Achouak W, Sutra L, Heulin T, Meyer J-M, Fromin N, Degraeve S, Christen R, Gardan L (2000) Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana. Int J Syst Evol Microbiol 50:9–18
Barelmann I, Fernandez DU, Budzikiewicz H, Meyer JM (2003) The pyoverdine from Pseudomonas chlororaphis D-TR133 showing mutual acceptance with the pyoverdine of Pseudomonas fluorescens CHA0. BioMetals 16:263–270
Bakker PAHM, Pieterse CMJ, van Loon LC (2007) Induced systemic resistance by fluorescent Pseudomonas spp. Phytopathol 97:239–243
Braun V (1997) Avoidance of iron toxicity through regulation of bacterial iron transport. Biol Chem 378:779–786
Briskot G, Taraz K, Budzikiewicz H (1989) Pyoverdine-type siderophores from Pseudomonas aeruginosa. Liebigs Ann Chem 1989:375–384
Brown SD, Utturkar SM, Klingeman DM, Johnson CM, Martin SL, Land ML, Lu T-YS, Schadt CW, Doktycz MJ, Pelletier DA (2012) Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoids. J Bacteriol 194:5991–5993
Budzikiewicz H (1997) Siderophores of fluorescent pseudomonads. Z Naturforsch 52:713–720
Budzikiewicz H (2004) Siderophores of the Pseudomonadaceae sensu stricto (fluorescent and non-fluorescent Pseudomonas spp.). Prog Chem Org Nat Prod 87:81–237
Budzikiewicz H, Schröder H, Taraz K (1992) Zur Biogenese der Pseudomonas-siderophore: der Nachweis analoger Strukturen eines Pyoverdin-Desferribactin-Paares. Z Naturforsch C 47:26–32
Budzikiewicz H, Schäfer M, Fernández DU, Matthijs S, Cornelis P (2007) Characterization of the chromophore of pyoverdins and related siderophores by electrospray tandem mass spectrometry. Biometals 20:135–144
Cheng X, de Bruijn I, van der Voort M, Loper JE, Raaijmakers JM (2013) The Gac regulon of Pseudomonas fluorescens SBW25. Environ Microbiol Rep 5:608–619
Cornelis P, Bodilis J (2009) A survey of TonB-dependent receptors in fluorescent pseudomonads. Environ Microbiol Rep 1:256–262
Cornelis P, Matthijs S (2002) Diversity of siderophore-mediated iron uptake systems in fluorescent pseudomonads: not only pyoverdines. Environ Microbiol 4:787–798
Cox CD, Graham R (1979) Isolation of an iron-binding compound from Pseudomonas aeruginosa. J Bacteriol 137:357–364
De Vleesschauwer D, Höfte M (2009) Rhizobacteria-induced systemic resistance. Plant Innate Immunity 51:223–281
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
Dennis JJ, Zylstra GJ (1998) Plasposons: modular self-cloning minitransposon derivatives for rapid genetic analysis of gram-negative bacterial genomes. Appl Environ Microbiol 64:2710–2715
Duijff BJ, Recorbet G, Bakker PAHM, Loper JE, Lemanceau P (1999) Microbial antagonism at the root level is involved in the suppression of fusarium wilt by the combination of nonpathogenic Fusarium oxysporum Fo47 and Pseudomonas putida WCS358. Phytopathol 89:1073–1079
Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes, characterization of a gene coding for 16S ribosomal RNA. Nucl Acids Res 17:7843–7853
Fernández DU, Fuchs R, Taraz K, Budzikiewicz H, Munsch P, Meyer J-M (2001) Structure of a pyoverdine produced by a Pseudomonas tolaasii-like isolate. Biometals 14:81–84
Fuchs R, Budzikiewicz H (2001) Rearrangement reactions in the electrospray ionization mass spectra of pyoverdins. Int J Mass Spectrom 201(211):603–612
Galet J, Deveau A, Hôtel L, Frey-Klett P, Leblond P, Aigle B (2015) Pseudomonas fluorescens pirates both ferrioxamine and ferri-coelichelin siderophores from Streptomyces ambofaciens. Appl Environ Microbiol 81:3132–3141
Gasser I, Müller H, Berg G (2009) Ecology and characterization of polyhydroxyalkanoate-producing microorganisms on and in plants. FEMS Microbiol Ecol 70:142–150
Hartney SL, Mazurier S, Kidarsa TA, Quecine MC, Lemanceau P, Loper JE (2011) TonB-dependent outer-membrane proteins and siderophore utilization in Pseudomonas fluorescens Pf-5. Biometals 24:193–213
