1887

Abstract

Three endophytic bacterial isolates were obtained in Italy from olive knots caused by pv. . Phenotypic tests in combination with 16S rRNA gene sequence analysis indicated a phylogenetic position for these isolates in the genera or , and revealed two other strains with highly similar 16S rRNA gene sequences (>99 %), CECT 5262 and CECT 5264, obtained in Spain from olive knots. Rep-PCR DNA fingerprinting of the five strains from olive knots with BOX, ERIC and REP primers revealed three groups of profiles that were highly similar to each other. Multilocus sequence analysis (MLSA) based on concatenated partial , , and gene sequences indicated that the strains constituted a single novel species in the genus . The strains showed general phenotypic characteristics typical of the genus and whole genome DNA–DNA hybridization data confirmed that they represented a single novel species of the genus . The strains showed DNA G+C contents ranging from 54.7 to 54.9 mol%. They could be discriminated from phylogenetically related species of the genus by their ability to utilize potassium gluconate, -rhamnose and -arabitol, but not glycerol, inositol or -sorbitol. The name sp. nov. (type strain DAPP-PG 531 = LMG 25322 = DSM 23398) is proposed for this novel taxon.

Funding
This study was supported by the:
  • Fondazione Cassa di Risparmio di Perugia
  • Federal Science Policy Office, Belgium
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2011-11-01
2024-03-28
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References

  1. Brady C. L., Cleenwerck I., Venter S., Vancanneyt M., Swings J., Coutinho T. A. 2008; Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA). Syst Appl Microbiol 31:447–460 [View Article][PubMed]
    [Google Scholar]
  2. Brady C. L., Venter S. N., Cleenwerck I., Engelbeen K., Vancanneyt M., Swings J., Coutinho T. A. 2009; Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov.. Int J Syst Evol Microbiol 59:2339–2345 [View Article][PubMed]
    [Google Scholar]
  3. Brady C. L., Cleenwerck I., Venter S. N., Engelbeen K., De Vos P., Coutinho T. A. 2010a; Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.. Int J Syst Evol Microbiol 60:2430–2440 [CrossRef]
    [Google Scholar]
  4. Brady C. L., Venter S. N., Cleenwerck I., Vandemeulebroecke K., De Vos P., Coutinho T. A. 2010b; Transfer of Pantoea citrea, Pantoea punctata and Pantoea terrea to the genus Tatumella emend. as Tatumella citrea comb. nov., Tatumella punctata comb. nov. and Tatumella terrea comb. nov. and description of Tatumella morbirosei sp. nov. Int J Syst Evol Microbiol 60:484–494 [CrossRef]
    [Google Scholar]
  5. Brady C. L., Goszczynska T., Venter S. N., Cleenwerck I., De Vos P., Gitaitis R. D., Coutinho T. A. 2010c; Pantoea allii sp. nov., a novel species isolated from onion and onion seed. Int J Syst Evol Microbiol 60:932–937 [CrossRef]
    [Google Scholar]
  6. Cleenwerck I., Vandemeulebroecke K., Janssens D., Swings J. 2002; Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. . Int J Syst Evol Microbiol 52:1551–1558 [View Article][PubMed]
    [Google Scholar]
  7. Coenye T., Falsen E., Vancanneyt M., Hoste B., Govan J. R. W., Kersters K., Vandamme P. 1999; Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. . Int J Syst Bacteriol 49:405–413 [View Article][PubMed]
    [Google Scholar]
  8. De Vuyst L., Camu N., De Winter T., Vandemeulebroecke K., Van de Perre V., Vancanneyt M., De Vos P., Cleenwerck I. 2008; Validation of the (GTG)(5)-rep-PCR fingerprinting technique for rapid classification and identification of acetic acid bacteria, with a focus on isolates from Ghanaian fermented cocoa beans. Int J Food Microbiol 125:79–90 [View Article][PubMed]
