Synchrotron X-rays for Metals in Plants, Soils, and Environmental Systems: Early Science and Community Building at XLEAP

Aug 5, 2026, 8:00 AM → Aug 7, 2026, 5:00 PM America/New_York

Bradfield 101 (Cornell University)

Olena K Vatamaniuk, Louisa Smieska, Ju-Chen Chia

This workshop brings together researchers from across disciplines to help shape the future scientific direction of the XLEAP beamline at CHESS.

XLEAP (X-rays for Life, Environment, Agriculture, and Plants) is a next-generation beamline currently under construction at CHESS, with user operations anticipated in 2028. This workshop will help define the science, build the community, and identify the opportunities that XLEAP will enable.

Participants will explore how advanced X-ray techniques can unlock new insights into complex biological, environmental, and agricultural systems - while helping guide the development of this new national resource.

Registration and abstract submission for full consideration is closed.

In person and virtual options:

In the spirit of building community, we hope that as many participants as possible will be able to attend in person. However, understanding that this may not be feasible for all, a remote viewing option is also available during registration.

CONFIRMED SESSION CHAIRS

• Mary Lou Guerinot (Dartmouth College)
• José Hernandez (University of Texas at El Paso)
• Vibha Kalra (Cornell University
• Tiina Roose (University of Southampton)
• Anne Sylvester (Marine Biological Laboratory)
• Olena Vatamaniuk (Cornell University)
• Louisa Smieska (CHESS)

 

CONFIRMED SPEAKERS

• David Mendoza-Cozatl (University of Missouri)
• Ute Krämer (Ruhr University Bochum)
• Kendal Hirschi (University of Texas at El Paso)
• Susan Zhang (Stanford University)
• Wolfgang Busch (Salk Institute for Biological Studies)
• Rachel Hestrin (University of Massachusetts Amherst)
• Josephine Loricco (Muhlenberg College)
• Jacqueline Gerson (Cornell University)
• Greeshma Gadikota (Columbia University)
• Buz Barstow (Cornell University)
• Amber Morey-Lanza (Beech-Nut)
• Harkamal Walia (University of Nebraska-Lincoln)
• Martina Ralle (Oregon State University)
• Margaret Frank (Cornell University)

SESSION TOPICS

• Plant nutrient homeostasis and transport
• Plant responses to environmental stress, pathogens, and emerging materials (e.g., nanoparticles)
• Plant–soil interfaces and biogeochemical cycling
• Nutrient cycling in aquatic systems
• Plants and critical minerals
• Food safety and nutritional quality
• Practical approaches to synchrotron measurements for life and environmental sciences

Synchrotron X-rays for Metals in Plants, Soils, and Environmental Systems: Early Science and Community Building at XLEAP

XLEAP2026_Detailed_Agenda_July20.pdf

Wed, August 5

8:00 AM Registration and breakfast (provided)

1 Welcome

Speakers: Joel Brock, Marcus Smolka, Olena K Vatamaniuk (Cornell University), Xingen Lei

2 Introduction to XLEAP

Speaker: Louisa Smieska

Fundamental processes in plant nutrient homeostasis

Chair: Mary Lou Guerinot

3 Plant interactions with soil composition in the extremophile Arabidopsis halleri

All ecosystems on land rely on plants to manage nutrient balancing in soils containing variable and largely non-optimal bioavailable levels of essential and non-essential inorganic compounds. Our research aims to understand the molecular and physiological mechanisms of the underlying physiological acclimations and evolutionary adaptations in plants. Arabidopsis halleri is a characteristic member of metallophyte plant communities found on soils containing toxic levels of the heavy metals zinc, cadmium, lead, and sometimes copper. In both polluted and pristine unpolluted habitats, natural populations of A. halleri are unusual in their ability to hyperaccumulate zinc and cadmium in their above-ground tissues at concentrations that are one or more orders of magnitude above the critical toxicity thresholds of ordinary plants. We confirmed exceptionally large edaphic and ionomic ranges across European A. halleri based on a biodiversity resource of ca. 1,000 accessions collected in the field. These A. halleri individuals are edaphically and ionomically indexed, meaning that the elemental composition of leaves and rhizosphere soil is known for each genotype at its site of origin. We address natural variation within A. halleri and compare across species with the closely related well-studied reference organism A. thaliana, a non-accumulator species exhibiting merely basal heavy metal tolerance which is common to all plants. We conducted genome-wide association mapping using our A. halleri collection, and we also mapped quantitative trait loci in segregating populations of targeted crosses between phenotypically contrasting individuals. I will present exemplary results highlighting the gap of knowledge between the molecular-cellular functions of decisive protein variants and associated phenotypes at the whole-plant level, which could be bridged through the localized quantification of metals and their chemical speciation. Our results can educate the improvement of crop safety and the development of plant-based technologies such as phytomining and phytoremediation.

