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Environmental Transformations and Interactions

Rhizosphere Function

The integrated “Earth system” comprises a complex set of interacting physical, chemical, biological, and societal processes. These include belowground interactions and activities, which are deeply coupled with climatic and environmental systems. Among these, plant roots are key factors for shaping the soil microbiome, soil organic matter formation, and soil carbon sequestration. The rhizosphere is the soil region influenced by plant roots where complex biological and ecological processes occur. 

The Environmental Molecular Sciences Laboratory (EMSL)'s Rhizosphere Function Integrated Research Platform (RF IRP) investigates the molecular mechanisms of interactions between roots, the soil, and microbes. It primarily studies the effects of root-controlled processes, including rhizodeposition, on belowground carbon flux, biogeochemical nutrient cycling, plant resilience, and microbial community structure and function. With this knowledge, we can better understand the role of belowground processes in terrestrial carbon and relevant biogeochemical cycles and their coupled feedbacks to Earth and environmental systems.

The science

Research in the RF IRP aims to dissect interactions between roots, the soil, and microbes to understand the impacts and mechanisms of root-controlled processes on plant resilience and biogeochemical cycling of carbon, nutrients, and mineral elements.  

Key science areas covered by this IRP include: 

  • Investigating the fate and flow of photosynthates and nutrients between roots, microbes, and the broader soil system. 
  • Discovering and decoding the chemical language and mechanisms of root–microbe interactions.  
  • Characterizing the spatiotemporal distribution of substances secreted by roots (exudates) at the root–soil interface and monitoring their impacts on microbial communities and the biogeochemical cycling of essential elements, such as carbon, nitrogen, and phosphorous.  
  • Understanding how biological diversity in plants interacts with structural and compositional diversity in roots and soil to influence rhizodeposition and rhizosphere microbial activity. 
  • Studying the effects of root exudate composition on plant–microbial interactions and plant resilience in response to environmental perturbations (e.g., drought, salinity) and under future climate scenarios (e.g., increased carbon dioxide levels).  

Synergy and relationship with other Environmental Transformations and Interactions IRPs:  

The RF IRP specifically addresses the impact of root system architecture and root exudates on highly interlinked rhizosphere components (microbial communities, organic matter, and soil mineralogy) in response to environmental perturbations. Research in the Biogeochemical Transformations IRP compliments Rhizosphere Functions by focusing more fundamentally on the processes common to all of these systems—including soil organic matter decomposition or mineral weathering—and on subsurface processes that occur outside of the rhizosphere. Research in the Terrestrial-Atmospheric Processes IRP examines interactions between volatiles and particles emitted by soils and plants, and subsequent atmospheric processes, starting within the rhizosphere and extending up to the top of the troposphere. 

How we do the science

EMSL’s phytotron allows us to grow plants under tightly controlled environmental conditions and climate scenarios. Novel synthetic soil habitats—such as rhizosphere-on-a-chip—as well as traditional rhizoboxes, rhizotrons, and gel-based systems are used to grow, monitor, and analyze plants and their developing roots, while multi-omics and mass spectrometry imaging capabilities enable molecular analyses of root tissue, exudates, soil, and associated microbiomes. Using the phytotron, we are also investigating the connection between plant phenotype and the carbon cycle. With stable isotope tracers, EMSL staff and users are examining how carbon gets fixed, incorporated into different biomolecules, partitioned throughout the plant, and leaches out into the microbiome and surrounding soils.