    [Google Scholar]
  9. Dice L. 1945; Measurement of the amount of ecological association between species. Ecology 26:297–302 [View Article]
    [Google Scholar]
  10. Dye D. W. 1968; A taxonomic study of the genus Erwinia. I. The “amylovora” group. N Z J Sci 11:590–607
    [Google Scholar]
  11. Ezaki T., Hashimoto Y., Yabuuchi E. 1989; Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229 [View Article]
    [Google Scholar]
  12. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  13. Gardan L., Christen R., Achouak W., Prior P. 2004; Erwinia papayae sp. nov., a pathogen of papaya (Carica papaya). Int J Syst Evol Microbiol 54:107–113 [View Article][PubMed]
    [Google Scholar]
  14. Geider K., Auling G., Du Z., Jakovljevic V., Jock S., Völksch B. 2006; Erwinia tasmaniensis sp. nov., a non-phytopathogenic bacterium from apple and pear trees. Int J Syst Evol Microbiol 56:2937–2943 [View Article][PubMed]
    [Google Scholar]
  15. Gevers D., Huys G., Swings J. 2001; Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205:31–36 [View Article][PubMed]
    [Google Scholar]
  16. Goris J., Suzuki K., De Vos P., Nakase T., Kersters K. 1998; Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44:1148–1153 [View Article]
    [Google Scholar]
  17. Goto M. 1976; Erwinia mallotovora sp. nov., the causal organism of bacterial leaf spot of Mallotus japonicus . Int J Syst Bacteriol 26:467–473 [View Article]
    [Google Scholar]
  18. Hao M. V., Brenner D. J., Steigerwalt A. G., Kosako Y., Komagata K. 1990; Erwinia persicinus, a new species isolated from plants. Int J Syst Bacteriol 40:379–383 [View Article][PubMed]
    [Google Scholar]
  19. Harada H., Oyaizu H., Kosako Y., Ishikawa H. 1997; Erwinia aphidicola, a new species isolated from pea aphid, Acyrthosiphon pisum . J Gen Appl Microbiol 43:349–354 [View Article][PubMed]
    [Google Scholar]
  20. Hauben L., Moore E. R. B., Vauterin L., Steenackers M., Mergaert J., Verdonck L., Swings J. 1998; Phylogenetic position of phytopathogens within the Enterobacteriaceae . Syst Appl Microbiol 21:384–397[PubMed] [CrossRef]
    [Google Scholar]
  21. Higgins C. F., Ames G. F. L., Barnes W. M., Clement J. M., Hofnung M. 1982; A novel intercistronic regulatory element of prokaryotic operons. Nature 298:760–762 [View Article][PubMed]
    [Google Scholar]
  22. Hosni T. 2010; Interaction between Pseudomonas savastanoi pv. savastanoi, the causal agent of olive knot, and the endophytic bacterial species associated with the knot . PhD thesis, University of Perugia, Italy, pp. 108
    [Google Scholar]
  23. Hulton C. S. J., Higgins C. F., Sharp P. M. 1991; ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 5:825–834 [View Article][PubMed]
    [Google Scholar]
  24. Kim W.-S., Gardan L., Rhim S.-L., Geider K. 1999; Erwinia pyrifoliae sp. nov., a novel pathogen that affects Asian pear trees (Pyrus pyrifolia Nakai). Int J Syst Bacteriol 49:899–906 [View Article][PubMed]
    [Google Scholar]
  25. López M. M., Roselló M., Llop P., Ferrer S., Christen R., Gardan L. 2011; Erwinia piriflorinigrans sp. nov., a novel pathogen that causes necrosis of pear blossoms. Int J Syst Evol Microbiol 61:561–567 [View Article][PubMed]
    [Google Scholar]
  26. Marchi G., Sisto A., Cimmino A., Andolfi A., Cipriani M. G., Evidente A., Surico G. 2006; Interaction between Pseudomonas savastanoi pv. savastanoi and Pantoea agglomerans in olive knots. Plant Pathol 55:614–624 [View Article]
