Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae

Standards in Genomic Sciences

Volumn 10, Issue FEBRUARY2015, 2015, Pages

  Martínez García, Pedro Manuel ^a,d   Ruano Rosa, David ^b   Schilirò, Elisabetta ^b   Prieto, Pilar ^c   Ramos, Cayo ^a   Rodríguez Palenzuela, Pablo ^d   Mercado Blanco, Jesús ^b  

^a INSTITUTO DE HORTOFRUTICULTURA SUBTROPICAL Y MEDITERRÁNEA LA MAYORA   (Spain)

^b Departmentos de Potección de Cultivos y Campus ^*  (Spain)

^c INSTITUTO DE AGRICULTURA SOSTENIBLE   (Spain)

^d ETSI MontesTechnical University of Madrid   (Spain)

Author keywords

Biocontrol; Detoxification systems; Endophyte; Olive; Pseudomonas fluorescens; Siderophores; Verticillium wilt

Indexed keywords

ESSENTIAL OIL; GENOMIC DNA; SIDEROPHORE;

AGROBACTERIUM; ARTICLE; BACTERIAL SECRETION SYSTEM; BIOLOGICAL CONTROL AGENT; DETOXIFICATION; DNA ISOLATION; ENDOPHYTE; FUNCTIONAL GENOMICS; GENE SEQUENCE; GENETIC ANALYSIS; NONHUMAN; OLIVE TREE; PSEUDOMONAS FLUORESCENS; VERTICILLIUM DAHLIAE;

EID: 84928116754     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.1186/1944-3277-10-10     Document Type: Article

References (50)

