (Grant No. 16A210012), the Key Scientific and Technological Project of Henan Province (Grant No. 172102110259) and the Youth Science Foundation of Gansu Province (18JR3RA023).

Author Contribution’s

Zhang ZD: He supported the procedures and methods for the characterization for the strain RS1T and the closest type strains. He also made the tables and figure and wrote the manuscript. He had prepared the lyophilized powder of strain RS1T and the closest related strains for analysis of polar lipids and isoprenoid quinone. Sun F: He had collected the samples for isolation of the strain RS1T, and isolated bacteria from the samples, and purified the strains. He was in charge of analysis of polar lipids, and isoprenoid quinone, and transmission electron micrograph of the strain. Chen Y: She had collected the samples, and conducted the PCR and sequencing of the 16S rRNA gene. Yao LG: He had constructed the phylogenetic trees, and Gram staining of the cells and determined the cellular fatty acids. Chen ZJ: He proposed strain RS1T as a new species. He had conducted the experiments for bacterial phenotypic characteristics using the API strips. He support the funding for the study. Tian W: He had performed the comparison of the genomes of RS1T and the closet related type strains. The Latin name was proposed by Wei Tian.

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

10482_2019_1242_MOESM1_ESM.docx (1.7 mb)
Supplementary material 1 (DOCX 1720 kb)

