Molecular Mechanisms of Plant and Microbe Coexistence pp 369-382

Part of the Soil Biology book series (SOILBIOL, volume 15) | Cite as

Siderotyping, a Straightforward Tool to Identify Soil and Plant-Related Pseudomonads

  • Jean-Marie Meyer
  • Christelle Gruffaz
  • Marion Fischer-LeSaux

Siderotyping is a method recently developed to characterize bacterial strains by the siderophore(s) they produce when grown under iron deficiency. First applied to fluorescent pseudomonads and their main siderophores, the pyoverdines, the method was primarily used for the recognition of new molecules among pyoverdines. Because of the huge diversity of molecules encountered among this siderophore family, the method became rapidly a useful prerequisite for starting novel structure investigations. Close to 50 structures have been already established and a total of more than 110 structurally different compounds are presently recognized by siderotyping.

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References

  1. Aagot N, Nybroe O, Nielsen P, Johnsen K (2001) An altered Pseudomonas diversity is recovered from soil by using nutrient-poor Pseudomonas-selective soil extract media. Appl Environ Microbiol 67:5233-5239. CrossRefPubMedGoogle Scholar
  2. Achouak W, Sutra L, Heulin T, Meyer JM, Fromin N, Degreave S, Christen R, Gardan L (2000) Description of Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., root-associated bacteria isolated from Arabidopsis thaliana and Brassica napus. Int J Syst Evol Microbiol 50:9-18. PubMedGoogle Scholar
  3. Ait Tayeb L, Ageron E, Grimont F, Grimont PAD (2005) Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 156:763-773. CrossRefPubMedGoogle Scholar
  4. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the pseu-domonads based on 16 S rRNA sequence. Int J Syst Evol Microbiol 50:1563-1589.PubMedGoogle Scholar
  5. Behrendt U, Ulrich A, Schumann P, Meyer JM, Spröer C (2007) Pseudomonas lurida sp. nov., a fluorescent species associated with the phyllosphere of grasses. Int J Syst Evol Microbiol 57:979-985. CrossRefPubMedGoogle Scholar
  6. Breed RS, Murray EGD, Smith NR (1957) Bergey’s manual of determinative bacteriology, 7th edn. The Williams and Wilkins Co. Baltimore, p 103.Google Scholar
  7. Budzikiewicz H (2004) Siderophores of the Pseudomonadaceae sensu stricto (fluorescent and non-fluorescent Pseudomonas spp.) Prog Chem Org Nat Prod 87:81-235.Google Scholar
  8. Cladera AM, Garcia-Valdes E, Lalucat J (2006) Genotype versus phenotype in the circumscription of bacterial species: the case of Pseudomonas stutzeri and Pseudomonas chloritidismutans. Arch Microbiol 184:353-361. CrossRefPubMedGoogle Scholar
  9. Clerc A, Manceau C, Nesme X (1998) Comparison of randomly amplified polymorphic DNA with amplified fragment length polymorphism to assess genetic diversity and genetic relatedness within genospecies III of Pseudomonas syringae. Appl Environ Microbiol 64:1180-1187.PubMedGoogle Scholar
  10. Dabboussi F, Hamzé M, Singer E, Geoffroy V, Meyer JM, Izard D (2002) Pseudomonas mosselii sp. nov., a new species isolated from clinical specimens. Int J Syst Evol Microbiol 52:363-376. PubMedGoogle Scholar
  11. Delorme S, Lemanceau P, Christen R, Corberand T, Meyer JM, Gardan L (2002) Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils. Int J Syst Evol Microbiol 52:513-523.PubMedGoogle Scholar
  12. Elliot RP (1958) Some properties of pyoverdine, the water-soluble pigment of the Pseudomonas. Appl Microbiol 6:241-246. Google Scholar
  13. Espinosa-Urgel M, Salido A, Ramos JL (2002) Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J Bacteriol 182:2363-2369. CrossRefGoogle Scholar
  14. Founoune H, Duponnois R, Meyer JM, Thioulouse J, Masse D, Chotte JL, Neyra M (2002) Interactions between ectomycorrhizal symbiosis and fluorescent pseudomonads on Acacia holosericea: isolation of Mycorrhiza Helper Bacteria (MHB) from a soudano-sahelian soil. FEMS Microbiol Ecol 41:37-46. CrossRefPubMedGoogle Scholar
  15. Frapolli M, Défago G, Moënne-Loccoz Y (2007) Multilocus sequence analysis of biocontrol fluo-rescent Pseudomonas spp. producing the antifungal compound 2,4-diacetylphloroglucinol. Env Microbiol (in press).Google Scholar
  16. Frey P, Frey-Klett P, Garbaye J, Berge O, Heulin T (1997) Metabolic and genotypic fingerprinting of fluorescent pseudomonads associated with the Douglas Fir-Laccaria bicolor myccorrhizo-sphere. Appl Environ Microbiol 63:1852-1860. PubMedGoogle Scholar
