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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 10

sp. nov., isolated from the rhizospheric soils of bell pepper ( L.) No Access

Abstract

Two separate bacterial strains, PMTSA4 and PMR2A8, were isolated from the rhizospheric soils of bell pepper plants grown in a plant nursery. These strains are Gram-negative, non-motile and rod-shaped and grow in aerobic conditions. They exhibit a positive reaction for catalase activity but negative results for oxidase activity. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the strains PMTSA4 and PMR2A8 are closely related to ICH-30 (95.6%, respectively), 10Alg 130 (95.5%) and KMM 9535 (95.3%), aligning them within the genus . Digital DNA–DNA hybridization (dDDH) values and average nucleotide identities (ANIs) of the whole-genome sequences for the two strains and related species were significantly below the established thresholds for prokaryotic species delineation (<70% for dDDH and <95% for ANI). The observed values were as follows: LMG 4008 (dDDH: 19.8% and ANI: 75.5%), ICH-30 (dDDH: 18.6% and ANI: 73.3%) and WWJ 16 (dDDH: 18.5% and ANI: 72.0%). The strains have genome sizes of 3 068 185 bp and 3 068 330 bp, with a G+C content of 32.5 mol%. In phenotypic characterization, the new strains grew at 10–35 °C and tolerated up to 4% NaCl at pH 5–9 (optimum pH 8). The predominant cellular fatty acids were observed to be iso-C, iso-C 3-OH and iso-C 3-OH. Menaquinone-6 was the predominant quinone. Considering the results from phenotypic, chemotaxonomic, phylogenetic and genomic analyses, it is proposed that the strains PMTSA4 and PMR2A8 represent a novel species within the genus .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Flavobacterium sp. nov. , novel species and pepper rhizosphere
Funding
This study was supported by the:
  • Korea Research Institute of Bioscience and Biotechnology (Award KGM5282331)
    • Principal Award Recipient: ChaYoung Kim
  • National Research Foundation of Korea (Award RS-2024-00352429)
    • Principal Award Recipient: JiyoungLee
© 2024 The Authors
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2024-10-23
2025-11-15

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References

  1. Bergey DH. Bergey’s Manual of Determinative Bacteriology Lippincott Williams & Wilkins; 1994
     [Google Scholar]
  2. Hu G, Zhang J, Yang G, Li Y-Y, Guan Y-T et al. Flavobacterium yanchengense sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:2848–2852 [View Article] [PubMed]
     [Google Scholar]
  3. Chen WM, Guo YP, Kwon SW, Sheu C, Sheu SY. Flavobacterium stagni sp. nov., isolated from a freshwater reservoir. Int J Syst Evol Microbiol 2019; 69:2372–2379 [View Article] [PubMed]
     [Google Scholar]
  4. Yoon J-H, Park S, Kang S-J, Oh S-J, Myung SC et al. Flavobacterium ponti sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2011; 61:81–85 [View Article]
     [Google Scholar]
  5. Zhang GQ, Yang LL, Liu Q, Liu HC, Zhou YG et al. Flavobacterium restrictum sp. nov., Flavobacterium rhamnosiphilum sp. nov., and Flavobacterium zepuense sp. nov. isolated from glaciers. Int J Syst Evol Microbiol 2020; 70:4583–4590 [View Article]
     [Google Scholar]
  6. Bernardet J-F, Bowman JP. The genus Flavobacterium. In The Prokaryotes vol 7 2006 pp 481–531 [View Article]
     [Google Scholar]
  7. 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]
     [Google Scholar]
  8. McBride MJ. The family Flavobacteriaceae. In The Prokaryotes vol 4 2014 pp 643–676 [View Article]
     [Google Scholar]
  9. 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]
     [Google Scholar]
  10. 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]
  11. Humaira Z, Cho D, Peng Y, Avila F, Park YL et al. Demequina capsici sp. nov., a novel plant growth-promoting actinomycete isolated from the rhizosphere of bell pepper (Capsicum annuum). Sci Rep 2024; 14:15830 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. Trees RP. The neighbor-joining method: a new method for. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  14. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967 [View Article]
     [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  17. Li Z, Mertens KN, Nézan E, Chomérat N, Bilien G et al. Discovery of a new clade nested within the genus Alexandrium (Dinophyceae): morpho-molecular characterization of Centrodinium punctatum (Cleve) F.J.R. Taylor. Protist 2019; 170:168–186 [View Article] [PubMed]
     [Google Scholar]
  18. Jiang L, Pheng S, Lee KC, Kang SW, Jeong JC et al. Cohnella abietis sp. nov., isolated from Korean fir (Abies koreana) rhizospheric soil of Halla mountain. J Microbiol 2019; 57:953–958 [View Article]
     [Google Scholar]
  19. 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]
  20. Collins MD, Shah HN, Minnikin DE. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin‐layer chromatography. J Appl Bacteriol 1980; 48:277–282 [View Article]
     [Google Scholar]
  21. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acids Methyl Esters (GC-FAME) Newark, NY: Microbial ID; 2006
     [Google Scholar]
  22. Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990; 28:1942–1946 [View Article] [PubMed]
     [Google Scholar]
  23. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
     [Google Scholar]
  24. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [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. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
     [Google Scholar]
  27. Yoon SH, Ha SM, 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]
  28. 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]
  29. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
     [Google Scholar]
  30. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 2014; 42:D231–9 [View Article] [PubMed]
     [Google Scholar]
  31. Kim M, Oh H-S, Park S-C, 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 [View Article] [PubMed]
     [Google Scholar]
  32. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
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Flavobacterium capsici sp. nov., isolated from the rhizospheric soils of bell pepper (Capsicum annuum L.)
Int J Syst Evol Microbiol 74, 006554 (2024); https://doi.org/10.1099/ijsem.0.006554
/content/journal/ijsem/10.1099/ijsem.0.006554
/content/journal/ijsem/10.1099/ijsem.0.006554
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