Complete Genome of the Plant Growth-Promoting RhizobacteriumPseudomonas putidaBIRD-1

Abstract

We report the complete sequence of the 5.7-Mbp genome of Pseudomonas putida BIRD-1, a metabolically versatile plant growth-promoting rhizobacterium that is highly tolerant to desiccation and capable of solubilizing inorganic phosphate and iron and of synthesizing phytohormones that stimulate seed germination and plant growth.Bacteria that efficiently colonize the rhizosphere and stimulate plant growth through direct or indirect mechanisms are referred to as plant growth-promoting rhizobacteria (PGPR). Plant growth promotion can be mediated by the synthesis of phytohormones, enhanced uptake of mineral nutrients, antagonizing of soilborne pathogens, induction of systemic resistance, etc. (1). The use of PGPR as inoculants for biofertilization, phytostimulation, and biocontrol avoids the use of chemical fertilizers and pesticides.Pseudomonas putida BIRD-1 is a soil bacterium that is efficient as a PGPR agent through the mobilization of nutrients and stimulation of secondary root proliferation. The complete genome sequence of BIRD-1 was obtained using 454 pyrosequencing technology. The sequences of 499,016 reads were assembled into 106 contigs to give 20ϫ coverage. Fifty-two contigs were longer than 3,000 bp. The complete genome of P. putida BIRD-1 is made up of a 61.74%-GC circular chromosome of 5,731,541 bp with no plasmid. The genome size is similar to that of P. putida W619 (5,774,330 Mb) (4) and smaller than those of P. putida KT2440 (6,181,860 Mb) (2), P. putida F1 (5,959,964 Mb), and P. putida GB-1 (6,078,430 Mb).The genome of BIRD-1 encodes 5,124 proteins, 64 tRNAs, eight 5S rRNAs, seven 16S rRNAs, and 23S rRNA. All essentially conditional genes identified in KT2440 (3) are present in the genome of BIRD-1, and functions were assigned to almost 60% of the total coding genes. The genome of P. putida BIRD-1 encodes a number of root colonization determinants (4) and a number of elements that favor plant growth. The ability of P. putida BIRD-1 to solubilize inorganic phosphate is related to the production of gluconic acid, whereas the ability to solubilize iron is related to the synthesis of pyoverdines. All genes required for these functions have been identified; BIRD-1 produces the indole-3-acetic acid (IAA) plant hormone, a trait associated with stimulation of root initiation and elongation. Two putative tryptophan-dependent IAA biosynthetic pathways have been identified in this strain. The genome of BIRD-1 also contains genes encoding proteins for the synthesis of salicylate, another compound that is relevant in plant responses.Nucleotide sequence accession number. The complete genome sequence of P. putida BIRD-1 is available in GenBank under accession number CP002290.

Stability of a Pseudomonas putida KT2440 Bacteriophage-Carried Genomic Island and Its Impact on Rhizosphere Fitness

“…Recently, it has been suggested that many of the resident GIs in a single prokaryotic genome originated from the same source, considering their similar genomic signature compositions (56). The identity of the donor microorganism(s) of the 12 GIs selected in this work is unknown, because the results from sequence alignments did not show homology with any sequence longer than 4 kb in the databases, including P. putida strains BIRD-1, S16, and B6-2 (41,64,72).…”

Iron Uptake Analysis in a Set of Clinical Isolates of Pseudomonas putida

“…Recently, a few P. putida strains have been isolated from hospital environments (von Graevenitz and Weinstein, 1971; Galli et al, 1992; Yoshino et al, 2011; Molina et al, 2013, 2014, 2016). The ubiquitous character of this microorganism has been linked to its broad metabolic potential, its ability to produce a large variety of secondary metabolites that may enable colonization of different environments and a complex array of sigma factors and two-component regulatory systems that allow a fast adaptation to environmental changes (Matilla et al, 2011; Udaondo et al, 2012, 2013, 2016; Planchamp et al, 2015). …”

Mechanisms of Resistance to Chloramphenicol in Pseudomonas putida KT2440

“…Genome annotation of several natural chloramphenicol-resistant P. putida strains failed to show any specific chloramphenicol-modifying enzymes (36,41,45,67); however, Godoy and colleagues (23) showed that P. putida mutants in the multidrug TtgABC pump exhibited compromised growth in the presence of chloramphenicol (21). Further studies in P. putida DOT-T1E confirmed the role of the TtgABC efflux pump in tolerance to chloramphenicol and other toxic compounds while unveiling the molecular mechanisms involved in the regulation of the expression of this pump in this strain (14,18,58).…”