Pseudomonas fluorescens Transportome Is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings under Nutrient Stress

Abstract

Diverse communities of bacteria colonize plant roots and the rhizosphere. Many of these rhizobacteria are symbionts and provide plant growth promotion (PGP) services, protecting the plant from biotic and abiotic stresses and increasing plant productivity by providing access to nutrients that would otherwise be unavailable to roots. In return, these symbiotic bacteria receive photosynthetically-derived carbon (C), in the form of sugars and organic acids, from plant root exudates. PGP activities have been characterized for a variety of forest tree species and are important in C cycling and sequestration in terrestrial ecosystems. The molecular mechanisms of these PGP activities, however, are less well-known. In a previous analysis of Pseudomonas genomes, we found that the bacterial transportome, the aggregate activity of a bacteria's transmembrane transporters, was most predictive for the ecological niche of Pseudomonads in the rhizosphere. Here, we used Populus tremuloides Michx. (trembling aspen) seedlings inoculated with one of three Pseudomonas fluorescens strains (Pf0-1, SBW25, and WH6) and one Pseudomonas protegens (Pf-5) as a laboratory model to further investigate the relationships between the predicted transportomic capacity of a bacterial strain and its observed PGP effects in laboratory cultures. Conditions of low nitrogen (N) or low phosphorus (P) availability and the corresponding replete media conditions were investigated. We measured phenotypic and biochemical parameters of P. tremuloides seedlings and correlated P. fluorescens strain-specific transportomic capacities with P. tremuloides seedling phenotype to predict the strain and nutrient environment-specific transporter functions that lead to experimentally observed, strain, and media-specific PGP activities and the capacity to protect plants against nutrient stress. These predicted transportomic functions fall in three groups: (i) transport of compounds that modulate aspen seedling root architecture, (ii) transport of compounds that help to mobilize nutrients for aspen roots, and (iii) transporters that enable bacterial acquisition of C sources from seedling root exudates. These predictions point to specific molecular mechanisms of PGP activities that can be directly tested through future, hypothesis-driven biological experiments.

Keywords: Pseudomonas; aspen; computational modeling; nitrogen; phosphorus; plant growth promotion; transportomics.

Figure 1

Impact of PGPB on aspen seedlings under conditions of low nitrogen (N) and phosphorus (P). Aspen seedlings inoculated with bacterial strains indicated on the left and grown under replete (4 mM N, 1.5 mM P) or nutrient limiting conditions (low N 150 μM, low P 25 μM) indicated on the top of the image.

Figure 2

Principal component analysis and hierarchical clustering of aspen seedling phenotypes. A scatter plot of the first two PC is shown. Each point is a single observation, drawn from average values of individual seedlings on a vertical plate. Shape indicates culture condition: no bacteria are circles, Pf-5 are triangles, Pf0-1 are crosses, SBW25 are × 's, and WH6 are diamonds. Nutrient condition is indicated by color: replete media is black, low N media is blue, and low P media is red. In PCA plot, blue, red, and black labels have been added to highlight the effects of colonization by bacteria and the effects of nutrient stress. Labeled arrows are the eigenvectors associated with seedling phenotype measure.

Figure 3

Heat map and hierarchical cluster of Pseudomonas strain PRTT-scores. In this heat map, rows are Pseudomonas strains and columns are specific ligands. Values in heat map are PRTT-scores.

Figure 4

Network of correlated aspen seedling phenotypes. In this network, nodes are measured seedling phenotypes, solid edges indicate strong positive correlations, and dashed edges indicate strong negative correlations. The phenotypes for root and shoot P concentration do not correlate strongly with any phenotypes.

Figure 5

Phenotype and Pseudomonas transportome correlation network. This is a graphical representation of the correlation network for aspen phenotypes and Pseudomonas transportome. Green rounded rectangles are aspen seedling phenotypes and diamonds are predicted ligands transported by Pseudomonas strains. Ligands are colored according to the specific Pseudomonas strain with the greatest (by PRTT-score) relative capacity for that ligand's transport: yellow for Pf-5, orange for Pf0-1, red for SBW25, and purple for WH6. Wavy green lines are strong correlations between aspen seedling phenotypic features. Solid straight lines are strong correlations between Pseudomonas transportomic capacity and aspen seedling phenotypes colored by culture condition: gray for replete media, blue for low N media, and yellow for low P media.