1887

Abstract

A novel bacterial strain, S40, with strong antifungal activity was isolated from the rhizosphere of green potato collected from Zealand, Denmark. Polyphasic analysis with a combined phenotypic, phylogenetic and genomic approach was used to characterize S40. Phylogenetic analysis based on the 16S rRNA gene and MLSA (concatenated , , and sequences) showed that strain S40 was affiliated with the genus and with PRI-2C as the closest related strain [average nucleotide identity (ANI), 99.26 %; DNA–DNA hybridization (dDDH), 99.20%]. However, whole genome sequence analyses revealed that S40 and PRI-2C genomes displayed lower similarities when compared to all other strains (ANI ≤94.34 %; dDDH ≤57.6 % relatedness). The DNA G+C content of strain S40 was determined to be 55.9 mol%. Cells of the strain were Gram-negative, rod-shaped, facultative anaerobic and displayed growth at 10–37 °C (optimum, 25–30 °C) and at pH 6–9 (optimum, pH 6–7). Major fatty acids were C (27.9 %), summed feature (C 6/C ω7; 18.0 %) and C cyclo (15.1 %). The respiratory quinone was determined to be Q8 (94 %) and MK8 (95 %) and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The results of phenotypic, phylogenetic and genomic analyses support the hypothesis that strain S40 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S40 (=LMG 31467=NCIMB 15235). In addition, we propose that PRI-2C is reclassified and transferred to the species as PRI-2C.

Funding
This study was supported by the:
  • Not Applicable , Innovationsfonden , (Award 5158-00001A)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004270
2020-06-17
2020-11-25
Loading full text...

Full text loading...

