Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Chemical Imaging of Plant-Soil-Microbe Systems at the Stanford Synchrotron Radiation Lightsource


Jocelyn Richardson1* David Weston2, Elizabeth Herndon2, Alyssa Carrell2, Arunima Bhattacharjee3, Christopher R. Anderton3, Ritimukta Sarangi1 and Keith Hodgson1


1SLAC National Accelerator Laboratory; 2Oak Ridge National Laboratory (ORNL); and 3Pacific Northwest National Laboratory


The Structural Molecular Biology resource at the Stanford Synchrotron Radiation Lightsource (SSRL) develops, operates, and supports synchrotron capabilities for biological and environmental research including macromolecular crystallography, small angle scattering, x-ray absorption spectroscopy (XAS) and x-ray fluorescence (XRF) imaging. Three dedicated XRF imaging beamlines cover a range of spatial scales (µm to cm) and elements of biological importance (P, S, K, Ca, and metals). A powerful aspect of the XRF imaging beamlines is that they can perform µ-XAS to characterize the oxidation state, or chemical species, at a single point within a sample. Combining XRF with XAS is a tool for generating spatial distribution images of individual chemical species of an element within a sample. Researchers will present examples of P, S, K, Mn and Fe chemical imaging from BER-relevant systems, such as microbial aggregates, plant components, mineral-organic matter complexes and soil cores as well as detailing the rich information that can be gained from synchrotron analyses using two specific examples.

Sphagnum moss is a key genus in terrestrial peatlands, responsible for most of the primary production and recalcitrant organic matter in these ecosystems, in turn impacting both C and N cycles. Sphagnum growth and production is partly dependent on a microbial symbiosis with N-fixing microbes. Researchers from ORNL used XRF imaging at SSRL to visualize the exchange of S compounds during stages of Sphagnum colonization by cyanobacteria. Data showed increased production of sulfate from Sphagnum as the percentage of colonization increased. Additionally, an increase in the local production of reduced S compounds (thiols/thio-ethers, likely in amino acids) and sulfonate (in either taurine or sulfoacetate) was observed within colonized hyaline cells only. These data support the hypothesis that Sphagnum produced choline-sulfate is being exchanged for microbially derived S and N bearing amino acids. Understanding the function of this relationship under warming conditions will provide insight into whether peatland ecosystems will remain net C sinks or become C sources due to climate change.

Potassium is persistently limited in most environments, however, studies of rhizosphere-phyllosphere K cycling are generally based on bulk measurements, which provide limited information on the biological processes that control K bioavailability. Researchers at EMSL have developed synthetic soil habitats (SSH), which simulate soil chemical and physical properties and are compatible with multi-modal imaging techniques. In collaboration with SSRL, researchers from EMSL are using SSH and multiple lines of synchrotron investigation to visualize the organic and inorganic processes controlling fungal sourcing, transport, and transformation of K during C-limitation, including: (i) XRF imaging of fungal hyphae on SSH in the presence and absence of an inorganic K source, (ii) XRF imaging of hyphae removed from SSH to determine the K phases and their role in hyphae, (iii) XRF imaging of the SSH surface to determine the availability of K resulting from fungal degradation of an inorganic K source, and (iv) XAS and theoretical calculations to determine the K bonding environment in organic K compounds to improve the knowledge of the dominant chelating ligands and properties. Combined with mass spectrometry imaging and multiomics analyses, these data indicate the importance of fungal exudated tartaric and citric acids, which are likely responsible for sensing K rich minerals and uptake/storage of K by fungi, respectively. Additionally, the formation of 10s µm size clay minerals on the SSH after 30 days of fungal growth provides insight into fungal mineral degradation over environmentally relevant spatial and temporal scales. This readily bioavailable pool of K could be a source for other microbes and plants in a more complex system.

The SSRL Structural Molecular Biology resource supports the development of advanced methodologies and research, collaborative research, service, training, and dissemination in structural molecular biology using synchrotron radiation at SSRL. The integrated program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894).