Nutrient and moisture limitation reveal keystone metabolites that link switchgrass rhizosphere metabolome and microbiome dynamics

Abstract

Plants exude large quantities of rhizosphere metabolites that can modulate composition and activity of microbial communities in response to environmental stress. While rhizodeposition dynamics have been associated with rhizosphere microbiome succession, and may be particularly impactful in stressful conditions, specific evidence of these connections has rarely been documented. Here, we grew the bioenergy crop switchgrass (Panicum virgatum) in a marginal soil, under nutrient limited, moisture limited, +nitrogen (N), and +phosphorus (P) conditions, to identify links between rhizosphere chemistry, microbiome dynamics, and abiotic stressors. To characterize links between rhizosphere microbial communities and metabolites, we used 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics. We measured significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of diverse bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions enhanced the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin, ectoine, and acetylcholine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were found in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant-microbe interactions.

Reproducible growth ofBrachypodium distachyonin fabricated ecosystems (EcoFAB 2.0) reveals that nitrogen form and starvation modulate root exudation

“…Another paper showed that the root exudation of p -coumaric acid in rice increased by 1.95-fold in iN-than iN+ conditions ( 21 ). Therefore, our results from B. distachyon combined with the previous result suggest conserved patterns of increased production of compounds from the shikimate-phenylpropanoid pathway in root exudates of grasses under N-deficiency ( 20, 21 ).…”

“…4A and B ). Similarly, switchgrass showed an increased amino acid exudation pattern under +N and +NP fertilization relative to unfertilized controls ( 20 ). Additionally, axenically grown maize under N deficiency lowered the amino acid amounts in root exudates ( 22 ).…”

“…To our knowledge, dopamine exudation in grasses remains to be shown experimentally. However, the production of another neurotransmitter, serotonin, was documented to be also N-dependent in the rhizosphere of switchgrass ( 20 ).…”

“…Keeping this classification in mind, the literature contains several examples where shikimates-phenylpropanoids increased in the exudates of grasses under N deficiency. Recent work showed an increase in several organic and aromatic acids in marginal N-limited soil of the switchgrass rhizosphere ( 20 ). Another paper showed that the root exudation of p -coumaric acid in rice increased by 1.95-fold in iN-than iN+ conditions ( 21 ).…”

“…Multiple studies showed exudate changes by N supply in several plant grass species. For example, a recent paper showed the increase of aromatic and other organic acids in marginal N-depleted soils of the switchgrass rhizosphere, while added nitrogen (+N) and nitrogen phosphate (+NP) fertilizer increased the abundance of amino acids ( 20 ). A study on rice ( Oryza sativa ) found that roots actively release many metabolites in response to N and P deficiency ( 21 ).…”