1887

Abstract

Phytopathogenic bacteria, MAFF 212426, MAFF 212427, MAFF 212428 and MAFF 212429, were isolated from head rot lesions of broccoli ( L. var. Plenck) in Hokkaido, Japan, and subjected to polyphasic taxonomic characterization. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella, rod-shaped and formed pale yellow colonies. Results of 16S rRNA gene sequence analysis showed that they belong to the genus with the highest similarity to ‘’ JJ3 (99.86 %), GSL-010 (99.22 %), WCHPs060044 (99.01 %), NBRC 103040 (98.87 %) and KL28 (98.73 %). The genomic DNA G+C content was 63.4 mol% and the major fatty acids (>5 % of the total fatty acids) were summed feature 3 (C ω7 / C ω6), C, summed feature 8 (C ω7 / C ω6) and C cyclo. Multilocus sequence analysis using the partial , and gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the group, but form a monophyletic, robust clade separated from their closest relatives. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values corroborated their novel species status, with 88.39 % (ANI) and 35.8 % (dDDH) as the highest scores with ‘’ JJ3. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity on broccoli, and whole-cell MALDI-TOF mass spectrometry profiles. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel species, for which the name sp. nov. is proposed. The type strain is MAFF 212427 (=ICMP 23635).

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2020-09-02
2020-09-28
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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 [CrossRef][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 [CrossRef][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 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  6. Peix A, Ramírez-Bahena M-H, Velázquez E. The current status on the taxonomy of Pseudomonas revisited: An update. Infect Genet Evol 2018; 57:106–116 [CrossRef][PubMed]
    [Google Scholar]
  7. Mulet M, Sánchez D, Lalucat J, Lee K, García-Valdés E. Pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol. Int J Syst Evol Microbiol 2015; 65:4013–4018 [CrossRef][PubMed]
    [Google Scholar]
  8. Tohya M, Watanabe S, Teramoto K, Uechi K, Tada T et al. Pseudomonas asiatica sp. nov., isolated from hospitalized patients in Japan and Myanmar. Int J Syst Evol Microbiol 2019; 69:1361–1368 [CrossRef][PubMed]
    [Google Scholar]
  9. Tohya M, Watanabe S, Teramoto K, Shimojima M, Tada T et al. Pseudomonas juntendi sp. nov., isolated from patients in Japan and Myanmar. Int J Syst Evol Microbiol 2019; 69:3377–3384 [CrossRef][PubMed]
    [Google Scholar]
  10. Wright MH, Hanna JG, Anthony Pica II D, Tebo BM. Pseudomonas laurentiana sp. nov., an Mn(III)-oxidizing bacterium isolated from the St. Lawrence Estuary. PC 2018; 8:153–157 [CrossRef]
    [Google Scholar]
  11. Wang M-Q, Wang Z, Yu L-N, Zhang C-S, Bi J et al. Pseudomonas qingdaonensis sp. nov., an aflatoxin-degrading bacterium, isolated from peanut rhizospheric soil. Arch Microbiol 2019; 201:673–678 [CrossRef][PubMed]
    [Google Scholar]
  12. Qin J, Hu Y, Feng Y, Xaioju L, Zong Z. Pseudomonas sichuanensis sp. nov., isolated from hospital sewage. Int J Syst Evol Microbiol 2019; 69:517–522 [CrossRef][PubMed]
    [Google Scholar]
  13. Qin J, Feng Y, Lu X, Zong Z. Pseudomonas huaxiensis sp. nov., isolated from hospital sewage. Int J Syst Evol Microbiol 2019; 69:3281–3286 [CrossRef][PubMed]
    [Google Scholar]
  14. Oh WT, Jun JW, Giri SS, Yun S, Kim HJ et al. Pseudomonas tructae sp. nov., novel species isolated from rainbow trout kidney. Int J Syst Evol Microbiol 2019; 69:3851–3856 [CrossRef][PubMed]
    [Google Scholar]
  15. Pungrasmi W, Lee H-S, Yokota A, Ohta A. Pseudomonas japonica sp. nov., a novel species that assimilates straight chain alkylphenols. J Gen Appl Microbiol 2008; 54:61–69 [CrossRef][PubMed]
    [Google Scholar]
  16. Espinosa-Urgel M, Salido A, Ramos JL. Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J Bacteriol 2000; 182:2363–2369 [CrossRef][PubMed]
    [Google Scholar]
  17. Canaday CH, Mullins CA, Wyatt JE, Coffey DL, Mullins JA et al. Bacterial soft rot of broccoli in Tennessee. Phytopathology 1987; 77:1712
    [Google Scholar]
  18. Wimalajeewa DLS, Hallam ND, Hayward AC, Price TV. The etiology of head rot disease of broccoli. Aust J Agric Res 1987; 38:735–742 [CrossRef]
    [Google Scholar]
  19. Hildebrand PD. Surfactant-like characteristics and identity of bacteria associated with broccoli head rot in Atlantic Canada. Cana J Plant Pathol 1989; 11:205–214 [CrossRef]
    [Google Scholar]
  20. Sakamoto K, Horita H, Maeda M, Tanaka T, Mino Y. Pathogenic bacteria isolated from the head rot of broccoli. Jpn J Phytopathol 1998; 64:374
    [Google Scholar]
  21. Horita H, Sumino A, Komatsu T, Noda T. Occurrence of head rot and soft rot of broccoli in Hokkaido. Jpn J Phytopathol 2000; 66:306
    [Google Scholar]
  22. The Phytopathological Society of Japan Common Names of Plant Diseases in Japan. Tokyo, Japan: The Phytopathological Society of Japan; 2020. https://www.ppsj.org/pdf/mokuroku/mokuroku202001.pdf.
  23. 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 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. 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]
  26. 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 [CrossRef][PubMed]
    [Google Scholar]
  27. 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 [CrossRef][PubMed]
    [Google Scholar]
  28. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 2004; 101:11030–11035 [CrossRef][PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  33. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the AD hoc committee on econciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [CrossRef]
    [Google Scholar]
  34. 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 [CrossRef][PubMed]
    [Google Scholar]
  35. 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 [CrossRef][PubMed]
    [Google Scholar]
  36. Beringer JE. R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 1974; 84:188–198 [CrossRef][PubMed]
    [Google Scholar]
  37. 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]
  38. Lelliott RA, Billing E, Hayward AC. A determinative scheme for the fluorescent plant pathogenic pseudomonads. J Appl Bacteriol 1966; 29:470–489 [CrossRef][PubMed]
    [Google Scholar]
  39. 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 [CrossRef]
    [Google Scholar]
  40. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Technical Note. 1990 pp 1–7
    [Google Scholar]
  41. Sawada H, Horita H, Nishimura F, Mori M. Pseudomonas salomonii, another causal agent of garlic spring rot in Japan. J Gen Plant Pathol 2020; 86:180–192 [CrossRef]
    [Google Scholar]
  42. Schulthess B, Brodner K, Bloemberg GV, Zbinden R, Böttger EC et al. Identification of Gram-positive cocci by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry: comparison of different preparation methods and implementation of a practical algorithm for routine diagnostics. J Clin Microbiol 2013; 51:1834–1840 [CrossRef][PubMed]
    [Google Scholar]
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