Rhizosphere Function

Earth’s integrated soil systems comprise a complex set of interacting physical, chemical, and biological processes strongly affected by weather, major perturbations such as drought, and land uses such as bioeconomy crop production. The Rhizosphere Function Integrated Research Platform (IRP) advances basic science by investigating the molecular mechanisms of interactions among the microbiome, soil, and roots. Rhizosphere microbes live in an environment profoundly shaped by plant roots, which deposit approximately half of all soil organic matter through exudation, triggering complex biological and ecological processes that are different from those processes (if any) that occur in bulk soil. This IRP primarily studies the effects of microbial community structure and function under the action of rhizodeposition on biogeochemical nutrient cycling. With this knowledge, we can better understand the role of rhizosphere processes in nutrient and biogeochemical cycles, critical material/mineral solubilization, and feedbacks on Earth systems and energy infrastructure. We can also discover new microbial processes for transforming biomass, growing critical American scientific leadership in the process. 

Rhizosphere vs. bulk soil: a unique microbiome community 

The rhizosphere microbiome, located around plant roots, ranks as one of the most biodiverse ecosystems on the planet. It is much denser and more diverse than the bulk soil microbiome and contains 10- to 100-fold more microbes. These microbes are fueled by plant root exudates that serve as nutrients, attract microorganisms, and drive distinctive metabolic processes. Compared with bulk soil, the rhizosphere shows greater temporal dynamics driven by rhizodeposition. Additionally, the rhizosphere demonstrates chemical and physical properties that are distinct from those in bulk soil. These properties are influenced by root exudates, nutrient availability, and microbial activity, resulting in a unique microbial community and functional profile. 

The science 

Research in this IRP aims to dissect interactions among roots, the soil, and microbes to understand the impacts and mechanisms of root-controlled microbial and soil processes on bioprocesses, plant resilience, and the biogeochemical cycling of nutrients, minerals, and elements. 

Key science areas covered by this IRP include the following: 

• Investigating the fate and flow of exuded photosynthates and nutrients among 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. 
• Understanding how structural and compositional diversity in rhizosphere microbiomes experiencing rhizodeposition is influenced by biological diversity in plants. 
• Studying the effects of root exudate composition on plant-microbe interactions and plant resilience in response to environmental perturbations (e.g., drought and salinity). 

Synergy and relationship with other Environmental Transformations and Interactions IRPs 

The RF IRP specifically addresses the impacts 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 focuses on the basic science of the processes common to all of these systems—including soil organic matter decomposition and 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. It also investigates subsequent atmospheric processes, starting within the rhizosphere and extending up to the top of the troposphere. 

How we do the science 

Phytotrons at the Environmental Molecular Sciences Laboratory (EMSL) allow us to grow plants under tightly controlled environmental conditions. We use novel synthetic soil habitats—such as rhizosphere-on-a-chip—as well as traditional rhizoboxes, rhizotrons, and gel-based systems to grow, monitor, and analyze plants and their developing roots. We also use multi-omics and mass spectrometry imaging capabilities to perform molecular analyses of root tissue, exudates, soil, and associated microbiomes. Using the phytotron, we are also investigating the connection among plant roots, the rhizosphere microbiome, and the nutrient cycle. With stable isotope tracers, staff and users at EMSL are examining how photosynthates get partitioned throughout the plant and leach out into the microbiome and surrounding soils. 

Research in action

Root–microbe interactions in a changing environment

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 water scarcity, plants are forced to adapt through a range of processes that affect soil organic matter turnover in the rhizosphere. A multi-institutional team of researchers examined how different types of plant species interact with microbes in the rhizosphere during drought. They found that 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 a greater understanding of 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 nanoscale secondary ion mass spectrometry, RhizoChips, fluctuation localization imaging-based fluorescence in situ hybridization, and stable isotope probing 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. 

The interplay between iron and plant–mycorrhiza interactions 

The role of different ectomycorrhizal fungi (EMF) species in plant iron uptake is important for understanding how EMF-plant interactions influence iron cycling in forests. A multi-institutional team of researchers found that inoculating plants with multiple EMF species enhances iron acquisition from the soil to the roots and starts a range of iron-dependent physiological and biochemical processes in the mycorrhizal roots, benefiting plant growth. These findings demonstrate the potential importance of EMF diversity in promoting forest health and improving the symbiotic relationship between mycorrhizae and host. 

The function of fine roots in the rhizosphere 

In root-microbiome studies, researchers rarely focus on fine roots—2 millimeters or less in diameter—and their different functional roles. 

A multi-institutional team of researchers used a 26-year-old common garden forest to collect fine root samples from four temperate tree species (three deciduous and one coniferous) with varying morphology. By performing transcriptomics analyses and using EMSL’s metabolomics capabilities, they discovered that fine roots compartmentalize their functions, with bacteria and fungi operating differently within each compartment. This variation is likely influenced by the availability and type of nutritional resources present in each area. This finding underscores the critical role of root function in root-microbe relationships, highlighting the distinct host-selective pressures exerted on various root-microbiome compartments. 

RhizoMAP 

Spatiotemporally mapping metabolites within the rhizosphere enables a wide range of research for the scientific community. Staff scientists at EMSL developed a platform called RhizoMAP to allow researchers to trace and visualize complex metabolomic processes in the rhizosphere. 

Using EMSL’s RhizoMAP coupled with Fourier-transform ion cyclotron resonance mass spectrometry capabilities, EMSL users can monitor key metabolites at root-soil-microbe interfaces across both spatial and temporal dimensions. Confident annotation of a wide range of molecules, including the identification of exudate profiles, provides information on complex rhizosphere processes in which plants secrete a variety of exudates depending on their growth cycles and environmental stimuli in the soil. RhizoMAP data help develop mechanistic models to improve the understanding of molecular and microscale processes in the rhizosphere.