  17. Gardan L, Shafik H, Belouin S, Grimont F, Grimont PAD (1999) 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. 49:469-478.PubMedGoogle Scholar
  18. Gardan L, Bella P, Meyer JM, Christen R, Rott P, Achouak W, Samson R (2002) Pseudomonas salomonii sp. nov. pathogenic on garlic, and Pseudomonas palleroniana sp. nov., isolated from rice. Int J Syst Evol Microbiol 52:2065-2074. CrossRefPubMedGoogle Scholar
  19. Grimont PAD, Vancanneyt M, Lefevre M, Vandemeulebroecke K, Vauterin L, Brosch R, Kersters K, Grimont F (1996) Ability of Biolog and Biotype-100 systems to reveal the taxonomic diversity of the pseudomonads. Syst Appl Microbiol 19:510-527. Google Scholar
  20. Guillot E, Leclerc H (1993) Bacterial flora in natural mineral waters: characterization by ribos-omal ribonucleic acid gene restriction patterns. Syst Appl Microbiol 16:483-493 Google Scholar
  21. Haas D, Défago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomon-ads. Nat Rev Microbiol 3:307-319. CrossRefPubMedGoogle Scholar
  22. Hilario E, Buckley TR, Young JM (2004) Improved resolution on the phylogenic relationship by the combined analysis of atpD, carA, recA and 16SrDNA. Antonie van Leeuwenhoek 86:51-64. CrossRefPubMedGoogle Scholar
  23. Hohnadel D, Meyer JM (1988) Specificity of pyoverdine-mediated iron uptake among fluorescent Pseudomonas strains. J Bacteriol 170:4865-4873. PubMedGoogle Scholar
  24. Janssen PH (2006) Identifying the dominant soil bacterial taxa in libraries of 16 s rRNA and 16S rRNA genes. Appl Environ Microbiol 72:1719-1728. CrossRefPubMedGoogle Scholar
  25. Kersters K, Ludwig W, Vancanneyt M, De Vos P, Gillis M, Schleifer KH (1996) Recent changes in the classification of the pseudomonads: an overview. Syst Appl Microbiol 19:465-477.Google Scholar
  26. Kessler B, Palleroni NJ (2000) Taxonomic implications of synthesis of poly-beta-hydroxybutyrate and other poly-beta-hydroxyalkanoates by aerobic pseudomonads Int J Syst Evol Microbiol 50:711-713. PubMedGoogle Scholar
  27. King EO, Ward MK, Raney DF (1954) Two simple media for the demonstration of pyocyanin and fluorescein. J Lab Clin Med 44:301-307. PubMedGoogle Scholar
  28. Kloepper JW, Leong J, Teintze M, Schroth MN (1980a) Enhanced plant growth by siderophores produced by plant growth promoting rhizobacteria. Nature 286:885-886. CrossRefGoogle Scholar
  29. Kloepper JW, Leong J, Teintze M, Schroth MN (1980b) Pseudomonas siderophores: a mechanism explaining disease suppressive soils. Curr Microbiol 4:317-320. CrossRefGoogle Scholar
  30. Koedam N, Wittouck E, Gaballa A, Gillis A, Höfte M, Cornelis P (1994) Detection and differen-ciation of microbial siderophores by isoelectric focusing and chrome azurol S overlay. BioMetals 7:287-291. CrossRefPubMedGoogle Scholar
  31. Kwon SW, Kim JS, Crowley DE, Lim CK (2005) Phylogenetic diversity of fluorescent pseu-domonads in agricultural soils from Korea. Lett Appl Microbiol 41:417-423.CrossRefPubMedGoogle Scholar
  32. Landa BB, Mavrodi OV, Raaijmakers JM, NcSpadden Gardener BB, Thomashow LS, Weller DM (2002) Differential ability of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains to colonize the roots of pea plants. Appl Environ Microbiol 68:3226-3237.CrossRefPubMedGoogle Scholar
  33. Lang E, Griese B, Spröer C, Schumann P, Steffen M, Verbarg S (2007) Characterization of ‘Pseudomonas azelaica’ DSM 9128, leading to emended descriptions of Pseudomonas cit-ronellolis Seubert 1960 (Approved Lists 1980) and Pseudomonas nitroreducens Iizuka and Komagata 1964 (Approved Lists 1980), including Pseudomonas multiresinivorans as its later heterotypic synonym. Int J Syst Evol Microbiol 57:878-882. CrossRefPubMedGoogle Scholar
  34. Lee CH, Lewis TA, Paszczynski A, Crawford RL (1999) Identification of an extracellular catalyst of carbon tetrachloride dehalogenation from Pseudomonas stutzeri strain KC as pyridine-2, 6-bis(thiocarboxyate). Biochem Biophys Res Commun 261:562-566; erratum 265:770.CrossRefPubMedGoogle Scholar
  35. Lelliott RA, Billing E, Hayward AC (1966) A determinative scheme for the fluorescent plant pathogenic pseudomonads. J Appl Bacteriol 29:470-489. PubMedGoogle Scholar
  36. Lemanceau P, Alabouvette C (1993) Biological control of Fusarium diseases by fluorescent Pseudomonas and non-pathogenic Fusarium. Crop Prot 10:279-286. CrossRefGoogle Scholar