Speaker: Ute Kraemer (Ruhr University Bochum)

4 Connecting mineral nutrient homeostasis to fertility and crop yield through synchrotron-based XRF microscopy

Advances in imaging technologies have opened new avenues for understanding the physiological basis of plant reproduction. Here, we apply synchrotron-based X-ray fluorescence (XRF) microscopy to investigate the spatial distribution of essential micronutrients, particularly copper (Cu), during reproductive development. Cu deficiency affects approximately 30% of arable land and significantly limits crop yield, yet the mechanisms by which Cu supports fertility remain poorly understood. By combining XRF imaging techniques with molecular genetics, we show that two transcription factors, Squamosa Promoter Binding Protein-Like 7 (SPL7) and Copper-Deficiency Induced Transcription Factor 1 (CITF1), are required for reproductive success in Arabidopsis thaliana. Using high-resolution XRF mapping and XRF-computed tomography, we find that the citf1 spl7 double mutant exhibits severely depleted Cu levels in flowers, particularly in pistils, anthers, and pollen grains, leading to both female and male infertility. We further demonstrate that the CITF1–SPL7 regulatory pathway is essential for stigma development, pollen viability, germination, seed Cu distribution, and embryo formation. Extending these findings to Brachypodium distachyon, we show that Cu delivery to florets is similarly critical for fertility, grain quality, and yield. This work highlights the power of synchrotron-based imaging to elucidate micronutrient function in reproductive biology and offers insights into improving crop fertility and resilience under Cu-deficient conditions.

Speaker: JU-CHEN CHIA

10:30 AM Coffee break

Fundamental processes in plant nutrient homeostasis

Chair: Mary Lou Guerinot

5 A tomato under the beam: Tackling the challenges of fresh-tissue SXRF analysis [virtual]

Synchrotron X-ray fluorescence (SXRF) is a powerful technique for investigating element distribution in plant tissues. However, the analysis of fresh, highly hydrated samples remains challenging, as water can attenuate fluorescence signals and dehydration during data acquisition may alter tissue structure and elemental distribution. While substantial anatomical and structural heterogeneity already complicates SXRF analyses of fresh roots, stems, and leaves, fleshy fruits pose an additional challenge due to their high water content. The combined effects of tissue hydration, structural fragility, and prolonged acquisition times hinder the development of robust sample-preparation protocols, thereby limiting the use of SXRF in horticultural fruit research. The aim of this work was to optimize sample preparation protocols for SXRF analysis of fresh tomato tissues, including roots, stems, leaves, and fruits. A range of preparation strategies was evaluated, including different mounting approaches, heat- and freeze-drying treatments, and hydration-preservation methods adapted to each tissue type. Protocol performance was assessed at the CHESS Facility at Cornell University according to sample stability during acquisition, resistance to dehydration, preservation of tissue morphology, and the quality of the resulting elemental maps. The optimized protocols enabled the acquisition of high-quality SXRF datasets from fresh tomato tissues with minimal dehydration-induced artifacts. Both heat-dried and freshly prepared fruit samples consistently revealed a Cu accumulation pattern associated with the pericarp vasculature across five tomato species, suggesting a possible link between Cu distribution, vascular lignification, and fruit firmness. High-quality elemental maps were also obtained from fresh leaves. In contrast, although the protocols developed for seedling roots and stems effectively maintained sample hydration, achieving an optimal balance between tissue preservation and spatial resolution remained challenging.
These findings provide practical guidelines for SXRF analysis of hydrated plant tissues and expand the applicability of synchrotron-based elemental imaging to fresh horticultural crops.

Speaker: Dr Paco ROMERO (Postharvest Physiology and Biotechnology for Food Sustainability Lab. Institute of Agrochemistry and Food Technology (IATA-CSIC), Paterna, Valencia, Spain.)

