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Abstract

Four Gram-stain-positive and two Gram-stain-negative bacterial strains, designated as W4, FW7, TW48, UW52, PT-3, and RJY3, were isolated from soil samples collected from the Republic of Korea. The 16S rRNA gene sequence analysis showed that strains W4 and FW7 belonged to the genus , strains TW48 and UW52 were affiliated to the genus strain PT-3 was related to the genus , and strain RJY3 was associated with the genus . The closest phylogenetic taxa to W4, FW7, TW48, UW52, PT-3, and RJY3 were NEAU-LLE (97.7 %), DFW100M-13 (97.9 %), JJ-7 (99.6 %), JJ-447 (95.7 %), T7 (97.1 %), and S2 (99.5 %), respectively. Average nucleotide identity and digital DNA–DNA hybridization values between the novel strains and related reference type strains were <95.0 % and <70.0 %, respectively. The major cellular fatty acid in strains W4, FW7 TW48, and UW52 was antiso-C. Similarly, strain PT-3 revealed iso-C, iso-C G, iso-C 3-OH, and iso-C 3-OH as its principal fatty acids. On the other hand, RJY3 exhibited summed feature 3 (C 7 and/or C 6), C, summed feature 8 (C 7 and/or C 6), and C as its predominant fatty acids. Overall, the polyphasic taxonomic data indicated that strains W4, FW7, TW48, UW52, PT-3, and RJY3 represent novel species within the genera , , , and . Accordingly, we propose the names sp. nov., with the type strain W4 (=KCTC 49888=NBRC 116001), sp. nov., with the type strain FW7 (=KCTC 49859=NBRC 116000), sp. nov., with the type strain TW48 (=KCTC 43470=NBRC 116017), sp. nov., with the type strain UW52 (=KCTC 43477=NBRC 116018), sp. nov., with the type strain PT-3 (=KCTC 92106=NBRC 116012), and sp. nov., with the type strain RJY3 (=KCTC 92105=NBRC 115831).

Funding
This study was supported by the:
  • National Institute of Biological Resources (Award NIBR202203112 and NIBR202102109)
    • Principle Award Recipient: Dong-UkKim
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2024-09-15
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References

  1. Orla-Jensen S. The Lactic Acid Bacteria Copenhagen: Høst and Son; 1919
    [Google Scholar]
  2. Alves A, Correia A, Igual JM, Trujillo ME. Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium. Syst Appl Microbiol 2014; 37:474–479
    [Google Scholar]
  3. Krishnamurthi S, Bhattacharya A, Schumann P, Dastager SG, Tang S-K et al. Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2012; 62:2187–2193 [View Article] [PubMed]
    [Google Scholar]
  4. Takeuchi M, Hatano K. Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium. Int J Syst Bacteriol 1998; 48:739–747 [View Article]
    [Google Scholar]
  5. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 1993; 64:253–260 [View Article] [PubMed]
    [Google Scholar]
  6. Tindall BJ. What is the type species of the genus Paenibacillus? Request for an opinion. Int J Syst Evol Microbiol 2000; 50:939–940 [View Article] [PubMed]
    [Google Scholar]
  7. Wu M, Zong Y, Guo W, Wang G, Li M. Paenibacillus montanisoli sp. nov., isolated from mountain area soil. Int J Syst Evol Microbiol 2018; 68:3569–3575 [View Article]
    [Google Scholar]
  8. 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 Evol Microbiol 1996; 46:128–148 [View Article]
    [Google Scholar]
  9. 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]
  10. Bergey D, Harrison F, Breed R, Hammer B. Genus II. Flavobacterium gen. nov. In Bergey’s Manual of Determinative Bacteriology vol 1923 Baltimore: The Williams & Wilkins Co; pp 97–117
    [Google Scholar]
  11. Kalmbach S, Manz W, Wecke J, Szewzyk U. Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system. Int J Syst Evol Microbiol 1999; 49:769–777 [View Article]
    [Google Scholar]
  12. Park M-J, Kim MK, Kim H-B, Im W-T, Yi T-H et al. Microbacterium ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2008; 58:429–433 [View Article] [PubMed]
    [Google Scholar]
  13. Shivaji S, Bhadra B, Rao RS, Chaturvedi P, Pindi PK et al. Microbacterium indicum sp. nov., isolated from a deep-sea sediment sample from the Chagos Trench, Indian Ocean. Int J Syst Evol Microbiol 2007; 57:1819–1822 [View Article] [PubMed]
    [Google Scholar]
  14. Heo J, Cho H, Kim MA, Hamada M, Tamura T et al. Microbacterium protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. Int J Syst Evol Microbiol 2020; 70:2226–2232 [View Article]
    [Google Scholar]
  15. Ling L, Zhao J, Li X, Zhang X, Jiang H et al. Microbacterium bovistercoris sp. nov., a novel actinomycete isolated from cow dung. Int J Syst Evol Microbiol 2019; 69:2703–2708 [View Article] [PubMed]