1. Mercado-Blanco J, Rodríguez-Jurado D, Hervas A, Jiménez-Díaz RM. Suppression of Verticillium wilt in olive planting stocks by root-associated fluorescent Pseudomonas spp. Biol Control. 2004; 30:474-86
2. Pegg GF, Brady BL. Verticillium wilts. Wallingford: CAB International. 2002
3. Prieto P, Navarro-Raya C, Valverde-Corredor A, Amyotte SG, Dobinson KF, Mercado-Blanco J. Colonization process of olive tissues by Verticillium dahliae and its in planta interaction with the biocontrol root endophyte Pseudomonas fluorescens PICF7. Microb Biotechnol. 2009; 2:499-511
4. López-Escudero FJ, Mercado-Blanco J. Verticillium wilt of olive: a case study to implement an integrated strategy to control a soil-borne pathogen. Plant Soil. 2011; 344:1-50
5. Prieto P, Mercado-Blanco J. Endophytic colonization of olive roots by the biocontrol strain Pseudomonas fluorescens PICF7. FEMS Microbiol Ecol. 2008; 64:297-306
6. Prieto P, Schilirò E, Maldonado-González M, Valderrama R, Barroso-Albarracín JB, Mercado-Blanco J. Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity. Microb Ecol. 2011; 62:435-45
7. Schilirò E, Ferrara M, Nigro F, Mercado-Blanco J. Genetic responses induced in olive roots upon colonization by the biocontrol endophytic bacterium Pseudomonas fluorescens PICF7. PLoS ONE. 2012; 7:e48646
8. Gómez-Lama Cabanás C, Schilirò E, Valverde-Corredor A, Mercado-Blanco J. The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots. Front Microbiol. 2014; 5:427
9. Maldonado-González MM, Prieto P, Ramos C, Mercado-Blanco J. From the root to the stem, interaction between the biocontrol root endophyte Pseudomonas fluorescens PICF7 and the pathogen Pseudomonas savastanoi NCPPB 3335 in olive knots. Microb Biotechnol. 2013; 6:275-87
10. Ramos C, Matas IM, Bardaji L, Aragón IM, Murillo J. Pseudomonas savastanoi pv. savastanoi: some like it knot. Mol Plant Pathol. 2012; 13:998-1009
11. King EO, Ward M, Raney D. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med. 1954; 44:301-7
12. Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic. J Bacteriol. 1951; 62:293-300
13. Meyer JM, Abdallah MA. The fluorescent pigment of Pseudomonas fluorescens: biosynthesis, purification and physicochemical properties. J Gen Microbiol. 1978; 107:319-28
14. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, Vos PD, dePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, et al: The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-7
15. Woese CR. Towards a natural system of organisms: Proposal for the domains Archea, Bacteria and Eucarya. Proc Natl Acad Sci USA. 1990; 87:4576-9
16. Garrity GM, Bell JA, Phylum LT, XIV. phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriol-ogy, Volume 2. 2nd ed. Springer, New York: Part B; 2005: p. 1
17. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106. Int J Syst Evol Microbiol. 2005; 55:2235-8. http://dx.doi.org/10.1099/ijs.0.64108-0
18. Garrity GM, Bell JA, Class LT, III. class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's Manual of Systematic Bacteriology, Volume 2. 2nd ed. Springer, New York: Part B; 2005: p. 1
19. Skerman VBD, McGowan V, Sneath PHA. Approved lists of bacterial names. Int J Syst Bacteriol. 1980; 30:225-420. http://dx.doi.org/10.1099/00207713-30-1-225
20. Orla-Jensen S. The main lines of the natural bacterial system. J Bacteriol. 1921; 6:263-73
21. Garrity G, Bell J, Lilburn T. In: Garrity G, Brenner D, Krieg N, Staley J, editors. Bergey’s Manual of Systematic Bacteriology, Volume 2, Part B. 2nd ed. New York: Springer; 2005: p. 323
22. Winslow CEA, Broadhurst J, Buchanan RE, Krumwiede C, Rogers LA, Smith GH. The fami-lies and genera of the bacteria. Preliminary report of the committee of the society of American Bacteriologists on characterization and classification of bacterial types. J Bacteriol. 1917; 2:505-66
23. Migula W. Über ein neues System der Bakterien. Arb Bakteriol Inst Karlsruhe. 1894; 1:235-8
24. Doudoroff M, Palleroni NJ. Genus Migula 1894, 237; Nom. cons. Opin. 5, Jud. Comm. 1952, 121. In: Buchanan RE, Gibbons NE, editors. Bergey's Manual of Determinative Bacteriology. 8th ed. Baltimore: The Williams and Wilkins Co.; 1974: p. 217-43
25. Commission J. Opinion 5: Conservation of the generic name Migula 1894 and designation of aeruginosa (Schroeter) Migula 1900 as type species. Int Bull Bacteriol Nomencl Taxon. 1952; 2:121-2
26. Palleroni NJ. Pseudomonadaceae. Bergey's Manual of Systematic Bacteriology. In: Krieg NR, Holt JG, editors. Baltimore: The Williams and Wilkins Co; 1984: p. 141-99
27. Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H. Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Intl J Sys Evol Microbiol. 2000; 50:1563-89
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25:25-9
29. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992; 8:275-82
30. Felsenstein J. Confidence limits on phylogenies -an approach using the bootstrap. Evolution. 1985; 39:783-91
31. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008; 36:D475-9
32. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010; 20:265-72
33. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008; 24:713
34. SOAP. denovo v.1.05. http://soap.genomics.org.cn/soapdenovo.html
35. Signal P. http://www.cbs.dtu.dk/services/SignalP/
36. Emanuelsson O, Brunak S, von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007; 2:953-71
37. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001; 305:567-80
38. TMHMM. Transmembrane domain prediction. www.cbs.dtu.dk/services/TMHMM/
39. Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997; 278:631-7
40. Clusters of Ortholog ous Groups. http://www.ncbi.nlm.nih.gov/COG
41. Hood RD, Singh P, Hsu F, Güvener T, Carl MA, Trinidad RR, Silverman JM, Ohlson BB, Hicks KG, Plemel RL, Li M, Schwarz S, Wang WY, Merz AJ, Goodlett DR, Mougous JD: A type VI secretion system of Pseudomonas aeruginosa targets a toxin to bacteria. Cell Host Microbe. 2010; 7:25-37
42. Matthysse AG, Jaeckel P, Jeter C. attG and attC mutations of Agrobacterium tumefaciens are dominant negative mutations that block attachment and virulence. Can J Microbiol. 2008; 54:241-7
43. Colburn-Clifford JM, Scherf JM, Allen C. Ralstonia solanacearum Dps contributes to oxidative stress tolerance and to colonization of and virulence on tomato plants. Appl Environ Microbiol. 2010; 76:7392-9
44. Guo M, Block A, Bryan CD, Becker DF, Alfano JR. Pseudomonas syringae Catalases Are Collectively Required for Plant Pathogenesis. J Bacteriol. 2012; 194:5054-64
45. Sudo T, Shinohara K, Dohmae N, Takio K, Usami R, Horikoshi K, Osada H. Isolation and characterization of the gene encoding an aminopeptidase involved in the selective toxicity of ascamycin toward Xanthomonas campestris pv. citri. Biochem J. 1996; 319(Pt 1):99-102
46. Peñaloza-Vázquez A, Kidambi SP, Chakrabarty AM, Bender CL. Characterization of the alginate biosynthetic gene cluster in Pseudomonas syringae pv. syringae. J Bacteriol. 1997; 179:4464-72
47. Ren Y, Strobel G, Sears J, Park M. Geobacillus sp., a thermophilic soil bacterium producing volatile antibiotics. Microb Ecol. 2010; 60:130-6
48. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Paré PW, Kloepper JW. Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci U S A. 2003; 100:4927-32
49. Ahmad F, Ahmad I, Khan MS. Screening of free-living rhizospheric bacteria for their multiple plant growth promoting activities. Microbiol Res. 2008; 163:173-81
50. Hardoim PR, van Overbeek LS, van Elsas JD. Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol. 2008; 16:463-71