Höfte M, Seong KY, Jurkevitch E, Verstraete W (1991) Pyoverdine production by the plant growth beneficial Pseudomonas strain 7NSK2: ecological significance in soil. Plant Soil 130:249–257
Jurkevitch E, Hadar Y, Chen Y (1992) Differential siderophore utilization and iron uptake by soil and rhizosphere bacteria. Appl Environ Microbiol 58:119–124
Kloepper JW, Leong J, Teintze M, Schroth MN (1980) Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature 286:885–886
Leeman M, den Ouden FM, van Pelt JA, Dirkx FPM, Steijl H, Bakker PAHM, Schippers B (1996) Iron availability affects induction of systemic resistance to Fusarium wilt of radish Pseudomonas fluorescens. Phytopathology 85:149–155
Lemanceau P, Expert D, Gaymard F, Bakker P, Briat JF (2009) Role of iron in plant-microbe interactions. Plant Innate Immunity 51:491–549
Long HH, Schmidt DD, Baldwin IT (2008) Native bacterial endophytes promote host growth in a species-specific manner; phytohormone manipulations do not results in common growth responses. PLoS One 3(7):e2702
Loper JE, Henkels MD (1997) Availability of iron to Pseudomonas fluorescens in rhizosphere and bulk soil evaluated with an ice nucleation reporter gene. Appl Environ Microbiol 63:99–105
Matthijs S, Baysse C, Koedam N, Abbaspour Tehrani K, Verheyden L, Budzikiewicz H, Schäfer M, Hoorelbeke B, Meyer J-M, De Greve H, Cornelis P (2004) The Pseudomonas siderophore quinolobactin is synthesized from xanthurenic acid, an intermediate of the kynurenine pathway. Mol Microbiol 52:371–384
Matthijs S, Abbaspour Tehrani K, Laus G, Jackson RW, Cooper RM, Cornelis P (2007) Thioquinolobactin, a Pseudomonas siderophore with antifungal and anti-Pythium activity. Environ Microbiol 9:425–434
Matthijs S, Budzikiewicz H, Schäfer M, Wathelet B, Cornelis P (2008) Ornicorrugatin, a new siderophore from Pseudomonas fluorescens AF76. Z Naturforsch C 63:8–12
Matthijs S, Laus G, Meyer JM, Abbaspour-Tehrani K, Schäfer M, Budzikiewicz H, Cornelis P (2009) Siderophore-mediated iron acquisition in the entomopathogenic bacterium Pseudomonas entomophila. Biometals 22:951–964
Matthijs S, Coorevits A, Gebrekidan TT, Tricot C, Vander Wauven C, Pirnay J-P, De Vos P, Cornelis P (2013) Evaluation of the oprI and oprL genes as molecular markers for the genus Pseudomonas and their use to study the biodiversity of a small Belgian River. Res Microbiol 164:254–261
Maurhofer M, Hase C, Meuwly P, Métraux JP, Défago G (1994) Induction of systemic resistance of tobacco to tobacco necrosis virus by the root-colonizing Pseudomonas fluorescens strain CHA0: influence of the gacA gene and of pyoverdine production. Phytopathol 84:39–146
Mercado-Blanco J, van der Drift KMGM, Olsson PE, Thomas-Oates JE, van Loon LC, Bakker PAHM (2001) Analysis of the pmsCEAB gene cluster involved in the biosynthesis of salicylic acid and the siderophore pseudomonine in the biocontrol strain Pseudomonas fluorescens WCS374. J Bacteriol 183:1909–1920
Meyer J-M, Abdallah MA (1978) The fluorescent pigment of Pseudomonas fluorescens: biosynthesis, purification and physicochemical properties. J Gen Microbiol 107:319–328
Meyer J-M, Geoffroy VA, Baida N, Gardan L, Izard D, Lemanceau P, Achouak W, Palleroni NJ (2002) Siderophore typing, a powerful tool for the identification of fluorescent and nonfluorescent pseudomonads. Appl Environ Microbiol 68:2745–2753
Meyer J-M, Gruffaz C, Raharinosy V, Bezverbnaya I, Schäfer M, Budzikiewicz H (2008) Siderotyping of fluorescent Pseudomonas: molecular mass determination by mass spectrometry as a powerful pyoverdine siderotyping method. Biometals 21:259–271
Moon CD, Zhang XX, Matthijs S, Schäfer M, Budzikiewicz H, Rainey PB (2008) Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. BMC Microbiol 8:7
Mulet M, Bennasar A, Lalucat J, García-Valdés E (2009) An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cellul Prob 23:140–147
Mulet M, Lalucat J, García-Valdés E (2010) DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 12:1513–1530
