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

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Molecular Mechanisms of Plant and Microbe Coexistence

Part of the book series: Soil Biology ((SOILBIOL,volume 15))

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

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Budzikiewicz H (2004) Siderophores of the Pseudomonadaceae sensu stricto (fluorescent and non-fluorescent Pseudomonas spp.) Prog Chem Org Nat Prod 87:81-235.

    CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Elliot RP (1958) Some properties of pyoverdine, the water-soluble pigment of the Pseudomonas. Appl Microbiol 6:241-246.

    Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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 

  • Haas D, Défago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomon-ads. Nat Rev Microbiol 3:307-319.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Hohnadel D, Meyer JM (1988) Specificity of pyoverdine-mediated iron uptake among fluorescent Pseudomonas strains. J Bacteriol 170:4865-4873.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • King EO, Ward MK, Raney DF (1954) Two simple media for the demonstration of pyocyanin and fluorescein. J Lab Clin Med 44:301-307.

    PubMed  CAS  Google Scholar 

  • Kloepper JW, Leong J, Teintze M, Schroth MN (1980a) Enhanced plant growth by siderophores produced by plant growth promoting rhizobacteria. Nature 286:885-886.

    Article  CAS  Google Scholar 

  • Kloepper JW, Leong J, Teintze M, Schroth MN (1980b) Pseudomonas siderophores: a mechanism explaining disease suppressive soils. Curr Microbiol 4:317-320.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Lelliott RA, Billing E, Hayward AC (1966) A determinative scheme for the fluorescent plant pathogenic pseudomonads. J Appl Bacteriol 29:470-489.

    PubMed  CAS  Google Scholar 

  • Lemanceau P, Alabouvette C (1993) Biological control of Fusarium diseases by fluorescent Pseudomonas and non-pathogenic Fusarium. Crop Prot 10:279-286.

    Article  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Meyer J-M (2000) Pyoverdines: pigments, siderophores and potential taxonomic markers of fluo-rescent Pseudomonas species. Arch Microbiol 174:135-142.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • Palleroni NJ, Kunisawa R, Contopoulos R, Doudoroff M (1973) Nucleic acid homologies in the genus Pseudomonas. Int J Syst Bacteriol 23:333-339.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Stanier RY, Palleroni NJ, Doudoroff M (1966) The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159-271.

    PubMed  CAS  Google Scholar 

  • Starr MP, Knackmuss HJ, Cosens G (1967) The intracellular blue pigment of Pseudomonas lem-onnieri. Arch Mikrobiol 59:287-294.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

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Meyer, JM., Gruffaz, C., Fischer-LeSaux, M. (2008). Siderotyping, a Straightforward Tool to Identify Soil and Plant-Related Pseudomonads. In: Nautiyal, C.S., Dion, P. (eds) Molecular Mechanisms of Plant and Microbe Coexistence. Soil Biology, vol 15. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75575-3_15

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