1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

sp. nov. and sp. nov., isolated from forest soil No Access

Abstract

Two Gram-stain-negative, yellow-pigmented and strictly aerobic bacteria, designated strains SE-s27 and SE-s28, were isolated from forest soil. Both strains were non-motile rods that were catalase-positive and oxidase-negative and grew optimally at 25–30 °C, pH 8.0 and with 0 % (w/v) NaCl. Strain SE-s28 produced flexirubin-type pigments, but strain SE-s27 did not produce them. Both strains contained menaquinone-6 as the sole respiratory quinone and phosphatidylethanolamine as a major polar lipid. As the major cellular fatty acids (>10 %), SE-s27 contained iso-C and iso-CG, whereas SE-s28 contained iso-C and summed feature 3 comprising Cωc and/or Cωc and/or iso-C 2-OH. The DNA G+C contents of strains SE-s27 and SE-s28 were 33.1 and 44.3 mol%, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that SE-s27 and SE-s28 formed respective distinct phylogenetic lineages within the genus . Strains SE-s27 and SE-s28 were most closely related to an-8 and ICH-30 with 98.0 and 94.5 % 16S rRNA gene sequence similarities, respectively. In conclusion, strains SE-s27 and SE-s28 represent novel species of the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains of and are SE-s27 (=KACC 18802=JCM 31544) and SE-s28 (=KACC 18803=JCM 31545), respectively.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Flavobacterium silvaticum , Flavobacterium solisilvae , forest soil , new taxa and taxonomy
Funding
This study was supported by the:
  • National Institute of Biological Resources (Award NIBR No. 2020-02-001)
    • Principle Award Recipient: CheOk Jeon
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004867
2021-07-13
2024-04-25
Loading full text...

Full text loading...

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Genus II Flavobacterium gen. nov. In Bergey’s Manual of Determinative Bacteriology, 1st. edn Baltimore: Williams & Wilkins; 1923 pp 97–117
     [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian Knot: Emended Classification and Description of the Genus Flavobacterium, Emended Description of the Family Flavobacteriaceae, and Proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978. Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  3. Ngo HT, Kook M, Yi T-H. Flavobacterium daemonensis sp. nov., isolated from Daemo Mountain soil. Int J Syst Evol Microbiol 2015; 65:983–989
     [Google Scholar]
  4. Lee Y, Jeon CO. Flavobacterium alvei sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2018; 68:1919–1924 [View Article] [PubMed]
     [Google Scholar]
  5. Li D-D, Liu C, Zhang Y-Q, Wang X-J, Wang N et al. Flavobacterium arcticum sp. nov., isolated from Arctic seawater. Int J Syst Evol Microbiol 2017; 67:1070–1074 [View Article]
     [Google Scholar]
  6. Ren Q, Yu M, Li Y, Zhang Y, Shi X et al. Flavobacterium ovatum sp. nov., a marine bacterium isolated from an Antarctic intertidal sandy beach. Int J Syst Evol Microbiol 2018; 68:795–800 [View Article] [PubMed]
     [Google Scholar]
  7. Kämpfer P, Lodders N, Martin K, Avendaño-Herrera R. Flavobacterium chilense sp. nov. and Flavobacterium araucananum sp. nov., isolated from farmed salmonid fish. Int J Syst Evol Microbiol 2012; 62:1402–1408 [View Article] [PubMed]
     [Google Scholar]
  8. Seo YL, Jeong SE, Jin HM, Jeon CO. Flavobacterium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa. Int J Syst Evol Microbiol 2020; 70:1037–1041 [View Article] [PubMed]
     [Google Scholar]
  9. Du J, Yi T-H. Flavobacterium tyrosinilyticum sp. nov., isolated from the rhizosphere of wild strawberry. Int J Syst Evol Microbiol 2016; 66:2629–2634
     [Google Scholar]
  10. 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
     [Google Scholar]
  11. Zhang Y, Jiang F, Chang X, Qiu X, Ren L et al. Flavobacterium collinsense sp. nov., isolated from a till sample of an Antarctic glacier. Int J Syst Evol Microbiol 2016; 66:172–177 [View Article] [PubMed]
     [Google Scholar]
  12. Zhang B, Liu ZQ, Zheng YG. Flavobacterium quisquiliarum sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2017; 67:3965–3970 [View Article] [PubMed]
     [Google Scholar]
  13. Chaudhary DK, Kim J. Flavobacterium naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:305–309 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. Wahli T, Lone M. Flavobacteria, a never ending threat for fish: a review. Curr Clin Microbiol Rep 2018; 5:26–37 [View Article]
     [Google Scholar]
  16. Baek K, Jeon CO. Mucilaginibacter vulcanisilvae sp. nov., isolated from a volcanic forest. Int J Syst Evol Microbiol 2015; 65:2036–2041
     [Google Scholar]
  17. 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
     [Google Scholar]
  18. Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article] [PubMed]
     [Google Scholar]
  19. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  20. 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 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  23. Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103
     [Google Scholar]
  24. 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]
  25. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 2017; 34:2115–2122 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955138–146
     [Google Scholar]
  28. Smibert R, Krieg N. Phenotypic characterization. Gerhardt P. eds In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  29. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  30. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of flavobacterium and cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. 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
     [Google Scholar]
  31. Jeong SH, Park MS, Jin HM, Lee K, Park W et al. Aestuariibaculum suncheonense gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a tidal flat and emended descriptions of the genera Gaetbulibacter and Tamlana. Int J Syst Evol Microbiol 2013; 63:332–338 [View Article] [PubMed]
     [Google Scholar]
  32. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
     [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  34. Minnikin D, Patel P, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117
     [Google Scholar]
  35. Nguyen TM, Kim J. A rapid and simple method for identifying bacterial polar lipid components in wet biomass. J Microbiol 2017; 55:635–639 [View Article] [PubMed]
     [Google Scholar]
  36. Lee S, Weon HY, Han K, Ahn TY. Flavobacterium dankookense sp. nov., isolated from a freshwater reservoir, and emended descriptions of Flavobacterium cheonanense, F. chungnamense, F. koreense and F. aquatile. Int J Syst Evol Microbiol 2012; 62:2378–2382 [View Article] [PubMed]
     [Google Scholar]
  37. Sheu SY, Chiu TF, Young CC, Arun AB, Chen WM. Flavobacterium macrobrachii sp. nov., isolated from a freshwater shrimp culture pond. Int J Syst Evol Microbiol 2011; 6:1402–1407
     [Google Scholar]
  38. Feng XM, Tan X, Jia L, Long PP, Han L et al. Flavobacterium buctense sp. nov., isolated from freshwater. Arch Microbiol 2015; 197:1109–1115 [View Article] [PubMed]
     [Google Scholar]
  39. Chen WM, Guo YP, Kwon SW, Sheu SY. Flavobacterium piscinae sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 2019; 69:1775–1782 [View Article] [PubMed]
     [Google Scholar]
  40. Jit S, Dadhwal M, Prakash O, Lal R. Flavobacterium lindanitolerans sp nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2008; 58:1665–1669 [View Article] [PubMed]
     [Google Scholar]
  41. Montero-Calasanz M del C, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea l.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense. Syst Appl Microbiol 2014; 37:342–350 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004867
Loading
Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov., isolated from forest soil
Int J Syst Evol Microbiol 71, 004867 (2021); https://doi.org/10.1099/ijsem.0.004867
/content/journal/ijsem/10.1099/ijsem.0.004867
/content/journal/ijsem/10.1099/ijsem.0.004867
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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