Ongena M, Jacques P, Thonart P, Gwose I, Fernandez DU, Schäfer M, Budzikiewicz H (2001) The pyoverdin of Pseudomonas fluorescens BTP2, a novel structural type. Tetrahedron Lett 42:5849–5851
Poole K, Young L, Neshat S (1990) Enterobactin-mediated iron transport in Pseudomonas aeruginosa. J Bacteriol 172:6991–6996
Raaijmakers JM, Van Der Sluis I, Koster M, Bakker PAHM, Weisbeek PJ, Schippers B (1995) Utilization of heterologous siderophores and rhizosphere competence of fluorescent Pseudomonas spp. Can J Microbiol 41:126–135
Rausch C, Weber T, Kohlbacher O, Wohlleben W, Huson DH (2005) Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVM). Nucleic Acids Res 33:5799–5808
Risse D, Beiderbeck H, Taraz K, Budzikiewicz H, Gustine D (1998) Corrugatin, a lipopeptide from Pseudomonas corrugata. Z Naturforsch C 53:295–304
Schlegel K, Fuchs R, Schäfer M, Taraz K, Budzikiewicz H, Geoffroy V, Meyer JM (2001) The pyoverdins of Pseudomonas sp. 96-312 and 96-318. Z Naturforsch C 56:680–686
Schnider-Keel U, Seematter A, Maurhofer M, Blumer C, Duffy B, Gigot-Bonnefoy C, Reimmann C, Notz R, Défago G, Haas D, Keel C (2000) Autoinduction of 2,4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin. J Bacteriol 182:1215–1225
Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56
Singh GM, Fortin PD, Koglin A, Walsh CT (2008) Beta-Hydroxylation of the aspartyl residue in the phytotoxin syringomycin E: characterization of two candidate hydroxylases AspH and SyrP in Pseudomonas syringae. Biochemistry 47:11310–11320
Stachelhaus T, Mootz HD, Marahiel MA (1999) The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem Biol 6:493–505
Sultana R, Fuchs R, Schmickler H, Schlegel K, Budzikiewicz H, Siddiqui BS, Geoffroy V, Meyer JM (2000) A pyoverdine from Pseudomonas sp. CFML 95-275. Z Naturforsch C 55:857–865
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum like-lihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Tappe R, Taraz K, Budzikiewicz H, Meyer JM, Lefèvre JF (1993) Structure elucidation of a pyoverdin produced by Pseudomonas aeruginosa ATCC 27853. J Prakt Chem 335:83–87
Uría-Fernández D, Geoffroy V, Schäfer M, Meyer JM, Budzikiewicz H (2003) Structure revision of pyoverdines produced by plant-growth promoting and plant deleterious Pseudomonas species. Monatsh Chem 134:1421–1431
Van Der Voort M, Meijer HJ, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM (2015) Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp SH-C52 for antimicrobial compounds. Front Microbiol 6:693
Vieira J, Messing J (1991) New pUC-derived cloning vectors with different selectable markers and DNA replication origins. Gene 100:189–194
Voisard C, Bull C, Keel C, Laville J, Maurhofer M, Schnider U, Défago G, Haas D (1994) Biocontrol of root diseases by Pseudomonas fluorescens CHA0: current concepts and experimental approaches. In: O’Gara F, Dowling D, Boesten B (eds) Molecular ecology of rhizosphere microorganisms. VCH, Weinheim, pp 67–89
Yamamoto S, Ksai 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
Ye L, Ballet S, Hildebrand F, Laus G, Guillemyn K, Raes J, Matthijs S, Martins J, Cornelis P (2013) A combinatorial approach to the structure elucidation of a pyoverdine siderophore produced by a Pseudomonas putida isolate and the use of pyoverdine as a taxonomic marker for typing P. putida subspecies. Biometals 26:561–575
Ye L, Matthijs S, Bodilis J, Hildebrand H, Raes J, Cornelis P (2014a) Analysis of the draft genome of Pseudomonas fluorescens ATCC 17400 indicates a capacity to take up iron from a wide range of sources, including different exogenous pyoverdines. Biometals 27:633–644
Ye L, Hildebrand F, Dingemans J, Ballet S, Laus G, Matthijs S, Berendsen R, Cornelis P (2014b) Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens. PLoS One 9(11):e110038
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
