The development of new phenomics approaches to image and process data from the subcellular to ecosystem-scale has accelerated over the past decade. Many of these tools are produced “in-house” within a single lab or a group of collaborating labs, making it hard to keep up with the state-of-the-art for phenomics hardware and software development. The Plant Cell Atlas Phenomics Committee is creating a collaborative space that connects phenomics developers with each other and with the greater plant science community, with the goal of facilitating wide-reaching collaborations. To do this, we will be hosting a video series called “How We Built It” where developers provide a short tour of their inventions and relevant biological applications. We will follow the series with a more in-depth networking event where plant scientists can connect with the inventors and discuss collaborative opportunities. Our goal is to streamline the invention of new phenotyping tools and broaden the application of existing tools.

To address some challenging biological and environmental problems, scientists at the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL) have been pairing scientific capabilities at their home institution with the bright, tunable energy x-rays and high-resolution instruments at several national synchrotron user facilities. Synchrotron techniques can help answer a variety questions, and two examples featuring synchrotron-based structural and chemical imaging in bio/geochemical systems will be presented. In the first example, x-ray fluorescence spectromicroscopy and microtomography were used to visualize and better understand phosphorous uptake in poplar trees. Endophyte-promoted phosphorous uptake was seen inside poplar roots, where the fixated phosphorous appeared to be in the form of an organic phosphate. Analysis of the tomography data showing increased root mass for the plants inoculated with the endophytes supported the picture of increased nutrient uptake in those plants. These results along with in-house proteomics characterization point to the biological relevance of the symbiosis between endophytes and the host plant. In the second example, scanning transmission x-ray microscopy (STXM) combined with x-ray absorption near edge structure (XANES) helped us investigate soil mineral – soil organic matter (SOM) interactions in an alkaline soil from Washington state. Ca mineral–organic associations were found to be predominant which may play a critical role in the stabilization/degradation of SOM and mineral. Micro- and nanoscale characterization of the chemical state of both Ca from the mineral and C from the organic matter are crucial for understanding such stabilization mechanisms as well as soil nutrient dynamics.