References

  1. Grimont PA, Grimont F, De Rosnay HL. Taxonomy of the genus Serratia . J Gen Microbiol 1977; 98:39–66 [CrossRef][PubMed]
    [Google Scholar]
  2. Kämpfer P, Glaeser SP. Serratia aquatilis sp. nov., isolated from drinking water systems. Int J Syst Evol Microbiol 2016; 66:407–413 [CrossRef][PubMed]
    [Google Scholar]
  3. Grimont PAD, Grimont F, Starr MP. Serratia species isolated from plants. Curr Microbiol 1981; 5:317–322 [CrossRef]
    [Google Scholar]
  4. Matilla MA, Drew A, Udaondo Z, Krell T, Salmond GPC. Genome Sequence of Serratia plymuthica A153, a Model Rhizobacterium for the Investigation of the Synthesis and Regulation of Haterumalides, Zeamine, and Andrimid. Genome Announc 2016; 4:pii: e00373-16 [CrossRef]
    [Google Scholar]
  5. Matilla MA, Udaondo Z, Salmond GPC. Genome Sequence of the Oocydin A-Producing Rhizobacterium Serratia plymuthica 4Rx5. Microbiol Resour Announc 2018; 7: [CrossRef][PubMed]
    [Google Scholar]
  6. Proença DN, Schwab S, Vidal MS, Baldani JI, Xavier GR et al. The nematicide Serratia plymuthica M24T3 colonizes Arabidopsis thaliana, stimulates plant growth, and presents plant beneficial potential. Braz J Microbiol 2019; 50:777–789 [CrossRef][PubMed]
    [Google Scholar]
  7. Zhang C-W, Zhang J, Zhao J-J, Zhao X, Zhao D-F et al. Serratia oryzae sp. nov., isolated from rice stems. Int J Syst Evol Microbiol 2017; 67:2928–2933 [CrossRef][PubMed]
    [Google Scholar]
  8. Clements T, Ndlovu T, Khan W. Broad-spectrum antimicrobial activity of secondary metabolites produced by Serratia marcescens strains. Microbiol Res 2019; 229:126329 [CrossRef][PubMed]
    [Google Scholar]
  9. Gerber NN. Prodigiosin-like pigments. CRC Crit Rev Microbiol 1975; 3:469–485 [CrossRef][PubMed]
    [Google Scholar]
  10. Ravindran A, Sunderrajan S, Pennathur G. Phylogenetic studies on the prodigiosin biosynthetic operon. Curr Microbiol 2019; 76:597–606 [CrossRef][PubMed]
    [Google Scholar]
  11. Domik D, Magnus N, Piechulla B. Analysis of a new cluster of genes involved in the synthesis of the unique volatile organic compound sodorifen of Serratia plymuthica 4Rx13. FEMS Microbiol Lett 2016; 363:fnw139 [CrossRef][PubMed]
    [Google Scholar]
  12. Weise T, Thürmer A, Brady S, Kai M, Daniel R et al. VOC emission of various Serratia species and isolates and genome analysis of Serratia plymuthica 4Rx13. FEMS Microbiol Lett 2014; 352:45–53 [CrossRef][PubMed]
    [Google Scholar]
  13. Su C, Xiang Z, Liu Y, Zhao X, Sun Y et al. Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25Tthat simultaneously produces prodigiosin and serrawettin W2. BMC Genomics 2016; 17:865 [CrossRef][PubMed]
    [Google Scholar]
  14. Sunaga S, Li H, Sato Y, Nakagawa Y, Matsuyama T. Identification and characterization of the pswP gene required for the parallel production of prodigiosin and serrawettin W1 in Serratia marcescens . Microbiol Immunol 2004; 48:723–728 [CrossRef][PubMed]
    [Google Scholar]
  15. Masschelein J, Mattheus W, Gao L-J, Moons P, Van Houdt R et al. A PKS/NRPS/FAS hybrid gene cluster from Serratia plymuthica RVH1 encoding the biosynthesis of three broad spectrum, zeamine-related antibiotics. PLoS One 2013; 8:e54143 [CrossRef][PubMed]
    [Google Scholar]
  16. Kalbe C, Marten P, Berg G. Strains of the genus Serratia as beneficial rhizobacteria of oilseed rape with antifungal properties. Microbiol Res 1996; 151:433–439 [CrossRef][PubMed]
    [Google Scholar]
  17. Liu X, Yu X, Yang Y, Heeb S, Gao S et al. Functional identification of the prnABCD operon and its regulation in Serratia plymuthica . Appl Microbiol Biotechnol 2018; 102:3711–3721 [CrossRef][PubMed]
    [Google Scholar]
  18. Garbeva P, van Elsas JD, de Boer W. Draft genome sequence of the antagonistic rhizosphere bacterium Serratia plymuthica strain PRI-2C. J Bacteriol 2012; 194:4119–4120 [CrossRef][PubMed]
    [Google Scholar]
  19. Dichmann SI, Park B, Pathiraja D, Choi I-G, Stougaard P et al. Draft Genome Sequence of a Novel Serratia sp. Strain with Antifungal Activity. Microbiol Resour Announc 2018; 7: [CrossRef][PubMed]
    [Google Scholar]
  20. Michelsen CF, Stougaard P. A novel antifungal Pseudomonas fluorescens isolated from potato soils in Greenland. Curr Microbiol 2011; 62:1185–1192 [CrossRef][PubMed]
    [Google Scholar]
  21. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 [CrossRef]
    [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. 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 [CrossRef][PubMed]
    [Google Scholar]
  26. Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. Isme J 2017; 11:2864–2868 [CrossRef][PubMed]
    [Google Scholar]
  27. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [CrossRef][PubMed]
    [Google Scholar]
  28. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [CrossRef][PubMed]
    [Google Scholar]
  31. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [CrossRef][PubMed]
    [Google Scholar]
  32. Suslow TV, Schroth MN, Isaka M. Application of a rapid method for Gram differentiation of plant pathogenic and saprophytic bacteria without staining. Phytopathology 1982; 72:917–918 [CrossRef]
    [Google Scholar]
  33. Miller LT. A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J. Clin. Microbiol 1982; 16:584–586
    [Google Scholar]
  34. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [CrossRef]
    [Google Scholar]
  35. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [CrossRef]
    [Google Scholar]
  36. Tindall BJ, Sikorski J, Smibert RM, Kreig NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd. Washington, DC., USA: ASM Press; 2007 pp 330–393
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004270
Loading
/content/journal/ijsem/10.1099/ijsem.0.004270
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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