Abstract
Nitrogen metabolism in the rhizosphere microbiome plays an important role in mediating plant nutrition, particularly under low inputs of mineral fertilizers. However, there is relatively little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to utilize diverse nitrogen substrates. Here we investigate nitrogen substrate utilization in three taxonomically diverse bacterial strains previously isolated from Arabidopsis roots. The three strains represent taxa that are consistently detected as core members of the plant microbiome: Pseudomonas, Streptomyces, and Rhizobium. We use phenotype microarrays to determine the nitrogen substrate preferences of these strains, and compare the experimental results vs. computational simulations of genome-scale metabolic network models obtained with EnsembleFBA. Results show that all three strains exhibit generalistic nitrogen substrate preferences, with substrate utilization being well predicted by EnsembleFBA. Using label-free quantitative proteomics, we document hundreds of proteins in each strain that exhibit differential abundance values following cultivation on five different nitrogen sources: ammonium, glutamate, lysine, serine, and urea. The proteomic response to these nitrogen sources was strongly strain-dependent, with lysine nutrition eliciting widespread protein-level changes in Pseudomonas sp. Root9, whereas Rhizobium sp. Root491 showed relatively stable proteome composition across different nitrogen sources. Our results give new protein-level information about the specific transporters and enzymes induced by diverse rhizosphere bacterial strains to utilize organic nitrogen substrates.
Highlights
Improved nitrogen management in agricultural systems is crucial for environmental sustainability
We studied nitrogen metabolism in three taxonomically diverse bacterial strains isolated from roots of field-grown Arabidopsis: Pseudomonas sp
The strains were selected for study based on two criteria: first that they were previously shown to correspond to highly abundant taxa in the root microbiome of field-grown Arabidopsis plants (Table 1); and second that they could be successfully cultivated on a set of minimal media using different N-sources, based on a preliminary experiment with a panel of 17 rhizosphere bacterial strains (Supplementary Table S1)
Summary
Improved nitrogen management in agricultural systems is crucial for environmental sustainability. One potential pathway to boost agricultural sustainability involves substituting mineral fertilizers with organic nutrients derived from recycling various waste streams. For low-input agricultural systems to provide sufficient bioavailable nitrogen to meet the demands of plant growth, future crop management practices will need to better incorporate microbial pathways of nitrogen mobilization. One specific suggestion involves engineering the rhizosphere microbiome to promote the mineralization of organic nitrogen, coupled with engineering of plant root metabolism to release rhizodeposits that recruit beneficial microbial strains (Bender et al, 2016). The ability to manipulate plant-microbe cooperation is limited by an incomplete knowledge of the specific microbial traits involved in root colonization and nutrient mobilization (Trivedi et al, 2017)
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