Plant-microbe interactions in the rhizosphere for smarter and more sustainable crop fertilization: the case of PGPR-based biofertilizers

Abstract

Biofertilizers based on plant growth promoting rhizobacteria (PGPR) are nowadays gaining increasingly attention as a modern tool for a more sustainable agriculture due to their ability in ameliorating root nutrient acquisition. For many years, most research was focused on the screening and characterization of PGPR functioning as nitrogen (N) or phosphorus (P) biofertilizers. However, with the increasing demand for food using far fewer chemical inputs, new investigations have been carried out to explore the potential use of such bacteria also as potassium (K), sulfur (S), zinc (Zn), or iron (Fe) biofertilizers. In this review, we update the use of PGPR as biofertilizers for a smarter and more sustainable crop production and deliberate the prospects of using microbiome engineering-based methods as potential tools to shed new light on the improvement of plant mineral nutrition. The current era of omics revolution has enabled the design of synthetic microbial communities (named SynComs), which are emerging as a promising tool that can allow the formulation of biofertilizers based on PGPR strains displaying multifarious and synergistic traits, thus leading to an increasingly efficient root acquisition of more than a single essential nutrient at the same time. Additionally, host-mediated microbiome engineering (HMME) leverages advanced omics techniques to reintroduce alleles coding for beneficial compounds, reinforcing positive plant-microbiome interactions and creating plants capable of producing their own biofertilizers. We also discusses the current use of PGPR-based biofertilizers and point out possible avenues of research for the future development of more efficient biofertilizers for a smarter and more precise crop fertilization. Furthermore, concerns have been raised about the effectiveness of PGPR-based biofertilizers in real field conditions, as their success in controlled experiments often contrasts with inconsistent field results. This discrepancy highlights the need for standardized protocols to ensure consistent application and reliable outcomes.

Keywords: bacterial siderophores; beneficial bacteria; crop nutrition; nitrogen biofertilizer; phosphate biofertilizer.

Figure 1

Biofertilizer-mediated nutrient availability. (A) N-biofertilizers. (B) P-, K-, and S-biofertilizers. (C) Cation-chelating biofertilizers based on siderophore-producing bacteria. Created with BioRender (https://biorender.com/).

Figure 2

Representation of the present and future of PGPR-based biofertilizer development. (A) Biofertilizers based on a single bacterial strain. (B) Biofertilizers containing multiple strains (two or more) which are selected by considering their ability in enhancing plant uptake of soil nutrients. (C) Biofertilizers produced by farmers in their own farms by using rudimentary bio-factories without appropriate control of contaminations, which may result in highly contaminated, non-effective products. (D) Biofertilizers containing multiple strains which are selected after analyzing the diversity profile of plant microbiome. Thus, SynComs are designed to recreate the core microbiome containing key microbial taxa carrying essential functional genes for the host plant. (E) Genetically modified biofertilizers where bacterial genes are modified with gene editing tools (e.g., CRISPR/Cas9, RNAi) to improve plant growth and nutrition. However, the incorporation of these products into farm systems remains controversial since their efficacy, survivability, and environmental hazards are not well understood (Qiu et al., 2019). (F) Genetically modified plants driving the selection/recruitment of PGPR biofertilizers. Created with BioRender (https://biorender.com/).

Figure 3

Guidelines for PGPR-based biofertilizers field trial design and implementation as proposed by Neuhoff et al. (2024).