    [Google Scholar]
  16. Young C-C, Busse H-J, Langer S, Chu J-N, Schumann P et al. Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei. Int J Syst Evol Microbiol 2010; 60:854–860 [View Article] [PubMed]
    [Google Scholar]
  17. Cho S-J, Lee S-S. Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea. Antonie van Leeuwenhoek 2017; 110:11–18 [View Article] [PubMed]
    [Google Scholar]
  18. Vaz-Moreira I, Lopes AR, Falsen E, Schumann P, Nunes OC et al. Microbacterium luticocti sp. nov., isolated from sewage sludge compost. Int J Syst Evol Microbiol 2008; 58:1700–1704 [View Article] [PubMed]
    [Google Scholar]
  19. Baik KS, Lim CH, Choe HN, Kim EM, Seong CN. Paenibacillus rigui sp. nov., isolated from a freshwater wetland. Int J Syst Evol Microbiol 2011; 61:529–534 [View Article] [PubMed]
    [Google Scholar]
  20. Sadaf K, Tushar L, Nirosha P, Podile AR, Sasikala C et al. Paenibacillus arachidis sp. nov., isolated from groundnut seeds. Int J Syst Evol Microbiol 2016; 66:2923–2928 [View Article] [PubMed]
    [Google Scholar]
  21. Wu Y-F, Wu Q-L, Liu S-J. Paenibacillus taihuensis sp. nov., isolated from an eutrophic lake. Int J Syst Evol Microbiol 2013; 63:3652–3658 [View Article] [PubMed]
    [Google Scholar]
  22. Kämpfer P, Busse H-J, McInroy JA, Clermont D, Criscuolo A et al. Paenibacillus allorhizosphaerae sp. nov., from soil of the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2021; 71:005051 [View Article]
    [Google Scholar]
  23. Kämpfer P, Lipski A, McInroy JA, Clermont D, Lamothe L et al. Paenibacillus auburnensis sp. nov. and Paenibacillus pseudetheri sp. nov., isolated from the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2023; 73:005808 [View Article]
    [Google Scholar]
  24. Kaur N, Seuylemezian A, Patil PP, Patil P, Krishnamurti S et al. Paenibacillus xerothermodurans sp. nov., an extremely dry heat resistant spore forming bacterium isolated from the soil of Cape Canaveral, Florida. Int J Syst Evol Microbiol 2018; 68:3190–3196 [View Article]
    [Google Scholar]
  25. Kong BH, Liu QF, Liu M, Liu Y, Liu L et al. Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L. Int J Syst Evol Microbiol 2013; 63:1037–1044 [View Article] [PubMed]
    [Google Scholar]
  26. Liu H, Lu L, Wang S, Yu M, Cao X et al. Paenibacillus tianjinensis sp. nov., isolated from corridor air. Int J Syst Evol Microbiol 2021; 71:005158 [View Article]
    [Google Scholar]
  27. Dahal RH, Chaudhary DK, Kim J, Kim D-U. Draft genome sequence of Flavobacterium silvisoli RD-2-33t isolated from forest soil. Korean J Microbiol 2020; 56:86–88
    [Google Scholar]
  28. Feng X-M, Tan X, Jia L, Long P-P, Han L et al. Flavobacterium buctense sp. nov., isolated from freshwater. Arch Microbiol 2015; 197:1109–1115 [View Article] [PubMed]
    [Google Scholar]
  29. Kitahara K, Muzembo BA, Morohoshi S, Kunihiro T, Tazato N et al. Flavobacterium okayamense sp. nov. isolated from surface seawater. Arch Microbiol 2023; 205:346 [View Article] [PubMed]
    [Google Scholar]
  30. Yin C-C, Yang L-L, Xin Y-H, Ye J, Liu Q. Identification of Flavobacterium algoritolerans sp. nov. and Flavobacterium yafengii sp. nov., two novel members of the genus Flavobacterium. Int J Syst Evol Microbiol 2023; 73:006072 [View Article]
    [Google Scholar]
  31. Seo J, Peng Y, Jiang L, Lee S-B, Jeong R-D et al. Flavobacterium endoglycinae sp. nov., an endophytic bacterium isolated from soybean (Glycine max L. cv. Gwangan) stems. Int J Syst Evol Microbiol 2022; 72:005220 [View Article] [PubMed]
    [Google Scholar]
  32. Loch TP, Faisal M. Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum. Int J Syst Evol Microbiol 2014; 64:406–412 [View Article] [PubMed]
    [Google Scholar]
  33. Irgang R, Poblete-Morales M, Avendaño-Herrera R. Flavobacterium pygoscelis sp. nov., isolated from a chinstrap penguin chick (Pygoscelis antarcticus). Int J Syst Evol Microbiol 2023; 73:005815 [View Article]
    [Google Scholar]
  34. Lin M-C, Jiang S-R, Chou J-H, Arun AB, Young C-C et al. Aquabacterium fontiphilum sp. nov., isolated from spring water. Int J Syst Evol Microbiol 2009; 59:681–685 [View Article] [PubMed]
    [Google Scholar]
  35. Chen W-M, Chen T-Y, Kwon S-W, Sheu S-Y. Aquabacterium lacunae sp. nov., isolated from a freshwater pond. Int J Syst Evol Microbiol 2020; 70:2888–2895 [View Article] [PubMed]
    [Google Scholar]
  36. Hirose S, Tank M, Hara E, Tamaki H, Mori K et al. Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria. Int J Syst Evol Microbiol 2020; 70:596–603 [View Article]
    [Google Scholar]