  37. Lemanceau P, Corberand T, Gardan L, Latour X, Laguerre G, Boeufgras JM, Alabouvette C (1995) Effect of two plant species, Flax (Linum usitatissinum L.) and tomato (Lycopersicon esculentum Mill.), on the diversity of soilborne populations of fluorescent pseudomonads. Appl Environ Microbiol 61:1004-1012. PubMedGoogle Scholar
  38. Louws FJ, Fulbright DW, Stephens CT, Debruijn FJ (1994) Specific genomic fingerprints of phy-topathogenic Xantomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Appl Environ Microbiol 60:2286-2295. PubMedGoogle Scholar
  39. Meyer J-M (2000) Pyoverdines: pigments, siderophores and potential taxonomic markers of fluo-rescent Pseudomonas species. Arch Microbiol 174:135-142. CrossRefPubMedGoogle Scholar
  40. Meyer J-M, Geoffroy VA, Baida N, Gardan L, Izard D, Lemanceau P et al. (2002) Siderophore typing, a powerful tool for the identification of fluorescent and non-fluorescent Pseudomonas. Appl Environ Microbiol 68:2745-2753. CrossRefPubMedGoogle Scholar
  41. Molina L, Ramos C, Ronchel MC, Molin S, Ramos JL (1998) Construction of an efficient biologi-cally contained Pseudomonas putida strain and its survival in outdoor assays. Appl Environ Microbiol 64:2072-2078. PubMedGoogle Scholar
  42. Moore ERB, Mau M, Arnscheidt A, Böttger EC, Hutson RA, Collins MD, Van De Peer Y, De Watcher R, Timmis KN (1996) The determination and comparison of the 16 S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst Appl Microbiol 19:478-492. Google Scholar
  43. Munsch P, Alatossava T, Meyer JM, Marttinen N, Christen R, Gardan L (2002) Pseudomonas costantinii sp. nov., another causal agent of brown blotch disease, isolated from cultivated mushroom sporophores in Finland. Int J Syst Evol Microbiol 52:1973-1983.CrossRefPubMedGoogle Scholar
  44. Nautiyal CS, Johri JK, Singh HB (2002) Survival of the rhizosphere-competent biocontrol strain Pseudomonas fluorescens NBRI2650 in the soil and phytosphere. Can J Microbiol 48:588-601. CrossRefGoogle Scholar
  45. Palleroni NJ (1984) Pseudomonas. In: Krieg NR (ed.) Bergey’s manual of systematic bacteriol-ogy, vol 1. Williams and Wilkins, Baltimore, pp 141-199. Google Scholar
  46. Palleroni NJ (2005) Genus I. Pseudomonas Migula 1894. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 2, pt B, 2nd edn. Springer, Berlin Heidelberg New York, pp 323-379.Google Scholar
  47. Palleroni NJ, Kunisawa R, Contopoulos R, Doudoroff M (1973) Nucleic acid homologies in the genus Pseudomonas. Int J Syst Bacteriol 23:333-339. CrossRefGoogle Scholar
  48. Risse D, Beiderbeck H, Taraz K, Budzikiewicz H, Gustine D (1998) Corrugatin, a lipopeptide siderophore from Pseudomonas corrugata. Z Naturforsch 53c:295-304. Google Scholar
  49. Ross IL, Alami Y, Harvey PR, Achouak W, Ryder MH (2000) Genetic diversity and biological control activity of novel species of closely related pseudomonads isolated from wheat field soils in South Australia. Appl Environ Microbiol 66:1609-1616. CrossRefPubMedGoogle Scholar
  50. Sikorski J, Lalucat J, Wackernagel W (2005) Genomovars 11 to 18 of Pseudomonas stutzeri, identified among isolates from soil and marine sediment. Int J Syst Evol Microbiol 55:1767-1770. CrossRefPubMedGoogle Scholar
  51. Sneath PHA, Stevens M, Sackin MJ (1981) Numerical taxonomy of Pseudomonas based on pub-lished records of substrate utilization. Antonie van Leeuwenhoek 47:423-448.CrossRefPubMedGoogle Scholar
  52. Stanier RY, Palleroni NJ, Doudoroff M (1966) The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159-271. PubMedGoogle Scholar
  53. Starr MP, Knackmuss HJ, Cosens G (1967) The intracellular blue pigment of Pseudomonas lem-onnieri. Arch Mikrobiol 59:287-294. CrossRefPubMedGoogle Scholar
  54. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464. Google Scholar
  55. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A, Harayama S (2000) Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146:2385-2394. PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Jean-Marie Meyer
    • 1
  • Christelle Gruffaz
    • 2
  • Marion Fischer-LeSaux
    • 3
  1. 1.Département Génétique Moléculaire, Génomique et MicrobiologieUMR 7156 Université Louis-Pasteur/CNRSStrasbourgFrance
  2. 2.Laboratoire de Microbiologie et GénétiqueUniversité Louis PasteurStrasbourg CedexFrance
  3. 3.UMR 077 de Pathologie VégétaleCentre INRA d’AngersBeaucouzéFrance

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