1887

Abstract

In a survey of endophytic bacteria in Miscanthus sinensis, a strain of Gram-negative, non-endospore-forming, rod-shaped, aerobic bacterium was isolated and designated as RS10. Phylogenetic analysis based on its 16S rRNA gene sequence showed that the strain RS10 was affiliated with the genus Pedobacter and exhibited the highest sequence similarities to Pedobacter kyungheensis KACC 16221 (97.78 %), Pedobacter roseus KCTC 22187 (97.75 %), Pedobacter humicola KACC 18452 (97.29 %) and Pedobacter soli KACC 14939 (97.23 %). The novel strain contained iso-C15 : 0, iso-C17 : 0-3OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as major fatty acids. The only isoprenoid quinone detected in strain RS10 was MK-7. Strain RS10 contains phosphatidylethanolamine and one kind of aminophospholipid as its major polar lipids. The DNA G+C content for RS10 was 39.8 mol%. Based on the results of phenotypic and genomic characterizations, we concluded that strains RS10 represents a novel species of Pedobacter , for which the name Pedobacter miscanthi sp. nov. is proposed. The type strain is RS10 (=KCTC 62786=GDMCC 1.1415).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003161
2018-12-12
2019-10-20
Loading full text...

Full text loading...

References

  1. Afzal M, Khan QM, Sessitsch A. Endophytic bacteria: prospects and applications for the phytoremediation of organic pollutants. Chemosphere 2014;117: 232– 242 [CrossRef] [PubMed]
    [Google Scholar]
  2. Rodriguez P, Gonzalez D, Rodríguez Giordano S. Endophytic microorganisms: A source of potentially useful biocatalysts. J Mol Catal B Enzym 2016;133: S569– S581 [CrossRef]
    [Google Scholar]
  3. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998;48: 165– 177 [CrossRef] [PubMed]
    [Google Scholar]
  4. Yoon SH, Ha SM, 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 [CrossRef] [PubMed]
    [Google Scholar]
  5. Rani A, Goyal A. A new member of family 8 polysaccharide lyase chondroitin AC lyase (Ps PL8A) from Pedobacter saltans displays endo- and exo-lytic catalysis. J Mol Catal B Enzym 2016;134: 215– 224 [CrossRef]
    [Google Scholar]
  6. Zhu B, Ni F, Ning L, Yao Z, du Y. Cloning and biochemical characterization of a novel κ-carrageenase from newly isolated marine bacterium Pedobacter hainanensis NJ-02. Int J Biol Macromol 2018;108: 1331– 1338 [CrossRef] [PubMed]
    [Google Scholar]
  7. Margesin R, Dieplinger H, Hofmann J, Sarg B, Lindner H. A cold-active extracellular metalloprotease from Pedobacter cryoconitis-production and properties. Res Microbiol 2005;156: 499– 505 [CrossRef] [PubMed]
    [Google Scholar]
  8. Blin K, Wolf T, Chevrette MG, Xw L, Schwalen J et al. High phylogenetic diversity of Flavobacterium spp. isolated from a hardwater creek Harz Mountains Germany. Org. Divers. Evol 2007;7: 145– 154
    [Google Scholar]
  9. Zhang YF, He LY, Chen ZJ, Zhang WH, Wang QY et al. Characterization of lead-resistant and ACC deaminase-producing endophytic bacteria and their potential in promoting lead accumulation of rape. J Hazard Mater 2011;186: 1720– 1725 [CrossRef] [PubMed]
    [Google Scholar]
  10. Heath LS, Sloan GL, Heath HE. A simple and generally applicable procedure for releasing DNA from bacterial cells. Appl Environ Microbiol 1986;51: 1138– 1140 [PubMed]
    [Google Scholar]
  11. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) In nucleic acid techniques in bacterial systematics Chichester: Wiley; 1991; pp. 115– 147
    [Google Scholar]
  12. Yoon SH, Ha SM, 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 [CrossRef] [PubMed]
    [Google Scholar]
  13. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef] [PubMed]
    [Google Scholar]
  14. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16: 111– 120 [CrossRef] [PubMed]
