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

Volume 75, Issue 7

Isolation and characterization of sp. nov. from freshwater, sp. nov. from moss on soil and sp. nov. from moss on a tree No Access

Abstract

Three Gram-negative, facultatively anaerobic, rod-shaped, non-motile and reddish-pigmented bacterial strains, designated GW2-5, WM1 and Tmos10, were isolated from distinct environments in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the three strains belonged to the genus . The type strain GW2-5ᵀ grew at temperatures of 10–35 °C (optimum: 25 °C), pH levels of 6.0–12.0 (optimum: pH 7.0) and NaCl concentrations of 0–0.5% (optimum: 0%). Strain WM1ᵀ grew at temperatures of 10–37 °C (optimum: 30 °C), pH levels of 5.0–12.0 (optimum: pH 7.0) and NaCl concentrations of 0–1% (optimum: 0%). Strain Tmos10ᵀ grew at temperatures of 10–35 °C (optimum: 25 °C), pH levels of 5.0–12.0 (optimum: pH 7.0) and NaCl concentrations of 0–0.5% (optimum: 0%). The three strains exhibited the highest 16S rRNA gene sequence similarity to HMF5405ᵀ (98.7%) for strain GW2-5ᵀ, BUZ 2ᵀ (98.7%) for strain WM1ᵀ and HMF5405ᵀ (96.6%) for strain Tmos10ᵀ. The average nucleotide identity values ranged from 73.5% to 86.6%, while the digital DNA–DNA hybridization values ranged from 19.5% to 31.4% between the three novel isolates and species belonging to the genus . Based on phenotypic, physiological, biochemical, genomic and phylogenetic characteristics, strains GW2-5, WM1 and Tmos10 are proposed as novel species within the genus . They are designated as sp. nov. (type strain GW2-5=KACC 23817=TBRC 19128), sp. nov. (type strain WM1=KACC 23815=TBRC 19127) and sp. nov. (type strain Tmos10=KACC 23816=TBRC 19129), respectively.

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Keyword(s): antibiotic resistance , Fibrella , freshwater , moss and novel species
© 2025 The Authors
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2025-07-14
2026-04-14

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References

  1. Filippini M, Svercel M, Laczko E, Kaech A, Ziegler U et al. Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008. Int J Syst Evol Microbiol 2011; 61:184–189 [View Article] [PubMed]
     [Google Scholar]
  2. Kang H, Kim H, Bae S, Joh K. Fibrella aquatilis sp. nov., Fibrella rubiginis sp. nov. and Fibrella forsythiae sp. nov., isolated from freshwater, rusty iron and forsythia flower. Int J Syst Evol Microbiol 2022; 72: Epub ahead of print 2022 [View Article]
     [Google Scholar]
  3. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  4. Ramesh C, Vinithkumar NV, Kirubagaran R, Venil CK, Dufossé L. Multifaceted applications of microbial pigments: current knowledge, challenges and future directions for public health implications. Microorganisms 2019; 7:186 [View Article] [PubMed]
     [Google Scholar]
  5. Woo H, Chhetri G, Kim I, So Y, Park S et al. Roseateles subflavus sp. nov. and Roseateles aquae sp. nov., isolated from artificial pond water and Roseateles violae sp. nov., isolated from a viola mandshurica root. Int J Syst Evol Microbiol 2024; 74: [View Article]
     [Google Scholar]
  6. Park S, Kim I, Chhetri G, So Y, Jung Y et al. Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov. Int J Syst Evol Microbiol 2023; 73:006043 [View Article]
     [Google Scholar]
  7. Kim I, Seo T. Pseudarthrobacter humi sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2023; 73:005671 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [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. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015; 31:3210–3212 [View Article] [PubMed]
     [Google Scholar]
  17. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  18. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:1–15 [View Article] [PubMed]
     [Google Scholar]
  19. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V et al. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 2021; 49:D1020–D1028 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  23. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [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; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  25. Blin K, Shaw S, Medema MH, Weber T. The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more. Nucleic Acids Res 2024; 52:D586–D589 [View Article] [PubMed]
     [Google Scholar]
  26. Lee H, Kim I, Park S, Woo H, Yook S et al. Sphingomonas rustica sp. nov. and Sphingomonas agrestis sp. nov., novel carotenoid-producing bacterial species isolated from farm soil. Int J Syst Evol Microbiol 2024; 74:006551 [View Article] [PubMed]
     [Google Scholar]
  27. Kim I, Chhetri G, Kim J, Kang M, Seo T. Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6180–6187 [View Article]
     [Google Scholar]
  28. Park S, Kim I, Woo H, Lee H, Yook S et al. Aurantiacibacter flavus sp. nov. and Aurantiacibacter gilvus sp. nov., isolated from the mudflat of Suaeda japonica colonies. Int J Syst Evol Microbiol 2024; 74:006578 [View Article]
     [Google Scholar]
  29. Bernardet J-F, Nakagawa Y, Holmes B. Prokaryotes S on the taxonomy of F and C bacteria of the IC on S of 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] [PubMed]
     [Google Scholar]
  30. Nonstaining BJD. Nonstaining (KOH) method for determination of gram reactions of marine bacteriat; 1982 https://journals.asm.org/journal/aem
  31. Lewis II JS, C and LSI Performance standards for antimicrobial susceptibility testing. n.d https://cir.nii.ac.jp/crid/1130578271562670753 accessed 19 August 2024
  32. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  33. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
     [Google Scholar]
  34. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  35. 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]
  36. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  37. Yoon S-H, Ha S, 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]
     [Google Scholar]
  38. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
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Isolation and characterization of Fibrella aquatica sp. nov. from freshwater, Fibrella musci sp. nov. from moss on soil and Fibrella arboris sp. nov. from moss on a tree
Int J Syst Evol Microbiol 75, 006842 (2025); https://doi.org/10.1099/ijsem.0.006842
/content/journal/ijsem/10.1099/ijsem.0.006842
/content/journal/ijsem/10.1099/ijsem.0.006842
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