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

Abstract

SummaryBacteria that inhabit the rhizosphere of agricultural crops can have a beneficial effect on crop growth. One such mechanism is the microbial‐driven solubilization and remineralization of complex forms of phosphorus (P). It is known that bacteria secrete various phosphatases in response to low P conditions. However, our understanding of their global proteomic response to P stress is limited. Here, exoproteomic analysis of Pseudomonas putida BIRD‐1 (BIRD‐1), Pseudomonas fluorescens SBW25 and Pseudomonas stutzeri DSM4166 was performed in unison with whole‐cell proteomic analysis of BIRD‐1 grown under phosphate (Pi) replete and Pi deplete conditions. Comparative exoproteomics revealed marked heterogeneity in the exoproteomes of each Pseudomonas strain in response to Pi depletion. In addition to well‐characterized members of the PHO regulon such as alkaline phosphatases, several proteins, previously not associated with the response to Pi depletion, were also identified. These included putative nucleases, phosphotriesterases, putative phosphonate transporters and outer membrane proteins. Moreover, in BIRD‐1, mutagenesis of the master regulator, phoBR, led us to confirm the addition of several novel PHO‐dependent proteins. Our data expands knowledge of the Pseudomonas PHO regulon, including species that are frequently used as bioinoculants, opening up the potential for more efficient and complete use of soil complexed P.

Quantification of bacterial non-specific acid ( phoC) and alkaline ( phoD ) phosphatase genes in bulk and rhizosphere soil from organically managed soybean fields

“…In addition, there are multiple genes in bacteria associated with the production of alkaline and acid phosphatases. Nonspecific acid phosphatases (NSAPs) can be grouped into Class A-C based on their taxonomic relatedness (Gandhi and Chandra, 2012), while ALK production has been associated with phoA, phoD, and phoX genes in bacteria (Apel et al, 2007;Gomez and Ingram, 1995;Lidbury et al, 2016). The phoC gene targeted in our study is of the Class A, although the relative contribution of each class to extracellular phosphatases activity in soil is unknown.…”

“…While excretion of ACP by plant roots (George et al, 2006;Li et al, 2002;Spohn et al, 2015;Tarafdar and Claassen, 1998), nodules (Li et al, 2012;Penheiter et al, 1997a), and soil microbes (Nannipieri et al, 2011;Spohn et al, 2015;Tarafdar and Claassen, 1998) has been well documented, production of ALK has been primarily reported from soil bacteria and some fungi (Nannipieri et al, 2011). Previous studies have confirmed the presence of a phosphate regulon (Pho) in some bacteria, consisting of a suite of genes responsible for phosphate acquisition induced under conditions of phosphate starvation, including phosphatase production (Apel et al, 2007;Krol and Becker, 2004;Lidbury et al, 2016;Vershinina and Znamenskaya, 2002). Some experiments have demonstrated increased phosphatase activity under phosphate-limited conditions (Fraser et al, 2015a,b;Kier et al, 1979;Zhang et al, 2012), although others have found no correlation (Fraser et al, 2015b).…”

Identification of extracellular glycerophosphodiesterases in Pseudomonas and their role in soil organic phosphorus remineralisation

“…20 . Briefly, a cell culture (n = 3) was incubated with 20 μL para -nitrophenyl phosphate ( p NPP) (final conc.…”

The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low‐pH soils

“…Microorganisms can have a beneficial effect on crop production, partly through the liberation of unavailable P in the rhizosphere and surrounding soil (Rodrıǵuez & Fraga, 1999). Various studies have revealed that upon depletion of extracellular Pi bacteria can undergo a regulatory and physiological response resulting in the secretion of various exoproteins involved in liberating and binding Pi (Hirani, Suzuki, Murata, Hayashi, & Eaton-Rye, 2001;Rittmann, Sorger-Herrmann, & Wendisch, 2005;Monds, Newell, Schwartzman, & O'Toole, 2006;Antelmann, Scharf, & Hecker, 2000;Lidbury et al, 2016). Through this process, numerous reports have revealed that various phosphatases play an important role in the bioavailability of P in soils (Nannipieri, Newell, Giagnoni, Landi, & Renella, 2011).…”

“…Usually, the most heavily secreted exoenzymes are alkaline phosphatases (APases), which cleave Pi from a plethora of complex organic P monoesters and diesters. The latter compounds account for the bulk (up to 90%) of organic P in soils (Condron, Turner, & Cade-Menun, 2005;Lidbury et al, 2016;Santos-Beneit, 2015;Zaheer, Morton, Proudfoot, Yakunin, & Finan, 2009).…”