1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 1

sp. nov., a pathogen causing soft rot of onion in Japan Free

Abstract

Six phytopathogenic bacterial strains, MAFF 301512, MAFF 301513, MAFF 301514, MAFF 301515, MAFF 301516 and MAFF 301517, were isolated from soft rot lesions of onion ( L.) in Japan. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. Analysis of their 16S rRNA gene sequences showed that they belong to the genus , with the highest similarities to DSM 14936 (99.86 %), OLi (99.85 %), DSM 14937 (99.79 %) and KMM 3447 (99.79 %). Their genomic DNA G+C content was 60.9 mol% and the major fatty acids (>5 % of the total fatty acids) present were C, summed feature 3 (C ω7/C ω6), summed feature 8 (C ω7 /C ω6) and C cyclo. Phylogenetic and phylogenomic analyses based on the gene and whole genome sequences, respectively, demonstrated that the strains belong to the subgroup, but form a monophyletic and robust clade, with as their neighbour. Between the strains and , the average nucleotide identity scores were 95.63–95.70 %, whereas the digital DNA–DNA hybridization scores of the strains against their closest relatives, including , were 65.4 % or less, which are lower than the 70 % cut-off for prokaryotic species delineation. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity in onion and cellular fatty acid composition. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel species, proposed to be named sp. nov., with MAFF 301514 (=ICMP 23680) being the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Allium cepa L. , onion , phylogenomic analysis , polyphasic taxonomy , Pseudomonas allii and soft rot disease
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004582
2020-12-03
2024-04-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/1/ijsem004582.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004582&mimeType=html&fmt=ahah

References

  1. Palleroni NJ. Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology 2, 2nd ed. Boston: Springer; 2005 pp 323–379
     [Google Scholar]
  2. Parte AC. LPSN - List of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
     [Google Scholar]
  3. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010; 12:1513–1530 [View Article][PubMed]
     [Google Scholar]
  4. Mulet M, Gomila M, Scotta C, Sánchez D, Lalucat J et al. Concordance between whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry and multilocus sequence analysis approaches in species discrimination within the genus Pseudomonas . Syst Appl Microbiol 2012; 35:455–464 [View Article][PubMed]
     [Google Scholar]
  5. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas . Front Microbiol 2015; 6:214 [View Article][PubMed]
     [Google Scholar]
  6. Peix A, Ramírez-Bahena MH, Velázquez E. The current status on the taxonomy of Pseudomonas revisited: An update. Infect Genet Evol 2018; 57:106–116 [View Article][PubMed]
     [Google Scholar]
  7. Sawada H, Fujikawa T, Nishiwaki Y, Horita H. Pseudomonas kitaguniensis sp. nov., a pathogen causing bacterial rot of Welsh onion in Japan. Int J Syst Evol Microbiol 2020; 70:3018–3026 [View Article][PubMed]
     [Google Scholar]
  8. Ohuchi A, Ohsawa T, Nishimura J. Two pathogenic bacteria, Erwinia rhapontici (Millard 1924) Burkholder 1948 and Pseudomonas marginalis pv. marginalis (Brown 1918) Stevens 1925, causing a soft rot of onion. Jpn J Phytopathol 1983; 49:619–626 [View Article]
     [Google Scholar]
  9. The Phytopathological Society of Japan Common Names of Plant Diseases in Japan Tokyo, Japan: The Phytopathological Society of Japan; 2020
     [Google Scholar]
  10. Sotokawa N, Takikawa Y. Occurrence of bacterial rot of onion bulbs caused by Burkholderia cepacia in Japan. J Gen Plant Pathol 2004; 70:348–352 [View Article]
     [Google Scholar]
  11. Tsuji M, Kadota I. Identification and phylogenetic analysis of Burkholderia cepacia complex bacteria isolated from rot of onion bulbs in Tohoku region of Japan. J Gen Plant Pathol 2020; 86:376–386 [View Article]
     [Google Scholar]
  12. Tsuji M, Nagasaka A, Kadota I. Causal agent of bacterial rot of onion (Allium cepa) bulbs in the Tohoku region of Japan. Jpn J Phytopathol 2019; 85:205–210 [View Article]
     [Google Scholar]
  13. Sawada H, Kunugi Y, Watauchi K, Kudo A, Sato T. Bacterial spot, a new disease of grapevine (Vitis vinifera) caused by Xanthomonas arboricola . Jpn J Phytopathol 2011; 77:7–22 [View Article]
     [Google Scholar]
  14. Yoon SH, Ha SM, 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]
  15. Sawada H, Fujikawa T, Horita H. Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan. Int J Syst Evol Microbiol 2020; 70:5319–5329 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. Parkinson N, Bryant R, Bew J, Elphinstone J. Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus. Plant Pathol 2011; 60:338–344 [View Article]
     [Google Scholar]
  18. Yoon SH, Ha SM, 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]
  19. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1
     [Google Scholar]
  20. 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]
  21. 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]
  22. 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 Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  23. Wu Y-W. ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes. BMC Genomics 2018; 19:921 [View Article][PubMed]
     [Google Scholar]
  24. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Beringer JE. R factor transfer in Rhizobium leguminosarum . J Gen Microbiol 1974; 84:188–198 [View Article][PubMed]
     [Google Scholar]
  27. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  28. Schaad NW, Jones JB, Chun W. Laboratory Guide for Identification of Plant Pathogenic Bacteria, 3rd ed. St. Paul, MN, USA: APS Press; 2001
     [Google Scholar]
  29. Lelliott RA, Billing E, Hayward AC. A determinative scheme for the fluorescent plant pathogenic pseudomonads. J Appl Bacteriol 1966; 29:470–489 [View Article][PubMed]
     [Google Scholar]
  30. Sawada H, Horita H, Misawa T, Takikawa Y. Pseudomonas grimontii, causal agent of turnip bacterial rot disease in Japan. J Gen Plant Pathol 2019; 85:413–423 [View Article]
     [Google Scholar]
  31. Ramírez-Bahena MH, Salazar S, Santín PJ, Sánchez-Rodríguez JA, Fernández-Pascual M et al. Pseudomonas edaphica sp. nov., isolated from rhizospheric soil of Cistus ladanifer L. in Spain. Int J Syst Evol Microbiol 2019; 69:3141–3147 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004582
Loading
Pseudomonas allii sp. nov., a pathogen causing soft rot of onion in Japan
Int J Syst Evol Microbiol 71, 004582 (2020); https://doi.org/10.1099/ijsem.0.004582
/content/journal/ijsem/10.1099/ijsem.0.004582
/content/journal/ijsem/10.1099/ijsem.0.004582
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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