Analysis of the plant growth‐promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD‐1

Abstract

Pseudomonas putida BIRD-1 is a plant growth-promoting rhizobacterium whose genome size is 5.7 Mbp. It adheres to plant roots and colonizes the rhizosphere to high cell densities even in soils with low moisture. This property is linked to its ability to synthesize trehalose, since a mutant deficient in the synthesis of trehalose exhibited less tolerance to desiccation than the parental strain. The genome of BIRD-1 encodes a wide range of proteins that help it to deal with reactive oxygen stress generated in the plant rhizosphere. BIRD-1 plant growth-promoting rhizobacteria properties derive from its ability to enhance phosphorous and iron solubilization and to produce phytohormones. BIRD-1 is capable of solubilizing insoluble inorganic phosphate forms through acid production. The genome of BIRD-1 encodes at least five phosphatases related to phosphorous solubilization, one of them being a phytase that facilitates the utilization of phytic acid, the main storage form of phosphorous in plants. Pyoverdine is the siderophore produced by this strain, a mutant that in the FvpD siderophore synthase failed to grow on medium without supplementary iron, but the mutant was as competitive as the parental strain in soils because it captures the siderophores produced by other microbes. BIRD-1 overproduces indole-3-acetic acid through convergent pathways.

Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria

“…Proteins for both starch (MalQ, GlgE, GlgX, GlpA and GlpB) and polyhydroxyalkanoic acid (PhaA, PhaG, PhaC) biosynthesis (carbon storage) were also enriched during Pi stress (Supporting Information Table S4). The abundance of a cytoplasmic glucose‐6‐phosphate dehydrogenase (Zwf), as well as two distinct membrane‐bound (PPUBIRD1_4115, PPYBiRD1_2225) glucose dehydrogenases (Gcd, GcdII respectively), all of which are known to play a role in Pi solubilization through gluconic acid production (Miller et al ., 2010; Roca et al ., 2013), was also greater in Pi‐deplete cells. Finally, another HAD‐family phosphatase (encoded by PPUBIRD1_3492), similar to PhnX was only detected in the proteome of Pi‐deplete cells (Table 2).…”

“…For example, a novel Pi‐responsive extracellular nuclease in SBW25 was discovered that was not identified through our comparative genomic analysis. Importantly, the genes (PPUBIRD1_5077, PPUBIRD1_0727, PPUBIRD1_2395, PPUBIRD1_0951, PPUBIRD1_0932) identified in BIRD‐1, based solely on in silico annotation (Roca et al ., 2013), were not members of the PHO regulon, highlighting the need for auxiliary studies to confirm genomic annotation. Furthermore, the strong secretion of exoproteins, such as PstS and PhoX, may serve as markers for characterizing complex communities in soil/rhizosphere to enable identification of the key microbial taxa involved in P recycling.…”

“…Various Pseudomonas strains can also degrade organic P compounds, such as phytate, phosphonates and phosphites (Ternan and Quinn, 1998; White and Metcalf, 2004, 2007). Three Pseudomonas strains , Pseudomonas putida BIRD‐1, Pseudomonas fluorescens SBW25 and Pseudomonas stutzeri DSM4166 (hereafter, BIRD‐1, SBW25 and DSM4166 respectively) are three examples of PGPR (Naseby et al ., 2001; Hass and Keel, 2003; Preston, 2004; Yu et al ., 2011; Roca et al ., 2013). SBW25 inhabits the rhizosphere of Pea plants and is antagonistic towards the pathogen Pythium ultimum (Naseby et al ., 2001), whereas DSM4166, an ‘unusual’ nitrogen‐fixing bacterium, was isolated from a cultivar of Sorghum nutans (Yu et al ., 2011).…”

“…SBW25 inhabits the rhizosphere of Pea plants and is antagonistic towards the pathogen Pythium ultimum (Naseby et al ., 2001), whereas DSM4166, an ‘unusual’ nitrogen‐fixing bacterium, was isolated from a cultivar of Sorghum nutans (Yu et al ., 2011). BIRD‐1, a P‐solubilising bacterium, has been previously utilized as a bioinoculant, since it can significantly improve the germination rates, growth and yields of various agricultural crops (Roca et al ., 2013). BIRD‐1 can remineralize Pi from the plant P‐storage compound phytate, a major source of organic P in some soils (up to 50%) (Stutter et al ., 2012).…”

“…BIRD‐1 can remineralize Pi from the plant P‐storage compound phytate, a major source of organic P in some soils (up to 50%) (Stutter et al ., 2012). Furthermore, when BIRD‐1 was used as an inoculant, phosphatase activity was greater in the rhizosphere compared with bulk soil (Roca et al ., 2013). Although Pseudomonas have been implicated in plant‐growth promotion, partially attributed to their effect on P mobilization, the precise mechanisms behind this process remain largely unknown.…”