sp. nov., a bacterial pathogen isolated from tomato Free

Abstract

An unusual fluorescent pseudomonad was isolated from tomato exhibiting leaf spot symptoms similar to bacterial speck. Strains were fluorescent, oxidase- and arginine-dihydrolase-negative, elicited a hypersensitive reaction on tobacco and produced a soft rot on potato slices. However, the strains produced an unusual yellow, mucoid growth on media containing 5 % sucrose that is not typical of levan. Based on multilocus sequence analysis using 16S rRNA, , , and , these strains formed a distinct phylogenetic group in the genus and were most closely related to within the complex. Whole-genome comparisons, using average nucleotide identity based on blast, of representative strain GEV388 and publicly available genomes representing the genus revealed phylogroup 7 strain UASW0038 and type strain ICMP 2848 as the closest relatives with 86.59 and 86.56 % nucleotide identity, respectively. DNA–DNA hybridization using the genome-to-genome distance calculation method estimated 31.1 % DNA relatedness between GEV388 and ATCC 13223, strongly suggesting the strains are representatives of different species. These results together with Biolog GEN III tests, fatty acid methyl ester profiles and phylogenetic analysis using 16S rRNA and multiple housekeeping gene sequences demonstrated that this group represents a novel species member of the genus The name sp. nov. is proposed with GEV388 (=LMG 30013=ATCC TSD-90) as the type strain.

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2018-01-01
2024-03-28
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References

