Skip to content
1887

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

Volume 75, Issue 1

sp. nov., sp. nov., sp. nov. and sp. nov., isolated from stagnant water in a clump of Steud No Access

Abstract

Four novel bacterial strains were isolated from stagnant water in a clump of Steud. The four Gram-negative, facultatively anaerobic, rod-shaped, non-motile and yellow-coloured strains were designated as DGU11, DGU38, DGU41 and DGU99. The four novel strains exhibited 16S rRNA gene similarities with their closest type strains, ranging from 95.7 to 98.7%, average nucleotide identity values from 75.3 to 95.6% and digital DNA–DNA hybridization values between 17.9 and 59.6%. The cells of strain DGU11 were non-motile and grew at 10−30°C (optimum 25 °C), a pH range of 4.0–12.0 (optimum 9.0) and in the presence of 0–1.0% sodium chloride (NaCl) (optimum 0%). The cells of strain DGU38 were non-motile and grew at 10−35°C (optimum 30 °C), a pH range of 4.0–8.0 (optimum 7.0) and at 0 –2.0% NaCl (optimum 0%). The cells of strain DGU41 were non-motile and grew at 15−50°C (optimum 30 °C), a pH range of 6.0–9.0 (optimum 7.0) and in the presence of 0% NaCl (optimum 0%). The cells of strain DGU99 were non-motile and grew at 15−35°C (optimum 25 °C), a pH range of 6.0–12.0 (optimum 9.0) and in the presence of 0 –2.0% NaCl (optimum 0%). The major fatty acid composition of the four novel strains was iso-C and C cC1 c, which is similar to other species. The proposed names of the novel strains are sp. nov. (type strain DGU11=KACC 23722=TBRC 19004), sp. nov. (type strain DGU38=KACC 23723=TBRC 19005), sp. nov. (type strain DGU41=KACC 23724=TBRC 19006) and sp. nov. (type strain DGU99=KACC 23725=TBRC 19007).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): carbohydrate-active enzyme , facultatively anaerobic bacteria , menaquinone-6 (MK-6) , Phragmites japonica , South Korea and stagnant water
Funding
This study was supported by the:
  • Dongguk University Research Fund of 2024
    • Principal Award Recipient: ParkSunho
  • National Research Foundation of Korea (Award 2022R1F1A1070108)
    • Principal Award Recipient: SeoTaegun
  • National Institute of Biological Resources (Award NIBR202402203)
    • Principal Award Recipient: SeoTaegun
© 2025 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006667
2025-01-31
2025-11-10

Metrics

Loading full text...

Full text loading...