6 Toward multimodal synchrotron imaging of pollen wall development in Arabidopsis [virtual]

The spore and pollen wall is among the most chemically complex and resilient biological materials, yet its composition and assembly remain poorly understood. Although genetic studies have identified many enzymes and transport pathways required for pollen wall development, the chemistry of sporopollenin remains debated, and the developmental processes linking biosynthesis, transport, and polymer assembly have remained largely inaccessible. Here, we present a multimodal synchrotron imaging framework to investigate pollen wall development within Arabidopsis thaliana anthers. Using cryosectioned anthers spanning key stages of pollen wall formation, we combined synchrotron mid-infrared (S-IR) spectromicroscopy with optical photothermal infrared (O-PTIR) spectroscopy to characterize chemical changes within the native anther environment. Principal component analysis of S-IR spectra resolved stage-specific chemical signatures that revealed progressive changes in molecular composition during sporopollenin deposition. Complementary O-PTIR measurements provided higher spatial resolution, enabling localized chemical features associated with the developing pollen wall to be examined. These approaches capture chemical transitions that are inaccessible using conventional analyses of isolated mature pollen. Beyond revealing the chemistry of pollen wall formation, this work establishes a multimodal imaging framework for studying complex metabolic and developmental processes in plants within their native spatial context. Building on this framework, ongoing integration of synchrotron X-ray fluorescence microscopy will provide complementary elemental information at cellular and tissue scales, creating opportunities to relate molecular and elemental dynamics during pollen wall development. These complementary approaches establish a foundation for linking genetic models of sporopollenin biosynthesis with their chemical outputs in situ and illustrate the broader potential of emerging multimodal synchrotron imaging platforms such as XLEAP to investigate complex developmental processes in plants.

Speaker: Teagen Quilichini (University of Saskatchewan)

7 Transgenerational effects of water limitation on seed morphology, ionome, and performance under nutrient limiting conditions [virtual]

One of the most damaging effects of drought on plants and crops is the reduction in yield and quality of seeds. Little is known, however, about the morphological changes happening in seeds at the cellular level when plants experience water limitation. And these changes include seed quality, composition, and offspring performance when the parental lines experience water limitation stress. Here we used electron microscopy and 3D X-ray tomography - two non-destructive high-definition phenotyping approaches - to evaluate the morphology and anatomy of well-watered and water-limited Arabidopsis seeds. When Arabidopsis plants grow under water limitation, plants produce a reduced number of seeds. Notably the reduction in seed number is also accompanied by a disarrangement of cell size and number. Interestingly, seeds from plants experiencing water limitation displayed lower number of cells but their size and volume were significantly different compared to well-watered plants. We also evaluated the performance of seeds, stressed or not, under different nutritional deficiencies and we found that seeds from plant experiencing water limitation had lower performance compared to well-watered plants. At the meeting we will further discuss our phenotyping and physiological approaches to understand the mechanistic basis of transgenerational effects of water limitation on seed biology.

Speaker: Prof. David Mendoza-Cozatl (University of Missouri)

11:45 AM Lunch (provided)

Plant–soil interfaces and biogeochemical cycling

Chair: Tiina Roose

8 Unraveling Dynamic Iron Regulation at the Plant–Microbe Interface

Iron is an essential micronutrient that supports core metabolic and defense processes in plants, yet its accumulation must be tightly controlled because excess iron promotes oxidative damage. In the rhizosphere, iron availability also profoundly influences plant–microbe interactions, creating a fundamental challenge for roots that must simultaneously acquire iron from the soil, maintain intracellular and organismal iron homeostasis, and restrict access to iron during immune responses. Understanding how plants coordinate these competing demands requires approaches capable of resolving iron dynamics across spatial and temporal scales. Our recent work has revealed multiple layers of regulation that coordinate iron homeostasis with immune signaling in roots. During sustained iron deficiency and microbial challenge, immune activation suppresses iron acquisition through spatial regulation of the iron deficiency signaling peptide IMA1, thereby limiting iron mobilization in the rhizosphere. In contrast, at much earlier timescales, perception of bacterial flagellin triggers rapid changes in intracellular iron availability that are coupled to receptor trafficking, membrane nano-clustering, and immune signaling of the receptorkinase SRF3. Together, these mechanisms enable roots to balance nutrient acquisition with defense while maintaining cellular iron homeostasis. These findings highlight both the importance and the difficulty of measuring highly dynamic metal distributions in living tissues. I will discuss our findings and emerging current bottlenecks in quantifying iron dynamics in plants and explore how emerging synchrotron- based approaches, including high resolution elemental mapping and chemical speciation analyses, could help elucidate the complex interactions of roots, iron and microbes.

