1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 12

sp. nov., isolated from sediment No Access

Abstract

A novel yellow-pigmented bacterial strain, designated YZ-48, was isolated from the sediment of the Yangtze River, PR China. Cells were Gram-stain-negative, non-motile, rod-shaped, strictly aerobic, catalase-positive and oxidase-positive. The strain grew optimally on R2A medium at 37 °C, pH 7.0 and with 1.0 % (w/v) NaCl. Strain YZ-48 showed the closest 16S rRNA gene sequence similarity to SE-s27 (96.4 %) and DSM 25687 (96.2 %). The phylogenetic trees based on 16S rRNA gene sequences showed that strain YZ-48 belonged to the genus but formed a distinct phylogenetic lineage. The obtained average nucleotide identity and digital DNA–DNA hybridization values between YZ-48 and the two closest strains were 75.0 and 74.5 % and 19.6 and 19.0 %, respectively. The sole respiratory quinone was MK-6. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and three unidentified polar lipids. The major cellular fatty acids were iso-C, iso-C, iso-C G, iso-C 3-OH, iso-C 3-OH and iso-C 3-OH. The DNA G+C content was 40.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain YZ-48 represents a novel species of the genus , for which the name sp. nov. is proposed, with strain YZ-48 (=KCTC 82329=CCTC AB 2023061=MCCC 1K08804) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Flavobacterium sedimenticola sp. nov. and polyphasic taxonomy
Funding
This study was supported by the:
  • Science and Technology Support Program of Jiangsu Province (Award BM2022019)
    • Principle Award Recipient: JianHe
  • National Natural Science Foundation of PR China (Award 32170128)
    • Principle Award Recipient: JianHe
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006180
2023-12-06
2024-05-08
Loading full text...

Full text loading...

References

  1. Bergey DH, Breed RS, Hammer BW, Huntoon F et al. Bergey’s Manual of Determinative Bacteriology Baltimore: Williams and & Wilkins Co; 1923
     [Google Scholar]
  2. Lee S, Oh J-H, Weon H-Y, Ahn T-Y. Flavobacterium cheonhonense sp. nov., isolated from a freshwater reservoir. J Microbiol 2012; 50:562–566 [View Article] [PubMed]
     [Google Scholar]
  3. Song L, Liu H, Huang Y, Dai X, Zhou Y. Flavobacterium marinum sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:3551–3555 [View Article] [PubMed]
     [Google Scholar]
  4. Xiao Y-P, Hui W, Lee J-S, Lee KC, Quan Z-X. Flavobacterium dongtanense sp. nov., isolated from the rhizosphere of a wetland reed. Int J Syst Evol Microbiol 2011; 61:343–346 [View Article] [PubMed]
     [Google Scholar]
  5. 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]
  6. Wahli T, Madsen L. Flavobacteria, a never ending threat for fish: a review. Curr Clin Micro Rpt 2018; 5:26–37 [View Article]
     [Google Scholar]
  7. Dahal RH, Chaudhary DK, Kim J. Flavobacterium flaviflagrans sp. nov., a bacterium of the family Flavobacteriaceae isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:2653–2659 [View Article] [PubMed]
     [Google Scholar]
  8. Dong K, Chen F, Du Y, Wang G. Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. Int J Syst Evol Microbiol 2013; 63:886–892 [View Article] [PubMed]
     [Google Scholar]
  9. Liu Y, Jin JH, Zhou YG, Liu HC, Liu ZP. Flavobacterium caeni sp. nov., isolated from a sequencing batch reactor for the treatment of malachite green effluents. Int J Syst Evol Microbiol 2010; 60:417–421 [View Article] [PubMed]
     [Google Scholar]
  10. Sambrock J, Russel DW. Molecular cloning: a laboratory manual. Anal Biochem 2001; 186:182–183 [View Article]
     [Google Scholar]
  11. Yoon JH, Lee ST, Park YH. Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 1998; 48:187–194 [View Article] [PubMed]
     [Google Scholar]
  12. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  13. Zhang W, Sun Z. Random local neighbor joining: a new method for reconstructing phylogenetic trees. Mol Phylogenet Evol 2008; 47:117–128 [View Article] [PubMed]
     [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. 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 [View Article] [PubMed]
     [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  18. Luo R, Liu B, Xie Y, Li Z, Huang W et al. Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2015; 4:30 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:206–214 [View Article] [PubMed]
     [Google Scholar]
  21. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article] [PubMed]
     [Google Scholar]
  22. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
     [Google Scholar]
  23. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note 101 Newark: MIDI; 1990
     [Google Scholar]
  26. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteri 1979; 47:87–95 [View Article]
     [Google Scholar]
  27. 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]
  28. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbio 1988; 19:161–207
     [Google Scholar]
  29. Beveridge TJ, Lawrence JR, Murray R. Sampling and Staining for Light Microscopy Wiley; 2007
     [Google Scholar]
  30. Li Y, Liang J, Liu R, Xue C-X, Zhou S et al. Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov., two marine bacteria isolated from the East China Sea. Int J Syst Evol Microbiol 2020; 70:889–896 [View Article]
     [Google Scholar]
  31. Bernardet JF, Nakagawa Y, Holmes B et al. 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 [View Article]
     [Google Scholar]
  32. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbio 1988; 19:1–67
     [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  34. 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]
  35. Jung HS, Chun BH, Kim HM, Jeon CO. Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2021; 71: [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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006180
Loading
Flavobacterium sedimenticola sp. nov., isolated from sediment
Int J Syst Evol Microbiol 73, 006180 (2023); https://doi.org/10.1099/ijsem.0.006180
/content/journal/ijsem/10.1099/ijsem.0.006180
/content/journal/ijsem/10.1099/ijsem.0.006180
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