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM et al. Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923
     [Google Scholar]
  2. Kang JY, Chun J, Jahng KY. Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:1633–1638 [View Article] [PubMed]
     [Google Scholar]
  3. 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]
  4. 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]
  5. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai’i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 2013; 63:3280–3286 [View Article] [PubMed]
     [Google Scholar]
  6. Chaudhary DK, Dahal RH, Kim D-U, Kim J. Flavobacterium sandaracinum sp. nov., Flavobacterium caseinilyticum sp. nov., and Flavobacterium hiemivividum sp. nov., novel psychrophilic bacteria isolated from Arctic soil. Int J Syst Evol Microbiol 2020; 70:2269–2280 [View Article]
     [Google Scholar]
  7. Zhang GQ, Yang LL, Liu Q, Liu HC, Zhou YG et al. 2020; Flavobacterium restrictum sp. nov., Flavobacterium rhamnosiphilum sp. nov., and Flavobacterium zepuense sp. nov. isolated from glaciers. Int J Syst Evol Microbiol 70:4583–4590 [View Article]
     [Google Scholar]
  8. Wu N, Liu L, Jiang X, Yuan Y, Mao D et al. Flavobacterium sedimenticola sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2023; 73:006180 [View Article] [PubMed]
     [Google Scholar]
  9. Liu Q, Siddiqi MZ, Liu Q, Huq MdA, Lee SY et al. Flavobacterium hankyongi sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2018; 68:1732–1736 [View Article]
     [Google Scholar]
  10. Starliper CE. Bacterial coldwater disease of fishes caused by Flavobacterium psychrophilum. J Adv Res 2011; 2:97–108 [View Article]
     [Google Scholar]
  11. 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]
     [Google Scholar]
  12. Zamora L, Fernández-Garayzábal JF, Svensson-Stadler LA, Palacios MA, Domínguez L et al. Flavobacterium oncorhynchi sp. nov., a new species isolated from rainbow trout (Oncorhynchus mykiss). Syst Appl Microbiol 2012; 35:86–91 [View Article]
     [Google Scholar]
  13. Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VGH et al. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnol Biofuels 2016; 9:260 [View Article] [PubMed]
     [Google Scholar]
  14. Nedashkovskaya OI, Balabanova LA, Zhukova NV, Kim S-J, Bakunina IY et al. Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga. Arch Microbiol 2014; 196:745–752 [View Article] [PubMed]
     [Google Scholar]
  15. Chaudhary DK, Kim DU, Kim D, Kim J. Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil. Sci Rep 2019; 9:4134 [View Article] [PubMed]
     [Google Scholar]
  16. Nayarisseri A, Suppahia A, Nadh AG, Nair AS. Identification and characterization of a pesticide degrading Flavobacterium species EMBS0145 by 16S rRNA gene sequencing. Interdiscip Sci 2015; 7:93–99 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. 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]
  19. Kolbek J, Jarolímek I. Phragmitetum japonicae in Korean Peninsula and Japan. Biologia 2010; 65:479–488 [View Article]
     [Google Scholar]
  20. Chhetri G, Kim I, Kim J, So Y, Park S et al. Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato). Front Microbiol 2023; 14:1140484 [View Article]
     [Google Scholar]
  21. Chhetri G, Kim I, Park S, Jung Y, Seo T. Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant. Arch Microbiol 2023; 205:1–9 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  31. 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]
  32. 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]
  33. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  34. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  35. 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]
  36. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genom 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  37. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
     [Google Scholar]
  38. Sun J, Lu F, Luo Y, Bie L, Xu L et al. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res 2023; 51:W397–W403 [View Article] [PubMed]
     [Google Scholar]
  39. Grant JR, Stothard P. The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Research 2008; 36:W181–W184 [View Article]
     [Google Scholar]
  40. Zheng J, Ge Q, Yan Y, Zhang X, Huang L et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res 2023; 51:W115–W121 [View Article]
     [Google Scholar]
  41. 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]
  42. 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]
     [Google Scholar]
  43. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  44. 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]
  45. Woo H, Kim I, Chhetri G, Park S, Lee H et al. Two novel bacterial species, Rhodanobacter lycopersici sp. nov. and Rhodanobacter geophilus sp. nov., isolated from the rhizosphere of Solanum lycopersicum with plant growth-promoting trait. Microorganisms 2024; 12:2227 [View Article]
     [Google Scholar]
  46. Moyes RB, Reynolds J, Breakwell DP. Differential staining of bacteria: gram stain. Curr Protoc Microbiol 2009; Appendix 3:Appendix 3C [View Article] [PubMed]
     [Google Scholar]
  47. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
     [Google Scholar]
  48. Bernardet J-F, 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 [View Article]
     [Google Scholar]
  49. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  50. 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]
  51. 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]
     [Google Scholar]
  52. 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]
  53. 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]
  54. Feng H, Zeng Y, Huang Y. Flavobacterium palustre sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2015; 65:1003–1007 [View Article] [PubMed]
     [Google Scholar]
  55. Ekwe AP, Kim SB. Flavobacterium commune sp. nov., isolated from freshwater and emended description of Flavobacterium seoulense. Int J Syst Evol Microbiol 2018; 68:93–98 [View Article] [PubMed]
     [Google Scholar]
  56. Chen WM, Su CL, Young CC, Sheu SY. Flavobacterium fluviatile sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018; 68:1244–1250 [View Article] [PubMed]
     [Google Scholar]
  57. Baek C, Shin SK, Yi H. Flavobacterium magnum sp. nov., Flavobacterium pallidum sp. nov., Flavobacterium crocinum sp. nov. and flavobacterium album sp. nov. Int J Syst Evol Microbiol 2018; 68:3837–3843 [View Article]
     [Google Scholar]
  58. Zhang B-Y, Yuan Y, Zhou J, Wang X-F, Li H-F et al. Flavobacterium lacisediminis sp. nov., a bacterium isolated from lake sediment. Int J Syst Evol Microbiol 2023; 73:005914 [View Article] [PubMed]
     [Google Scholar]
  59. Qu JH, Li HF, Yang JS, Yuan HL. Flavobacterium cheniae sp. nov., isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 2008; 58:2186–2190 [View Article] [PubMed]
     [Google Scholar]
  60. Ali Z, Cousin S, Frühling A, Brambilla E, Schumann P et al. Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov. isolated from a hard water rivulet. Int J Syst Evol Microbiol 2009; 59:2610–2617 [View Article] [PubMed]
     [Google Scholar]
  61. Cai H, Zeng Y, Wang Y, Cui H, Jiang H. Flavobacterium cyanobacteriorum sp. nov., isolated from cyanobacterial aggregates in a eutrophic lake. Int J Syst Evol Microbiol 2018; 68:1279–1284 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006667
Loading
Flavobacterium arundinis sp. nov., Flavobacterium calami sp. nov., Flavobacterium helocola sp. nov. and Flavobacterium flavipallidum sp. nov., isolated from stagnant water in a clump of Phragmites japonica Steud
Int J Syst Evol Microbiol 75, 006667 (2025); https://doi.org/10.1099/ijsem.0.006667
/content/journal/ijsem/10.1099/ijsem.0.006667
/content/journal/ijsem/10.1099/ijsem.0.006667
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