Genome-based identification of phosphate-solubilizing capacities of soil bacterial isolates

Abstract

Identifying genomic markers for phosphate-solubilizing bacteria (PSB) is vital for advancing agricultural sustainability. This study utilizes whole-genome sequencing and comprehensive bioinformatics analysis, examining the genomes of 76 PSB strains with the aid of specialized genomic databases and analytical tools. We have identified the pqq gene cluster, particularly the pqqC gene, as a key marker for (P) solubilization capabilities. The pqqC gene encodes an enzyme that catalyzes the conversion of precursors to 2-keto-D-gluconic acid, which significantly enhances P solubilization in soil. This gene's importance lies not only in its biochemical function but also in its prevalence and effectiveness across various PSB strains, distinguishing it from other potential markers. Our study focuses on Burkholderia cepacia 51-Y1415, known for its potent solubilization activity, and demonstrates a direct correlation between the abundance of the pqqC gene, the quantitative release of P, and the production of 2-keto-D-gluconic acid over a standard 144-h cultivation period under standardized conditions. This research not only underscores the role of the pqqC gene as a universal marker for the rapid screening and functional annotation of PSB strains but also highlights its implications for enhancing soil fertility and crop yields, thereby contributing to more sustainable agricultural practices. Our findings provide a foundation for future research aimed at developing targeted strategies to optimize phosphate solubilization, suggesting areas for further investigation such as the integration of these genomic insights into practical agricultural applications to maximize the effectiveness of PSB strains in real-world soil environments.

Keywords: Burkholderia cepacia; Pqq gene cluster; Genome sequence; Phosphate-solubilizing bacteria.

Fig. 1

The genetic structures of thepqqoperon inBurkholderia cepacia51-Y1415 and other strains, showing the conserved nature of these genes across different species.Genetic structures of pqq operon of Burkholderia cepacian 51-Y1415, B. ubonensis, B. ambifaria, B. anthina, B. territorii, B. contaminans and B. latens with a Pesudomonas species as reference. The location and polarity of genes are showed with arrows

Fig. 2

Biochemical and genetic analysis of strain 51-Y1415 cultivated in PVK medium over 144 h. a Average values of triplicate measurements with standard deviations. The line graph illustrates P release into the medium, while the bar chart quantifies the concentrations of various organic acids produced. Significant differences between groups indicated by different letters were determined by ANOVA (P < 0.05). b Radar charts depicting the relative expression levels (fold change) of the pqq gene cluster in strain 51-Y1415, with expression normalized to conditions in LB medium over 144 h

Fig. 3

The schematic diagram of the proposed pyrroloquinoline quinone (PQQ) biosynthetic pathway and glucose to gluconic acid conversion via PQQ-GDH (PQQ-dependent glucose dehydrogenase). (Adapted from Martins et al. ; Mi et al. 2020). Depicts the biosynthesis of PQQ from the peptide PqqA through four conserved enzymes: PqqE (radical SAM enzyme), PqqD (peptide chaperone), PqqB (dual hydroxylase), and PqqC (eight-electron, eight-proton oxidase), alongside an alternative pathway involving PqqF/G. This process underscores PQQ’s role in the conversion of glucose to gluconic acid