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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 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) 

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-Atmosphere 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. 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.

Research in action

Root–microbe interactions in a changing environment

a transparent, round RhizoChip holds a growing plant

Plant–soil–microbe interactions play a crucial role in processes that take place in the soil directly around plant roots, i.e., the rhizosphere. These processes contribute to nutrient cycling and metabolite turnover in the environment. Amid the water scarcity, plants are forced to adapt through a range of processes that impact soil organic matter turnover in the rhizosphere. A multi-institutional team of researchers examined how different types of plant species interacted with the microbes in the rhizosphere during drought. They found that the root exudation by plant roots can maintain specific microbe partnerships in a changing environment, revealing a new level of resilience. This knowledge highlights how plant-associated microbes enable tropical plants to better handle drought conditions and provides greater understanding about the drought-related impacts on rhizosphere processes.

In another study, researchers studied the molecular mechanisms of biological nitrogen fixation and beneficial plant–endophyte interactions. The team used the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, which colonizes the intercellular spaces and vascular tissues of the host plant, Populus trichocarpa, to identify the regulatory mechanisms of biological nitrogen fixation in vitro and in planta. Using several advanced technologies including secondary ion mass spectrometry (NanoSIMS), RhizoChips, fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH), and stable isotope probing (SIP) coupled with proteomics and metabolomics analyses, the team discovered novel mechanisms of biological nitrogen fixation by endophytic bacteria. Specifically, the new findings include the required conditions for nitrogenase activity and bacterial colonization in plant roots, and the potential nitrogenous signals or transfer molecules between microbial community members and the host plant.

Carbon transport and release to belowground

view from ground of trees above

Understanding the mechanism of carbon transport from plant leaf tissues (sites of photosynthesis) to belowground, and then carbon transformation between plant roots, microbes, and soil is important to the health of plant ecosystems and carbon sequestration. Researchers decoded how these interactions impact microbial communities and essential carbon cycles by analyzing root metabolites and fluid released through plant roots.

A study at EMSL was the first to comprehensively examine relationships between carbon sources (leaves) and sinks (roots) at the molecular level by applying synthetic auxins to poplar foliage, opening doors for additional research on ways to enhance the strength of the carbon sink in poplar roots.

Plant roots and the associated microbes release a diverse range of chemical compounds (i.e., exudates) into the surrounding rhizosphere with direct impacts on soil carbon storage and transformation. Researchers used EMSL’s high-resolution mass spectrometry capabilities to measure biogeochemical dynamics and changing exudation profile along single growing plant roots (Avena sativa) monitored with in situ microsensors. The team discovered that there are significant spatial variances in metabolites, dissolved organic carbon (DOC) concentrations, microbial growth, redox potential, and pH dynamics among bulk soil, root tip, and more mature root zones. Overall, this work highlights how different exudates like sugars or organic acids released along growing roots create functionally distinct soil microenvironments that evolve over time.

The impact of root-controlled processes on carbon and nutrient cycling at the ecosystem scale

Diagram comparing tree health and soil conditions before and during a drought. On the left, a tree with green leaves and a detailed cross-section showing healthy soil layers and active root systems. On the right, a tree with brown leaves and soil cross-section showing dry, compact layers with less active roots.

There is limited information about how different plant species respond to environmental stressors and how that impacts rhizosphere processes, nutrient cycling, and the larger ecosystem. Researchers studied three tropical rainforest plants to improve our understanding of how drought impacts root chemistry and carbon pathways. They used EMSL’s analytical tools including bulk omics and spatial chemical imaging technologies to study the impact of the microbial community on the root metabolome and carbon allocation pathways in the rhizosphere. Through this research, the team concluded that different plant species use specific mechanisms and drought-tolerance strategies to cope with stress, resulting in various effects on belowground organic matter composition.

In another study at EMSL, researchers examined how microbial–mineral interactions stabilize carbon in the rhizosphere. They filled mesh bags with a mineral called biotite, put them in the root zone of ponderosa pines for six months, and then compared them with surrounding soil. Using EMSL’s high-resolution electron microscopy and X-ray diffraction analysis coupled with mass spectrometry analyses, this study revealed the roles of rhizosphere microbial communities in the formation and stabilization of soil organic carbon, microaggregation, and mineral weathering at the micro- and nanoscales. This research highlights the significant impact of root-zone-specific microbes on shaping the soil structure and on carbon storage and transformation in soil.