  37. Pham VHT, Jeong S-W, Kim J. Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3597–3602 [View Article] [PubMed]
    [Google Scholar]
  38. Khan IU, Habib N, Asem MD, Salam N, Xiao M et al. Aquabacterium tepidiphilum sp. nov., a moderately thermophilic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2019; 69:337–342 [View Article] [PubMed]
    [Google Scholar]
  39. Dahal RH, Han JY, Lee H, Chaudhary DK, Kim D-U. Aquabacterium terrae sp. nov., isolated from soil. Arch Microbiol 2021; 203:3183–3189 [View Article] [PubMed]
    [Google Scholar]
  40. Sun L, Chen W, Huang K, Lyu W, Gao X. Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin. Int J Syst Evol Microbiol 2021; 71:004768 [View Article] [PubMed]
    [Google Scholar]
  41. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
    [Google Scholar]
  42. Chaudhary DK, Kim D-U, 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]
  43. 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]
  44. 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]
  45. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  46. 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]
  47. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  48. 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]
  49. Stackebrandt E. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  50. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article] [PubMed]
    [Google Scholar]
  51. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
    [Google Scholar]
  52. 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]
  53. 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]
  54. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000; 7:203–214 [View Article] [PubMed]
    [Google Scholar]
  55. 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]
  56. 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]
  57. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
    [Google Scholar]
  58. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  59. Yoon S-H, Ha S-M, 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]
  60. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  61. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
    [Google Scholar]
  62. Máté R, Kutasi J, Bata-Vidács I, Kosztik J, Kukolya J et al. Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field. Arch Microbiol 2022; 204:301 [View Article] [PubMed]
    [Google Scholar]
  63. Hu A, Chen X, Luo S, Zou Q, Xie J et al. Rhizobium leguminosarum glutathione peroxidase is essential for oxidative stress resistance and efficient nodulation. Front Microbiol 2021; 12:627562 [View Article] [PubMed]
    [Google Scholar]
  64. Zhou Z, Tang H, Wang W, Zhang L, Su F et al. A cold shock protein promotes high-temperature microbial growth through binding to diverse RNA species. Cell Discov 2021; 7:15 [View Article]
    [Google Scholar]
  65. Tong H, Hu Q, Zhu L, Dong X. Prokaryotic aquaporins. Cells 2019; 8:1316 [View Article] [PubMed]
    [Google Scholar]
  66. 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]
  67. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  68. 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] [PubMed]
    [Google Scholar]
  69. Oktari A, Supriatin Y, Kamal M, Syafrullah H. The bacterial endospore stain on Schaeffer Fulton using variation of methylene blue solution. J Phys: Conf Ser 2017; 812:012066 [View Article]
    [Google Scholar]
  70. Lee H, Chaudhary DK, Lim OB, Lee KE, Cha IT et al. Paenibacillus caseinilyticus sp. nov., isolated forest soil. Int J Syst Evol Microbiol 2023; 73: [View Article]
    [Google Scholar]
  71. Smibert R. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. eds Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  72. Sasser M. Bacterial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME). In MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  73. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  74. 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]
  75. 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]
  76. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial systematics. Method Micrbiol 1988; 19:161–207 [View Article]
    [Google Scholar]
  77. Kim M, Lee B-H, Lee K-E, Park W. Flavobacterium phycosphaerae sp. nov. isolated from the phycosphere of Microcystis aeruginosa. Int J Syst Evol Microbiol 2019; 71:004735 [View Article]
    [Google Scholar]
  78. Lee S, Weon H-Y, Han K, Ahn T-Y. 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]
    [Google Scholar]
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