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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 4

sp. nov., isolated from plastic waste landfill soil No Access

Abstract

A Gram-stain-negative, yellow-pigmented and facultatively aerobic bacterium, designated strain U1, was isolated from plastic dumped soil sampled in the Republic of Korea. Cell of strain U1 were non-motile rods showing catalase-negative and oxidase-positive activities. Strain U1 was shown to grow at 10–37 °C (optimum, 25–30 °C) and pH 6.0–9.0 (optimum, pH 8.0), and in the presence of 0–0.5 % (w/v) NaCl (optimum, 0 %). Strain U1 contained iso-C, C, C ω5 and summed feature 3 (comprising C 6 and/or C ω7) as the major cellular fatty acids (>5 %) and menaquinone-7 as the sole respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids were identified as the major polar lipids. The DNA G+C content of strain U1 calculated from the whole-genome sequence was 45.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain U1 formed a distinct phylogenetic lineage within the genus . Strain U1 has the highest 16S rRNA sequence similarity to QTA69 (97.9 %). Average nucleotide identity and digital DNA–DNA hybridization values between strain U1 and QTA69 were 74.6 % and 18.9 %, respectively. Based on phenotypic, chemotaxonomic and molecular features, strain U1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is U1 (= KACC 22210=JCM 34491).

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  • Accepted:
  • Published Online:
Keyword(s): Bacteroidota , Dyadobacter pollutisoli , new taxa and waste landfill
Funding
This study was supported by the:
  • National Institute of Biological Resources (Award NIBR No. 2021-02-001)
    • Principle Award Recipient: CheOk Jeon
  • Chung-Ang University
    • Principle Award Recipient: CheOk Jeon
© 2023 The Authors
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2023-04-20
2024-05-14
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References

  1. Chelius MK, Triplett EW. Dyadobacter fermentans gen. nov., sp. nov., a novel Gram-negative bacterium isolated from surface-sterilized Zea mays stems. Int J Syst Evol Microbiol 2000; 50 Pt 2:751–758 [View Article] [PubMed]
     [Google Scholar]
  2. Chen L, Jiang F, Xiao M, Dai J, Kan W et al. Dyadobacter arcticus sp. nov., isolated from Arctic soil. Int J Syst Evol Microbiol 2013; 63:1616–1620 [View Article] [PubMed]
     [Google Scholar]
  3. Zhang Y, Peng X, Qin K, Liu J, Xu Q et al. Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus. Int J Syst Evol Microbiol 2021; 71:005103 [View Article] [PubMed]
     [Google Scholar]
  4. Chaudhary DK, Dahal RH, Kim J. Dyadobacter psychrotolerans sp. nov. and Dyadobacter frigoris sp. nov., two novel psychrotolerant members of the family Cytophagaceae isolated from Arctic soil. Int J Syst Evol Microbiol 2020; 70:569–575 [View Article]
     [Google Scholar]
  5. Dahal RH, Kim J. Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil. Arch Microbiol 2018; 200:1067–1074 [View Article] [PubMed]
     [Google Scholar]
  6. Chen L, Gao X, Ma Q, Liu H, Wang X et al. Dyadobacter luteus sp. nov., isolated from rose rhizosphere soil. Arch Microbiol 2020; 202:191–196 [View Article] [PubMed]
     [Google Scholar]
  7. Liu QM, Im WT, Lee M, Yang DC, Lee ST. Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2006; 56:1939–1944 [View Article] [PubMed]
     [Google Scholar]
  8. Gao J-L, Sun P, Wang X-M, Qiu T-L, Lv F-Y et al. Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:4022–4026 [View Article] [PubMed]
     [Google Scholar]
  9. He X-L, Zhou D, Gao H, Huang F-Q, Li H et al. Dyadobacter bucti sp. nov., isolated from subsurface sediment. Int J Syst Evol Microbiol 2020; 70:2281–2287 [View Article] [PubMed]
     [Google Scholar]
  10. Qu JH, Yue YF, Zhou J, Qu LB, Wang LF. Dyadobacter flavalbus sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2020; 70:1064–1070 [View Article] [PubMed]
     [Google Scholar]
  11. Song Z, Song Y, Yu Y, Choi L, Wang G et al. Dyadobacter luticola sp. nov., isolated from a sewage sediment sample. Int J Syst Evol Microbiol 2019; 69:465–469 [View Article] [PubMed]
     [Google Scholar]
  12. Baik KS, Kim MS, Kim EM, Kim HR, Seong CN. Dyadobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2007; 57:1227–1231 [View Article] [PubMed]
     [Google Scholar]
  13. Szabó I, Al-Omari J, Szerdahelyi GS, Radó J, Kaszab E et al. Dyadobacter subterraneus sp. nov., isolated from hydrocarbon-polluted groundwater from an oil refinery in hungary. Int J Syst Evol Microbiol 2021; 71:004916 [View Article]
     [Google Scholar]
  14. Chun J, Kang JY, Joung Y, Kim H, Joh K et al. Dyadobacter jejuensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2013; 63:1788–1792 [View Article] [PubMed]
     [Google Scholar]
  15. Baek JH, Baek W, Ruan W, Jung HS, Lee SC et al. Massilia soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2022; 72:005227 [View Article]
     [Google Scholar]
  16. 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]
  17. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007; 3:e56 [View Article]
     [Google Scholar]
  18. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
     [Google Scholar]
  19. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
     [Google Scholar]
  20. Kim KR, Kim KH, Khan SA, Kim HM, Han DM et al. Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil. J Microbiol 2021; 59:709–717 [View Article]
     [Google Scholar]
  21. Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M et al. Assembly of long error-prone reads using de Bruijn graphs. Proc Natl Acad Sci 2016; 113:E8396–E8405 [View Article]
     [Google Scholar]
  22. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 2014; 9:e112963 [View Article]
     [Google Scholar]
  23. 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]
     [Google Scholar]
  24. 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]
     [Google Scholar]
  25. Kim J, Na SI, Kim D, Chun J. UBCG2: up- to- date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615
     [Google Scholar]
  26. Lee I, Ouk Kim Y, Park SC, 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]
  27. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Varjani SJ, Gnansounou E, Pandey A. Comprehensive review on toxicity of persistent organic pollutants from petroleum refinery waste and their degradation by microorganisms. Chemosphere 2017; 188:280–291 [View Article] [PubMed]
     [Google Scholar]
  30. Lagedroste M, Reiners J, Knospe CV, Smits SHJ, Schmitt L. A structural view on the maturation of lanthipeptides. Front Microbiol 2020; 11:1183 [View Article]
     [Google Scholar]
  31. Johnston I, Osborn LJ, Markley RL, McManus EA, Kadam A et al. Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation. NPJ Biofilms Microbiomes 2021; 7:56 [View Article] [PubMed]
     [Google Scholar]
  32. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955; 1:138–146
     [Google Scholar]
  33. Bernardet JF, 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]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  35. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
     [Google Scholar]
  36. 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]
  37. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  38. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI Inc; 1990
     [Google Scholar]
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Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil
Int J Syst Evol Microbiol 73, 005778 (2023); https://doi.org/10.1099/ijsem.0.005778
/content/journal/ijsem/10.1099/ijsem.0.005778
/content/journal/ijsem/10.1099/ijsem.0.005778
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