Stable isotope labeling to trace carbon flow from switchgrass to rhizosphere soil exometabolites and microbial communities

Switchgrass (SG) is a perennial grass with significant potential for US biofuel production and also potential benefits for increased soil carbon (C) stocks. SG is well-adapted to resource-limited environments, such as low-nutrient or droughty soils. This study investigates which plant-associated microbes are associated with improved plant performance and C flow in marginal soils, using ¹³CO₂ stable-isotope labeling, genomics and exometabolomics to identify the nature and fate of C in the SG rhizosphere.

We grew Alamo SG clones in reconstituted nutrient-deplete soil horizons in greenhouse mesocosms. Soil columns were 1 m deep and contained three soil horizons with different physio-chemical properties. The top horizon of soil was subjected to N and/or P amendments and two watering regimes. We collected rhizosphere and bulk soil from ¹²CO₂- and ¹³CO₂-labeled SG and extracted DNA and exometabolites. Plant shoot and root biomass were also measured.

Relative to controls, we observed significantly higher SG shoot and root biomass when N and/or P were added, and significantly lower biomass in the water-limited treatment. Using mass spectrometry-based metabolomics (LC-MS), we identified three main patterns of change in metabolite profiles: (i) N-containing metabolites (e.g. amino acids, nucleosides) were abundant in treatments where N and N/P were added, but depleted in treatments without any added nutrients. (ii) Osmolytes (e.g. betaines) increased in abundance in the rhizosphere of water-limited plants. (iii) Aromatic acids were abundant in non-amended control soil.

We used stable isotope probing (SIP) to link identified metabolite chemistries to the abundance and activity of rhizosphere bacteria. We found a significant shift in density of DNA from specific bacterial taxa when comparing the rhizosphere DNA recovered from ¹³CO₂-labeled plants to that recovered from ¹²CO₂ controls. In this presentation we demonstrate how a combined SIP, genomics and metabolomics approach enables us to trace C flow through root exudates into microbes actively respiring plant photosynthate. This approach uncovers the mechanistic basis for SG-microbe interactions in marginal soil and shows how root-derived metabolites structure SG rhizosphere community under different stresses.