Speaker: Wolfgang Busch (Salk Institute for Biological Studies)

9 Mycorrhizal-Bacterial Interactions and Resource Fluxes at the Plant-Soil Interface

Interactions between roots and soil microorganisms regulate resource movement through terrestrial ecosystems, influencing plant productivity, stress tolerance, and global biogeochemical cycling. Our research focuses on arbuscular mycorrhizal fungi—ubiquitous root symbionts that enhance plant nutrient acquisition while distributing plant-derived carbon below ground. Because these processes occur on fine spatiotemporal scales within a complex matrix, many biologically meaningful responses are difficult to detect using bulk soil measurements or traditional DNA sequencing approaches alone. We combine stable isotope tracing (15N, 13C, and 18O), genomics, and imaging to quantify resource dynamics in the rhizosphere and hyphosphere—the zones of soil influenced by roots and fungal hyphae. These methods allow us to identify the specific organisms involved in resource transfer, quantify their contributions to ecosystem processes, and reveal biological responses that would otherwise remain obscured. In this presentation, I will highlight how synergistic interactions between mycorrhizal fungi and free-living soil microorganisms enhance plant nitrogen acquisition from organic matter, and how mycorrhizal fungi facilitate the transfer of plant-derived carbon to soil bacterial communities, increasing their drought tolerance. Finally, I will discuss how synchrotron-based X-ray imaging and spectroscopy can complement these approaches by resolving the microscale distributions of roots, microbes, minerals, and organic matter—ultimately connecting resource dynamics at the plant-soil interface with ecosystem-scale biogeochemical cycling.

Speaker: Rachel Hestrin (University of Massachusetts Amherst)

10 Root-secreted Coumarins Increase Phosphorus Bioavailability to Plants through Reductive Dissolution of Iron

The essential nutrient phosphorus often has low bioavailability in soils because of adsorption to iron minerals. This can be especially problematic in agricultural soils, where large amounts of “legacy” phosphorus accumulate. Eudicot plants are known to access iron by secreting redox-active organic molecules, e.g. coumarins, from their roots. However, the ability of these metabolites to desorb phosphorus from the surfaces of iron minerals has not been explored. To test this, we reacted phosphate-doped ferrihydrite with fraxetin, a widely produced coumarin, across soil-relevant pH and oxygen gradients. Fraxetin solubilized both phosphorus and iron at every tested pH in anoxic experiments but was ineffective at high pH in the presence of oxygen. We also used P XANES to determine whether this reaction changed the bonding environment of phosphorus; after 48 hours, no changes were detected. Next, we tested differences in tissue nutrient concentrations between coumarin-producing wild type Arabidopsis thaliana and a coumarin-deficient A. thaliana mutant to determine whether our abiotic results translated to enhanced iron and phosphorus bioavailability. Plants were grown in potting soil amended with varying concentrations of ferrihydrite, to tune phosphorus availability, and calcium carbonate, to tune iron availability. Coumarin production improved tissue iron content in high pH soils; in low pH soils, coumarin production increased tissue phosphorus content. We also used XRF microprobe analysis to investigate the distribution and speciation of iron and phosphorus in the rhizosphere of coumarin-producing and coumarin-null plants. Phosphorus-rich iron phases were concentrated on the outside of roots relative to bulk soil, suggesting that root mucilage has an important role in entraining these nutrient sources in accessible locations. This work shows that coumarins increase phosphorus bioavailability via the reductive dissolution of iron minerals, enhancing our understanding of the strategies plants employ to access soil phosphorus.

