1887

Abstract

A Gram-stain-positive, aerobic bacterium, designated as YPD9-1, was isolated from the gut contents of a spotty belly greenling, , collected near Dokdo island, South Korea. The rod-shaped cells were oxidase-positive, and catalase-negative. The major cellular fatty acids were anteiso-C, iso-C, C, iso-C and iso-C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content was 47.6 mol% and the predominant respiratory quinone was menaquinone MK-7. The 16S rRNA gene sequence of YPD9-1 showed low sequence similarities to species of the genus , Gsoil 1138 (97.21 % of sequence similarity), CJ25 (97.12 %) and JJ-42 (96.89 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that YPD9-1 formed a distinct branch among other species of the genus . The digital DNA–DNA hybridisation, average nucleotide identity, and average amino acid identity values between YPD9-1 and the related species were in the ranges of 15.3–16.2 %, 74.1–78.4 %, and 71.1–71.9 %, respectively, which are below the species cutoff values. On the basis of the results of the polyphasic analysis, we conclude that strain YPD9-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of is YPD9-1 (=KCTC 43424 =LMG 32988).

Funding
This study was supported by the:
  • Ministry of Oceans and Fisheries (Award R2024019)
    • Principle Award Recipient: HeeJeong Kong
  • Ministry of Oceans and Fisheries (Award R2024053)
    • Principle Award Recipient: Dong-GyunKim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006419
2024-06-13
2024-07-15
Loading full text...

Full text loading...

References

  1. 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]
  2. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  3. Lal S, Tabacchioni S. Ecology and biotechnological potential of Paenibacillus polymyxa: a minireview. Indian J Microbiol 2009; 49:2–10 [View Article] [PubMed]
    [Google Scholar]
  4. Baek SH, Yi TH, Lee ST, Im WT. Paenibacillus pocheonensis sp. nov., a facultative anaerobe isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:1163–1167 [View Article] [PubMed]
    [Google Scholar]
  5. Bae J-Y, Kim K-Y, Kim J-H, Lee K, Cho J-C et al. Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland. Int J Syst Evol Microbiol 2010; 60:644–647 [View Article] [PubMed]
    [Google Scholar]
  6. Ravi AV, Musthafa KS, Jegathammbal G, Kathiresan K, Pandian SK. Screening and evaluation of probiotics as a biocontrol agent against pathogenic Vibrios in marine aquaculture. Lett Appl Microbiol 2007; 45:219–223 [View Article] [PubMed]
    [Google Scholar]
  7. He Z, Kisla D, Zhang L, Yuan C, Green-Church KB et al. Isolation and identification of a Paenibacillus polymyxa strain that coproduces a novel lantibiotic and polymyxin. Appl Environ Microbiol 2007; 73:168–178 [View Article] [PubMed]
    [Google Scholar]
  8. Park D-S, Jeong W-J, Lee KH, Oh H-W, Kim B-C et al. Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis. Int J Syst Evol Microbiol 2009; 59:1342–1347 [View Article] [PubMed]
    [Google Scholar]
  9. Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203 [View Article] [PubMed]
    [Google Scholar]
  10. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 2019; 20:129 [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  17. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 20162167–9843 [View Article]
    [Google Scholar]
  18. 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]
  19. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  20. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN:a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  23. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  24. Vater J, Herfort S, Doellinger J, Weydmann M, Borriss R et al. Genome mining of the lipopeptide biosynthesis of Paenibacillus polymyxa E681 in combination with mass spectrometry: discovery of the lipoheptapeptide paenilipoheptin. Chembiochem 2018; 19:744–753 [View Article] [PubMed]
    [Google Scholar]
  25. Zhu S, Hegemann JD, Fage CD, Zimmermann M, Xie X et al. Insights into the unique phosphorylation of the lasso peptide paeninodin. J Biol Chem 2016; 291:13662–13678 [View Article] [PubMed]
    [Google Scholar]
  26. Eltokhy MA, Saad BT, Eltayeb WN, Yahia IS, Aboshanab KM et al. Exploring the nature of the antimicrobial metabolites produced by Paenibacillus ehimensis soil isolate MZ921932 using a metagenomic nanopore sequencing coupled with LC-mass analysis. Antibiotics 2021; 11:12 [View Article] [PubMed]
    [Google Scholar]
  27. Ellatif SA, Abdel Razik ES, Al-Surhanee AA, Al-Sarraj F, Daigham GE et al. Enhanced production, cloning, and expression of a xylanase gene from endophytic fungal strain Trichoderma harzianum kj831197.1: unveiling the in vitro anti-fungal activity against phytopathogenic fungi. J Fungi 2022; 8:447 [View Article] [PubMed]
    [Google Scholar]
  28. Hong TY, Meng M. Biochemical characterization and antifungal activity of an endo-1,3-β-glucanase of Paenibacillus sp. isolated from garden soil. Appl Microbiol Biotechnol 2003; 61:472–478 [View Article] [PubMed]
    [Google Scholar]
  29. Stjohn FJ, Rice JD, Preston JF. Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization. Appl Environ Microbiol 2006; 72:1496–1506 [View Article] [PubMed]
    [Google Scholar]
  30. Logan NA, Berge O, Bishop AH, Busse H-J, De Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article] [PubMed]
    [Google Scholar]
  31. DeVos P, Ludwig W, Schleifer KH, Whitman WB. Family IV. Paenibacillaceae fam. nov. In DeVos P, Garrity GM, Jones D, Krieg NR, Ludwig W. eds Bergey’s Manual of Systematic Bacteriology: Volume 3 the Firmicutes, 2nd edn. vol 3 New York: Springer New York; pp 269–295
    [Google Scholar]
  32. Yan L, Shi J, Cao J, Zhang M, Chen L et al. Paenibacillus sedimenti sp. nov., isolated from freshwater wetland sediment. Curr Microbiol 2023; 73: [View Article]
    [Google Scholar]
  33. Hwang YJ, Ghim SY. Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea. Int J Syst Evol Microbiol 2017; 67:1039–1045 [View Article] [PubMed]
    [Google Scholar]
  34. Cao Y, Chen F, Li Y, Wei S, Wang G. Paenibacillus ferrarius sp. nov., isolated from iron mineral soil. Int J Syst Evol Microbiol 2015; 65:165–170 [View Article] [PubMed]
    [Google Scholar]
  35. Huq MA. Paenibacillus anseongense sp. nov. a silver nanoparticle producing bacterium isolated from rhizospheric soil. Curr Microbiol 2020; 77:2023–2030 [View Article] [PubMed]
    [Google Scholar]
  36. Lee H, Yoshizawa S, Kogure K, Kim HS, Yoon J. Pelagitalea pacifica gen. nov., sp. nov., a new marine bacterium isolated from seawater. Curr Microbiol 2015; 70:514–519 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006419
Loading
/content/journal/ijsem/10.1099/ijsem.0.006419
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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