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Volume 73, Issue 5

sp. nov., isolated from soil No Access

Abstract

A white-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated CYS-01, was obtained from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 28 °C. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain CYS-01 formed a lineage within the family and clustered with members of the genus . The closest relatives were CGMCC 1.12803 (95.70 % sequence similarity), THG-T11 (95.35 %), P-25 (95.28 %), CM134L-2 (94.94 %), Q-4 (94.73 %) and TDMA-5 (94.07 %). The principal respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine, an unidentified aminolipid, unidentified lipids and an unidentified glycolipid. The predominant cellular fatty acids were iso-C, summed feature 3 (C 7 and/or C 6) and iso-C 3-OH. The DNA G+C content was 36.6 mol%. Based on the results of genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain CYS-01 represents novel species in the genus , for which the name sp. nov. is proposed. The type strain is CYS-01 (=KACC 22655=NBRC 115630).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidetes , Pedobacter montanisoli , soil and Sphingobacteriaceae
Funding
This study was supported by the:
  • Kyonggi University
    • Principle Award Recipient: YelimYou
© 2023 The Authors
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2023-05-22
2024-09-19
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References

  1. 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 Pt 1:165–177 [View Article] [PubMed]
     [Google Scholar]
  2. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. Int J Syst Evol Microbiol 2012; 62:1963–1969 [View Article] [PubMed]
     [Google Scholar]
  3. Kook M, Park Y, Yi TH. Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2014; 64:1789–1794 [View Article] [PubMed]
     [Google Scholar]
  4. Vanparys B, Heylen K, Lebbe L, De Vos P. Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 2005; 55:1315–1318 [View Article] [PubMed]
     [Google Scholar]
  5. Hwang CY, Choi DH, Cho BC. Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2006; 56:1831–1836 [View Article] [PubMed]
     [Google Scholar]
  6. Gallego V, García MT, Ventosa A. Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2006; 56:1853–1858 [View Article] [PubMed]
     [Google Scholar]
  7. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. Int J Syst Evol Microbiol 2012; 62:1963–1969 [View Article] [PubMed]
     [Google Scholar]
  8. Kook M, Park Y, Yi TH. Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2014; 64:1789–1794 [View Article] [PubMed]
     [Google Scholar]
  9. Du J, Singh H, Ngo HTT, Won K-H, Kim K-Y et al. Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2015; 65:1241–1246 [View Article] [PubMed]
     [Google Scholar]
  10. Wei Y, Wang B, Zhang L, Zhang J, Chen S. Pedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2018; 68:2523–2529 [View Article] [PubMed]
     [Google Scholar]
  11. Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL et al. Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 2009; 59:1720–1726 [View Article] [PubMed]
     [Google Scholar]
  12. Dahal RH, Chaudhary DK, Kim D-U, Kim J. Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities. Int J Syst Evol Microbiol 2020; 70:2537–2553 [View Article] [PubMed]
     [Google Scholar]
  13. Dahal RH, Chaudhary DK, Kim J. Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968. Int J Syst Evol Microbiol 2018; 68:1955–1962 [View Article] [PubMed]
     [Google Scholar]
  14. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
     [Google Scholar]
  15. Yoon S-H, Ha S-M, 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 [View Article] [PubMed]
     [Google Scholar]
  16. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article] [PubMed]
     [Google Scholar]
  17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  18. Doetsch RN. Determinative methods of light microscopy. In Gerdhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA. eds Manual of Methods for General Bacteriology Washington, DC, USA: American Society for Microbiology; 1981 pp 21–33
     [Google Scholar]
  19. Breznak JA, Costilow RN et al. Physicochemical factors in growth. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. eds Methods for General and Molecular Bacteriology Washinton, DC, USA: American Society of Microbiology; 2007 pp 309–329
     [Google Scholar]
  20. Sasser M. Technical Note 101: Bacterial Identification by Gas Chromatographic Analysis of Fatty Acid Methyl Esters (GC-FAME) Newark, NE: MIDI Inc; 1990
     [Google Scholar]
  21. 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 [View Article]
     [Google Scholar]
  22. Komagata K, Suzuki K. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  23. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  24. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article] [PubMed]
     [Google Scholar]
  25. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
     [Google Scholar]
  26. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  27. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  28. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
     [Google Scholar]
  29. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  30. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  31. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  32. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  33. Hu S-L, Huang J-W, Yang M-J, Jia W-B, Ke Z et al. Pedobacter helvus sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2019; 69:3806–3811 [View Article]
     [Google Scholar]
  34. Zhang L-L, Gan L-Z, Xu Z-B, Yang F, Li Y et al. Pedobacter chitinilyticus sp. nov., a chitin-degrading bacterium isolated from wheat leaf tissue. Int J Syst Evol Microbiol 2018; 68:3713–3719 [View Article] [PubMed]
     [Google Scholar]
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Pedobacter montanisoli sp. nov., isolated from soil
Int J Syst Evol Microbiol 73, 005887 (2023); https://doi.org/10.1099/ijsem.0.005887
/content/journal/ijsem/10.1099/ijsem.0.005887
/content/journal/ijsem/10.1099/ijsem.0.005887
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