1887

Abstract

Two Gram-negative, aerobic, motile bacteria strains were isolated from leaf spot disease of . Strain hsmgli-8 has 99.86 % 16S rRNA gene sequence similarity to LY10J, and the highest 16S rRNA gene sequence similarity to 58 (97.2 %), then JCM 2400 (97.18 %), CFBP 3225, CFBP 6111 and DSM 14939 (all 97.12 %), and less than 97.1 % similarity to other recognized species. In phylogenetic trees based on 16S rRNA gene and multilocus sequence data, the two novel strains form a separate branch, indicating that they do not belong to any group and subgroup, and should belong to a novel species within the genus . This assertion is also supported by the results of genome average nucleotide identity analysis. The major fatty acids are C, C 7 and/or C 6, C 7 and/or C 6. Polar lipids include phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, aminolipid and seven uncharacterized phospholipids. The predominant respiratory quinone is Q-9. The DNA G+C content is 59.45–59.50 mol%. Based on these data, we propose that the two novel strains should be assigned as a novel species within the genus . We propose that the novel strains be named sp. nov. The type strain is hsmgli-8 (=CFCC 15739=LMG 31544).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004800
2021-05-17
2024-04-25
Loading full text...

Full text loading...

References

  1. Migula W. Über ein neues system der bakterien. Arb Bakteriol Inst Karlsruhe 1894; 1:235–238
    [Google Scholar]
  2. Höfte M, De Vos P. Plant pathogenic Pseudomonas species. Plant-Associated Bacteria Dordrecht, the Netherlands: Springer; 2007 pp 507–533
    [Google Scholar]
  3. Gomila M, Busquets A, Mulet M, García-Valdés E, Lalucat J. Clarification of taxonomic status within the Pseudomonas syringae species group based on a phylogenomic analysis. Front Microbiol 2017; 8:2422 [View Article][PubMed]
    [Google Scholar]
  4. Baker GC, Smith JJ, Cowan DA. Review and reanalysis of domain-specific 16S primers. J Microbiol Methods 2003; 55:541–555 [View Article][PubMed]
    [Google Scholar]
  5. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–175
    [Google Scholar]
  6. 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]
    [Google Scholar]
  7. Lalucat J, Mulet M, Gomila M, García-Valdés E. Genomics in bacterial taxonomy: impact on the genus Pseudomonas. Genes 2020; 11:139 [View Article][PubMed]
    [Google Scholar]
  8. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  9. Li Y, Song L-M, Guo M-W, Wang L-F, Liang W-X. Sphingobacterium populi sp. nov., isolated from bark of Populus × euramericana. Int J Syst Evol Microbiol 2016; 66:3456–3462 [View Article][PubMed]
    [Google Scholar]
  10. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article][PubMed]
    [Google Scholar]
  13. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 [View Article][PubMed]
    [Google Scholar]
  14. Lee I, Ouk Kim Y, Park S-C, 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]
  15. 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]
  16. Eichinger V, Nussbaumer T, Platzer A, Jehl M-A, Arnold R et al. Effective DB-updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Nucleic Acids Res 2016; 44:D669–D674 [View Article][PubMed]
    [Google Scholar]
  17. Urban M, Pant R, Raghunath A, Irvine AG, Pedro H et al. The Pathogen-Host interactions database (PHI-base): additions and future developments. Nucleic Acids Res 2015; 43:D645–D655 [View Article][PubMed]
    [Google Scholar]
  18. Chen L, Xiong Z, Sun L, Yang J, Jin Q. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 2012; 40:D641–D645 [View Article][PubMed]
    [Google Scholar]
  19. Jenkins D, Richard MG, Daigger GT. Manual on the causes and control of activated sludge bulking and foaming. Water Research Commission; 1986
  20. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI, Technical notes 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  21. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  22. Du H-J, Zhang Y-Q, Liu H-Y, Su J, Wei Y-Z et al. Allonocardiopsis opalescens gen. nov., sp. nov., a new member of the suborder Streptosporangineae, from the surface-sterilized fruit of a medicinal plant. Int J Syst Evol Microbiol 2013; 63:900–904 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  25. Moore EB, Tindall B, Santos MD, Pieper VP, Ramos DJL et al. Nonmedical: Pseudomonas. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. (editors) The Prokaryotes 6, 3rd ed. New York: Springer; 2006 pp 646–703
    [Google Scholar]
  26. Ramette A, Frapolli M, Fischer-Le Saux M, Gruffaz C, Meyer J-M et al. Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin. Syst Appl Microbiol 2011; 34:180–188 [View Article][PubMed]
    [Google Scholar]
  27. Lang E, Burghartz M, Spring S, Swiderski J, Spröer C. Pseudomonas benzenivorans sp. nov. and Pseudomonas saponiphila sp. nov., represented by xenobiotics degrading type strains. Curr Microbiol 2010; 60:85–91 [View Article][PubMed]
    [Google Scholar]
  28. Madhaiyan M, Poonguzhali S, Saravanan VS, Selvapravin K, Duraipandiyan V et al. Pseudomonas sesami sp. nov., a plant growth-promoting Gammaproteobacteria isolated from the rhizosphere of Sesamum indicum L. Antonie van Leeuwenhoek 2017; 110:843–852 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004800
Loading
/content/journal/ijsem/10.1099/ijsem.0.004800
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