    [Google Scholar]
  15. 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 [CrossRef] [PubMed]
    [Google Scholar]
  16. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64: 346– 351 [CrossRef] [PubMed]
    [Google Scholar]
  17. Handley PS, Carter PL, Wyatt JE, Hesketh LM. Surface structures (peritrichous fibrils and tufts of fibrils) found on Streptococcus sanguis strains may be related to their ability to coaggregate with other oral genera. Infect Immun 1985;47: 217– 227 [PubMed]
    [Google Scholar]
  18. Murray RGE, Doetsch RN, Robinow F. Determinative and cytological light microscopy. In Gerhardt RGE, Wood Murray, Krieg NR. (editors) Methods for general and molecular bacteriology Washington, DC: Am Society Microbiol.,; 1994; pp. 21– 41
    [Google Scholar]
  19. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52: 1049– 1070 [CrossRef] [PubMed]
    [Google Scholar]
  20. Xy D, Jiang F, Chang XL, Ren LZ, Qiu X et al. Pedobacter ardleyensis sp. nov., isolated from soil of the Ardley Island, South Shetland Islands in Antarctica. Int. J. Syst. Evol. Microbiol 2015;65: 3841– 3846
    [Google Scholar]
  21. Qiu X, Qu Z, Jiang F, Ren L, Chang X et al. Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 2014;64: 2431– 2436 [CrossRef] [PubMed]
    [Google Scholar]
  22. Zimmermann JJ, Langer R, Cooney CL. Specific plate assay for bacterial heparinase. Appl Environ Microbiol 1990;56: 3593– 3594 [PubMed]
    [Google Scholar]
  23. Zheng R, Zhao Y, Wang L, Chang X, Zhang Y et al. Mucilaginibacter antarcticus sp. nov., isolated from tundra soil. Int J Syst Evol Microbiol 2016;66: 5140– 5144 [CrossRef] [PubMed]
    [Google Scholar]
  24. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936;31: 575– 580 [PubMed]
    [Google Scholar]
  25. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical note 101. Newark DE: MIDI Inc; 1990
    [Google Scholar]
  26. Kroppenstedt RM. Separation of Bacterial Menaquinones by HPLC Using Reverse Phase (RP18) and a Silver Loaded Ion Exchanger as Stationary Phases. J Liq Chromatogr 1982;5: 2359– 2367 [CrossRef]
    [Google Scholar]
  27. Dahal RH, Kim J, Nov P. a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016;66: 2205– 2211
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010; http://www.bioinformatics.babraham.ac.uk/projects/fastqc
  30. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012;1: 18 [CrossRef] [PubMed]
    [Google Scholar]
  31. Li R, Yu C, Li Y, Lam TW, Yiu SM et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009;25: 1966– 1967 [CrossRef] [PubMed]
    [Google Scholar]
  32. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003;4: 41 [CrossRef] [PubMed]
    [Google Scholar]
  33. Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 2002;18: 77– 82 [CrossRef] [PubMed]
    [Google Scholar]
  34. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000;28: 45– 48 [CrossRef] [PubMed]
    [Google Scholar]
  35. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 2009;37: D233– D238 [CrossRef] [PubMed]
    [Google Scholar]
  36. Guo S, Li X, He P, Ho H, Wu Y et al. Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants. J Ind Microbiol Biotechnol 2015;42: 925– 937 [CrossRef] [PubMed]
    [Google Scholar]
  37. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 2017;45: W36– W41 [CrossRef] [PubMed]
    [Google Scholar]
  38. 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 [CrossRef] [PubMed]
    [Google Scholar]
  39. 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 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003161
Loading
/content/journal/ijsem/10.1099/ijsem.0.003161
Loading

Data & Media loading...

Supplements

Supplementary data

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error