    [Google Scholar]
  27. Mergaert J., Hauben L., Cnockaert M. C., Swings J. 1999; Reclassification of non-pigmented Erwinia herbicola strains from trees as Erwinia billingiae sp. nov.. Int J Syst Bacteriol 49:377–383 [View Article][PubMed]
    [Google Scholar]
  28. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [View Article]
    [Google Scholar]
  29. Neto J. R., Robbs C. F., Yamashiro T. 1987; A bacterial disease of guava (Psidium guajava) caused by Erwinia psidii sp. nov.. Fitopatol Bras 12:345–350
    [Google Scholar]
  30. Niemann S., Pühler A., Tichy H.-V., Simon R., Selbitschka W. 1997; Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 82:477–484 [View Article][PubMed]
    [Google Scholar]
  31. Ouzari H., Khsairi A., Raddadi N., Jaoua L., Hassen A., Zarrouk M., Daffonchio D., Boudabous A. 2008; Diversity of auxin-producing bacteria associated to Pseudomonas savastanoi-induced olive knots. J Basic Microbiol 48:370–377 [View Article][PubMed]
    [Google Scholar]
  32. Quesada J. M., García A., Bertolini E., López M. M., Penyalver R. 2007; Recovery of Pseudomonas savastanoi pv. savastanoi from symptomless shoots of naturally infected olive trees. Int Microbiol 10:77–84[PubMed]
    [Google Scholar]
  33. Rademaker J. L. W., de Bruijn F. J. 1997; Characterization and classification of microbes by rep-PCR genomic fingerprinting and computer-assisted pattern analysis. In Protocols, Application and Overviews pp. 151–171 Edited by Caetano-Anolles G., Gressfoff P. New York: J. Wiley and Sons;
    [Google Scholar]
  34. Roberts P. 1974; Erwinia rhapontici (Millard) Burkholder associated with pink grain of wheat. J Appl Bacteriol 37:353–358[PubMed] [CrossRef]
    [Google Scholar]
  35. Rojas A. M., de los Rios J. E., Fischer-Le Saux M., Jimenez P., Reche P., Bonneau S., Sutra L., Mathieu-Daudé F., McClelland M. 2004; Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots. Int J Syst Evol Microbiol 54:2217–2222 [View Article][PubMed]
    [Google Scholar]
  36. Schaad N. W., Jones J. B., Chun W. 2001; Initial identification of common genera. In Laboratory Guide for Identification of Plant Pathogenic Bacteria, 3rd edn. pp. 84–120 Edited by Schaad N. W., Jones J. B., Chun W. St Paul, MN: APS;
    [Google Scholar]
  37. Sisto A., Cipriani M. G., Morea M. 2004; Knot formation caused by Pseudomonas savastanoi subsp. savastanoi on olive plants is hrp-dependent. Phytopathology 94:484–489 [View Article][PubMed]
    [Google Scholar]
  38. Stackebrandt E., Goebel B. M. 1994; A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [View Article]
    [Google Scholar]
  39. Suslow T. V., Schroth M. N., Isaka M. 1982; Application of a rapid method for Gram differentiation of plant pathogenic and saprophytic bacteria without staining. Phytopathology 72:917–918 [View Article]
    [Google Scholar]
  40. Versalovic J., Koeuth T., Lupski J. R. 1991; Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 19:6823–6831 [View Article][PubMed]
    [Google Scholar]
  41. Versalovic J., Schneider M., de Bruijn F. P., Lupski J. R. 1994; Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5:25–40
    [Google Scholar]
  42. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al. 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [View Article]
    [Google Scholar]
  43. Wilson K. 1987; Preparation of genomic DNA from bacteria. In Current Protocols in Molecular Biology pp. 2.4.1–2.4.5 Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. New York: Green Publishing and Wiley-Interscience;
    [Google Scholar]
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