  1. Palleroni NJ. Introduction to the family pseudomonadaceae. In Stolp H, Trüper HG, Balows A, Starr MP, Schlegel HG. (editors) The Prokaryotes Berlin Heidelberg: Springer; 1981 pp. 655–665 [Crossref]
    [Google Scholar]
  2. Anwar N, Abaydulla G, Zayadan B, Abdurahman M, Hamood B et al. Pseudomonas populi sp. nov., an endophytic bacterium isolated from Populus euphratica . Int J Syst Evol Microbiol 2016; 66:1419–1425 [View Article]
    [Google Scholar]
  3. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas . Front Microbiol 2015; 6: [View Article][PubMed]
    [Google Scholar]
  4. González AJ, Cleenwerck I, de Vos P, Fernández-Sanz AM. Pseudomonas asturiensis sp. nov., isolated from soybean and weeds. Syst Appl Microbiol 2013; 36:320–324 [View Article][PubMed]
    [Google Scholar]
  5. Parte AC. LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  6. Bull CT, Koike ST. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria. Annu Rev Phytopathol 2015; 53:157–180 [View Article][PubMed]
    [Google Scholar]
  7. Cho JC, Tiedje JM. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 2001; 67:3677–3682 [View Article][PubMed]
    [Google Scholar]
  8. Jonasson J, Olofsson M, Monstein HJ. Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 2002; 110:263–272 [View Article][PubMed]
    [Google Scholar]
  9. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A et al. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000; 146:2385–2394 [View Article][PubMed]
    [Google Scholar]
  10. Bartoli C, Berge O, Monteil CL, Guilbaud C, Balestra GM et al. The Pseudomonas viridiflava phylogroups in the P. syringae species complex are characterized by genetic variability and phenotypic plasticity of pathogenicity-related traits. Environ Microbiol 2014; 16:2301–2315 [View Article][PubMed]
    [Google Scholar]
  11. Berge O, Monteil CL, Bartoli C, Chandeysson C, Guilbaud C et al. A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. PLoS One 2014; 9:e105547 [View Article][PubMed]
    [Google Scholar]
  12. Hwang MS, Morgan RL, Sarkar SF, Wang PW, Guttman DS. Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae . Appl Environ Microbiol 2005; 71:5182–5191 [View Article][PubMed]
    [Google Scholar]
  13. Auch AF, von Jan M, Klenk HP, 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]
  14. Konstantinidis KT, Ramette A, Tiedje JM. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 2006; 361:1929–1940 [View Article][PubMed]
    [Google Scholar]
  15. Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. Defining bacterial species in the genomic era: insights from the genus Acinetobacter . BMC Microbiol 2012; 12:302 [View Article][PubMed]
    [Google Scholar]
  16. von Neubeck M, Huptas C, Glück C, Krewinkel M, Stoeckel M et al. Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow's milk. Int J Syst Evol Microbiol 2016; 66:1163–1173 [View Article][PubMed]
    [Google Scholar]
  17. Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M et al. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014; 64:384–391 [View Article][PubMed]
    [Google Scholar]
  18. Lamichhane JR, Messéan A, Morris CE. Insights into epidemiology and control of diseases of annual plants caused by the Pseudomonas syringae species complex. J Gen Plant Pathol 2015; 81:331–350 [View Article]
    [Google Scholar]
  19. Bull CT, Clarke CR, Cai R, Vinatzer BA, Jardini TM et al. Multilocus sequence typing of Pseudomonas syringae sensu lato confirms previously described genomospecies and permits rapid identification of P. syringae pv. coriandricola and P. syringae pv. apii causing bacterial leaf spot on parsley. Phytopathology 2011; 101:847–858 [View Article][PubMed]
    [Google Scholar]
  20. Gardan L, Shafik H, Belouin S, Broch R, Grimont F et al. DNA relatedness among the pathovars of Pseudomonas syringae and description of Pseudomonas tremae sp. nov. and Pseudomonas cannabina sp. nov. (ex Sutic and Dowson 1959). Int J Syst Bacteriol 1999; 49:469–478 [View Article]
    [Google Scholar]
  21. Marcelletti S, Scortichini M. Definition of plant-pathogenic Pseudomonas genomospecies of the Pseudomonas syringae complex through multiple comparative approaches. Phytopathology 2014; 104:1274–1282 [View Article][PubMed]
    [Google Scholar]
  22. Kałużna M, Willems A, Pothier JF, Ruinelli M, Sobiczewski P et al. Pseudomonas cerasi sp. nov. (non Griffin, 1911) isolated from diseased tissue of cherry. Syst Appl Microbiol 2016; 39:370–377 [View Article][PubMed]
    [Google Scholar]
  23. Jones JB. Pseudomonas viridiflava: causal agent of bacterial leaf blight of Tomato. Plant Disease 1984; 68:341–342 [View Article]
    [Google Scholar]
  24. Jones JB. Occurrence of stem necrosis on field-grown tomatoes incited by Pseudomonas corrugata in Florida. Plant Dis 1983; 67:425–426 [View Article]
    [Google Scholar]
  25. Timilsina S, Adkison H, Testen AL, Newberry EA, Miller SA et al. A novel phylogroup of Pseudomonas cichorii identified following an unusual disease outbreak on tomato. Phytopathology 2017PHYTO-05-17-017 in press doi: [View Article][PubMed]
    [Google Scholar]
  26. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301–307[PubMed]
    [Google Scholar]
  27. 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]
  28. González AJ, Rodicio MR, Mendoza MC. Identification of an emergent and atypical Pseudomonas viridiflava lineage causing bacteriosis in plants of agronomic importance in a Spanish region. Appl Environ Microbiol 2003; 69:2936–2941 [View Article][PubMed]
    [Google Scholar]
  29. Laue H, Schenk A, Li H, Lambertsen L, Neu TR et al. Contribution of alginate and levan production to biofilm formation by Pseudomonas syringae . Microbiology 2006; 152:2909–2918 [View Article][PubMed]
    [Google Scholar]
  30. Leriche V, Sibille P, Carpentier B. Use of an enzyme-linked lectinsorbent assay to monitor the shift in polysaccharide composition in bacterial biofilms. Appl Environ Microbiol 2000; 66:1851–1856 [View Article][PubMed]
    [Google Scholar]
  31. Gregersen T. Rapid method for distinction of gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  32. Chen WP, Kuo TT. A simple and rapid method for the preparation of Gram-negative bacterial genomic DNA. Nucleic Acids Res 1993; 21:2260 [View Article][PubMed]
    [Google Scholar]
  33. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC et al. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl Environ Microbiol 1998; 64:795–799[PubMed]
    [Google Scholar]
  34. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. Almeida NF, Yan S, Cai R, Clarke CR, Morris CE et al. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 2010; 100:208–215 [View Article][PubMed]
    [Google Scholar]
  37. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012; 9:772 [View Article][PubMed]
    [Google Scholar]
  38. Deshmukh AM. Handbook of Media, Stains and Reagents in Microbiology Pama Publication; 1997
    [Google Scholar]
  39. Palleroni NJ. Genus I. Pseudomonas Migula 1984. In Brenner DJ, Kreig NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 2 The Proteobacteria, part B, the Gammaproteobacteria New York, USA: Spriner; pp. 323–379
    [Google Scholar]
  40. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 2012; 40:D115–D122 [View Article][PubMed]
    [Google Scholar]
  41. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  42. 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]
  43. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species: culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe Wash DC 2014; 9:111–118
    [Google Scholar]
  44. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
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