References

  1. Baik KS, Park SC, Kim EM, Lim CH, Seong CN (2010) Mucilaginibacter rigui sp. nov. isolated from wetland freshwater and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 60:134–139CrossRefGoogle Scholar
  2. Bianciotto V, Bandi C, Minerdi D, Sironi M, Tichy HV, Bonfante P (1996) An obligately endosymbiotic mycorrhizal fungus itself harbors obligately intracellular bacteria. Appl Environ Microbiol 62(8):3005–3010Google Scholar
  3. Bowman JP (2000) Description of Cellulophaga algicola sp. nov. isolated from the surfaces of Antarctic algae and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50(5):1861–1868CrossRefGoogle Scholar
  4. Breitling R, Takano E, Lee SY, Weber T, Medema MH (2017) AntiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 45:W36–W41CrossRefGoogle Scholar
  5. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68(1):461–466CrossRefGoogle Scholar
  6. Cui CH, Choi TE, Yu H, Jin F, Lee ST, Kim SC, Im WT (2011) Mucilaginibacter composti sp. nov. with ginsenoside converting activity isolated from compost. J Microbiol 49:393–398CrossRefGoogle Scholar
  7. Da XY, Jiang F, Chang XL, Ren LZ, Qiu X, Kan WJ, Zhang YM, Deng SS, Fang CX, Peng F (2015) Pedobacter ardleyensis sp. nov., isolated from soil of the Ardley Island, South Shetland Islands in Antarctica. Int J Syst Evol Microbiol 65:3841–3846CrossRefGoogle Scholar
  8. Dahal RH, Kim J (2016) Pedobacter humicola sp. nov. a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 66(6):2205–2211CrossRefGoogle Scholar
  9. Doetsch RN (1981) Determinative method of light microscopy. In: Manual of methods for general bacteriology Washington DC, pp 21–33Google Scholar
  10. Handley PS, Carter PL, Wyatt JE (1985) Surface structures (peritrichous fibrils and tufts of fibrils) found on Streptococcus sanguisstrains may be related to their ability to coaggregate with 242 other oral genera. Infect Immun 47(1):217–227Google Scholar
  11. Joshi NA, Fass JN (2011) Sickle: a sliding-window adaptive quality-based trimming tool for FastQ files (Version 1.33) [software]. Available at: https://github.com/najoshi/sickle
  12. Joung Y, Kim H, Kang H, Lee BI, Ahn TS, Joh K (2014) Mucilaginibacter soyangensis sp. nov. isolated from a lake. Int J Syst Evol Microbiol 64:413–419CrossRefGoogle Scholar
  13. 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(Pt 2):346–351CrossRefGoogle Scholar
  14. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33(7):1870–1874CrossRefGoogle Scholar
  15. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–147Google Scholar
  16. Lee JH, Kim MS, Kang JW, Baik KS, Seong CN (2016) Mucilaginibacter puniceus sp. nov. isolated from wetland freshwater. Int J Syst Evol Microbiol 66:4549–4554CrossRefGoogle Scholar
  17. Luo RB, Liu BH, Xie YL, Li ZY, Huang WH, Yuan JY, He GZ, Chen YX, Pan Q, Liu YJ, Tang JB, Wu GX, Zhang H, Shi YJ, Liu Y, Yu C, Wang B, Lu Y, Han CL, Cheung DW, Yiu SM, Peng SL, Zhu XQ, Liu GM, Liao XK, Li YR, Yang HM, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1(1):18CrossRefGoogle Scholar
  18. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distancefunctions. BMC Bioinform 14:60CrossRefGoogle Scholar
  19. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaala A, Parletta JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  20. Moscovici M (2015) Present and future medical applications of microbial exopolysaccharides. Front Microbiol 6:1012CrossRefGoogle Scholar
  21. Murray RGE, Doetsch RN, Robinow F (1994) Determinative and cytological light microscopy. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for generaland molecular bacteriology. American Society Microbiol, Washington, pp 21–41Google Scholar
  22. Pankratov TA, Tindall BJ, Liesack W, Dedysh SN (2007) Mucilaginibacter paludis gen nov sp. nov. and Mucilaginibacter gracilis sp. nov. pectin- xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog. Int J Syst Evol Microbiol 57:2349–2354CrossRefGoogle Scholar
  23. Parte AC (2013) LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616CrossRefGoogle Scholar
  24. Qiu X, Qu ZH, Jiang F, Ren LZ, Chang XL, Kan W, Fang C, Peng F (2014) Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov. isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 64(Pt 7):2431–2436CrossRefGoogle Scholar
  25. Richter M, Rosselló-Móra R, Glöckner RO, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6):929–931CrossRefGoogle Scholar
  26. Rosselló-Móra R (2011) Towards a taxonomy of bacteria and archaea based on interactive and cumulative data repositories. Environ Microbiol 14(2):318–334CrossRefGoogle Scholar
  27. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical note 101. MIDI Inc, NewarkGoogle Scholar
  28. Sheng XF, Xia JJ, Jiang CY, He LY, Qian M (2008) Characterization of heavy metal-resistant endophytic bacteria from rape (Brassica napus) roots and their potential in promoting the growth and lead accumulation of rape. Environ Pollut 156(3):1164–1170CrossRefGoogle Scholar
  29. Tittsler RP, Sandholzer LA (1936) The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31(6):575–580Google Scholar
  30. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefGoogle Scholar
  31. Zhao Y, Lee HG, Kim SK, Yu HS, Jin FX, Im WT (2016) Mucilaginibacter pocheonensis sp. nov. with ginsenoside-converting activity isolated from soil of a ginseng-cultivating field. Int J Syst Evol Microbiol 66:2862–2868CrossRefGoogle Scholar
  32. Zheng RC, Zhao YM, Wang LQ, Chang XL, Zhang YM, Da ZY, Peng F (2016) Mucilaginibacter antarcticus sp. nov. isolated from tundra soil. Int J Syst Evol Microbiol 66:5140–5144CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Northwest Hubei Research Institute of Traditional Fermented Food, College of Food Science and TechnologyHubei University of Arts and ScienceXiangyangPeople’s Republic of China
  2. 2.Innovation Center of Water Security for Water Source Region of Mid-route Project of South-North Water Diversion of Henan Province, Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, School of Agricultural EngineeringNanyang Normal UniversityNanyangPeople’s Republic of China
  3. 3.Nanjing Institute of Environmental SciencesMinistry of Environmental ProtectionNanjingPeople’s Republic of China

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