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Rhizosphere Promoted Rock Weathering and Nutrient Cycling in Deep Shale Fractures

EMSL Project ID


This project seeks to use EMSL metabolomic and imaging approaches to determine the biogeochemical processes driven by plant roots (sagebrush and lupin) in deep, fractured weathering shale, to test the hypothesis that plant root-driven shale weathering confers ecological advantages to deep-rooted plants by increasing access to water and geogenic nutrients, and to quantify the importance of the fractured shale environment to carbon and nutrient cycling in the watershed. This is part of the BER-funded project that seeks to establish a predictive understanding of how mountainous watersheds retain and release water, nutrients, carbon, and metals. To achieve this goal, an interdisciplinary team is studying canopy-to-bedrock processes at the East River and neighboring watersheds, Colorado, and developing and coupling predictive numerical models of how hydrology, vegetation, microorganisms, and geochemical processes respond to climate trends and perturbations. Project fieldwork has shown that weathering shale bedrock, particularly in the fluctuating water table zone, releases significant quantities of nutrients and metals into the watershed. Informed by field observations, we have developed flow and reaction models that reproduce the temporal patterns of element discharge into the river and that recreate the reaction network at weathering fracture surfaces. However, recent fieldwork discovered that several common plants establish root networks in fractured shale that extend down to subsurface regions where shale weathering processes are initiated (figure 1). Although it is well established that plants direct photosynthetic organic carbon to the rhizosphere in order to promote synergistic microbial processes in soils, the relationship between rhizosphere biogeochemistry, bedrock weathering processes and rock nutrient acquisition remain poorly understood.
Here, we seek to determine the geologic, biological and biochemical structure of the rhizosphere that develops in deep shale fractures and correlate that information with geochemical signatures of shale weathering. Working with EMSL, we will use X-ray tomography to reveal how plant roots penetrate rock fractures and determine the structure and composition of the soils that develop in these sub-millimeter spatially confined environments. We will apply approaches developed at EMSL to extract organic molecules from small soil volumes (e.g., 100 ×100 µm2) for mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. For selected samples, 2D mass spectroscopy imaging (MSI) will be performed by transferring metabolites to prewetted polyvinylidene fluoride (PVDF) membrane for MALDI-MSI. We have developed a protocol for DNA extraction from fracture-surface soils and will apply a metagenomic analysis pipeline developed to reveal the variations in soil microbial communities across the East River watershed. The locations and pathway of shale weathering will be established using 2D chemical imaging methods including Nano-SIMS at EMSL, X-ray microprobe analysis at ALS beamline 10.3.2, and FTIR microspectroscopy. These combined observations will enable unprecedented insight into the earliest stages of plant-influenced bedrock weathering and soil formation.

Project Details

Project type
Exploratory Research
Start Date
End Date


Principal Investigator

Benjamin Gilbert
Lawrence Berkeley National Laboratory


Eoin Brodie
Lawrence Berkeley National Laboratory

Team Members

Brooke Newell
Lawrence Berkeley National Laboratory

Langlang Li
Lawrence Berkeley National Laboratory