Optimizing Crop Production with Bacterial Inputs: Insights into Chemical Dialogue between Sphingomonas sediminicola and Pisum sativum

Abstract

The use of biological inputs is an interesting approach to optimize crop production and reduce the use of chemical inputs. Understanding the chemical communication between bacteria and plants is critical to optimizing this approach. Recently, we have shown that Sphingomonas (S.) sediminicola can improve both nitrogen supply and yield in pea. Here, we used biochemical methods and untargeted metabolomics to investigate the chemical dialog between S. sediminicola and pea. We also evaluated the metabolic capacities of S. sediminicola by metabolic profiling. Our results showed that peas release a wide range of hexoses, organic acids, and amino acids during their development, which can generally recruit and select fast-growing organisms. In the presence of S. sediminicola, a more specific pattern of these molecules took place, gradually adapting to the metabolic capabilities of the bacterium, especially for pentoses and flavonoids. In turn, S. sediminicola is able to produce several compounds involved in cell differentiation, biofilm formation, and quorum sensing to shape its environment, as well as several molecules that stimulate pea growth and plant defense mechanisms.

Keywords: Sphingomonas sediminicola; molecular dialogue plant–bacteria; pea; plant–bacteria interaction; root exudates.

Figure 1

Principal component analysis (PCA) of polyphenol, flavonoid, amino acid, and carbohydrate content in hydroponic solutions of peas inoculated or not with Sphingomonas sediminicola at the time of first leaf emergence, second internode, and flowering.

Figure 2

Metabolic potential of S. sediminicola against PM substrates. For each source, the level of substrate degradation, expressed in Omnilog units, was considered only if it reached a minimum value of 500 Omnilog units in at least two of the three replicates. For degraded substrates, the value given is the average of the three replicates; otherwise, a red cross indicates that the substrate was not degraded by S. sediminicola.

Figure 3

Untargeted metabolomics of Sphingomonas sediminicola in R2A medium. (a,b) Heatmap of differential metabolites in positive (a) and negative (b) ion modes. Each row corresponds to a differentially expressed metabolite, while each column represents a specific sample. The color gradient, ranging from green to red, indicates the abundance level of the differentially expressed metabolites, with green representing low abundance and red representing high abundance. (c,d) Volcano plot of differential metabolites in positive (a) and negative (b) ion modes. Each point represents a metabolite, horizontal coordinates indicate different multiplicities of differential metabolites (log₂ values), vertical coordinates indicate p-values (−log₁₀ values), grey indicates metabolites with no significant differences, red indicates up-regulated metabolites (Up), and green indicates down-regulated metabolites (Down). (e,f) bubble plots of metabolic pathway enrichment in positive (e) and negative (f) ion modes. The x-axis in the figure represents the ratio of differentiated metabolites in a specific metabolic pathway to the total number of identified metabolites within that pathway (RichFactor). A higher value indicates a greater enrichment of differential metabolites in the pathway. The color of the dots corresponds to the p-value obtained from the hypergeometric test. A smaller p-value indicates a more reliable test. The size of the dots represents the number of differential metabolites present in the respective metabolic pathway.