Speaker: Christopher Schuler (Massachusetts Institute of Technology)

11 Tracing Mineral Copper Acquisition in Grasses through Imaging and Reduction Kinetics

Understanding the uptake and localization of micronutrients in plant-soil systems is essential for improving crop nutrient efficiency and agricultural production. Copper (Cu) is an essential micronutrient required for fertility and grain production in grasses; however, its limited solubility in soils restricts plant acquisition and complicates efforts to understand Cu bioavailability in the rhizosphere. We investigated matrix-dependent Cu uptake in the model grass species Brachypodium distachyon by combining synchrotron-based imaging with physiological assays.
Synchrotron μXRF analyses of root and shoot tissues from plants grown in CuO-amended soil demonstrated that Brachypodium acquires and redistributes Cu from sparingly soluble mineral sources. Complementary μXRF and μXRD measurements of intact roots growing in CuO-amended field soil further demonstrated the utility of simultaneously mapping elemental distributions and mineral phases to investigate Cu localization at the soil-root interface.
To investigate the physiological basis of mineral-associated Cu uptake, we performed time-resolved spectrophotometric analyses of Cu(II) reduction by intact Brachypodium roots using CuO and Cu-citrate. These assays revealed matrix-dependent differences in Cu reduction kinetics, with reduction activity enhanced under Cu deficiency and exhibiting saturation behavior consistent with a finite, enzyme-like reduction capacity. Together, these complementary approaches link Cu distribution in complex soil environments with a candidate physiological mechanism for Cu acquisition, providing new insight into matrix-dependent Cu uptake in grasses and demonstrating the value of multimodal synchrotron imaging for investigating plant-soil interactions.

Speaker: Luna Natoli (Cornell University)

2:15 PM Coffee break

Metals and nutrient cycling in aquatic systems

Chair: Arthur Woll

12 Cell Wall Architecture and Dynamics in the Streptophyte Alga, Penium margaritaceum

Salt stress is one of the major and most common challenges that confront plants, and also would have been a major stressor during the colonization of land by Streptophyte algae ~500 million years ago. Penium margaritaceum is one of the closest known algal relatives to land plants, and its cell wall closely resembles the primary cell wall of higher plants. The inner layer of the cell wall is composed of cellulose, which is the major structural component of the cell wall. The outer layer is composed mainly of pectin (homogalacturonan), which cross-links with calcium to form a rigid lattice-like structure. Treatment of Penium with various salts has been shown to disrupt pectin architecture, possibly due to incorporation of different metal ions into the cell wall. Structural insights into cell wall composition, dynamics, or repair in Penium may also provide insights into the cell walls of land plants and/or their evolution. Additionally, if algae such Penium, are able to incorporate metals besides calcium into their cell wall, this could provide a possible bioremediation strategy.

Speaker: Josephine LoRicco (Muhlenberg College)

13 Selenium exposure differentially influences methylmercury retention in mayflies

High concentrations of mercury and selenium are individually toxic to organisms. However, it is proposed that high levels of environmental Se can reduce Hg bioaccumulation and biomagnification in aquatic food webs, though this potential interaction has been under-studied in aquatic macroinvertebrates. We examined the proposed effect of selenium on methylmercury accumulation, along with the transfer of methylmercury, between four lifestages for a parthenogenetic mayfly (Neocloeon triangulifer). We found support for the mercury-selenium interaction hypothesis, but it is context-specific. At high dietary methylmercury, elevated aqueous selenium lowered mayfly methylmercury concentrations; however, at low methylmercury treatments, there was no effect of selenium on mayfly methylmercury accumulation. Additionally, though we found higher methylmercury concentrations in terrestrial adult lifestages compared to aquatic larval lifestages at both methylmercury treatment levels, the cumulative life history transfer factor (the ratio of methylmercury in the final adult imago stage compared to late instar larvae) differed by treatment. These results suggest predators of adult mayflies would be exposed to greater methylmercury than predators of larval mayflies for all selenium and methylmercury levels, but that the ameliorative effect of selenium on methylmercury accumulation only occurs at high dietary methylmercury levels. To date, this research has focused on the use of mercury and selenium concentrations; this talk will highlight ways in which CHESS capabilities can be leveraged to better understand the fundamental mechanisms of mercury and selenium interactions within these systems.

Speaker: Jacqueline Gerson (Cornell University)

14 Imaging Elements in Fish “Hard Parts” To Make Discoveries About Their Secret Lives [virtual]

Fish bodies contain numerous sclerochronological structures that have been used for routine age determination (from annual increment deposition) and increasingly, to study elemental and isotopic composition for life history interpretation. The most widely used structures are otoliths (literally, ear-stones), made of aragonite (CaCO3) precipitated on a protein framework, that are part of the hearing/balance system in modern fishes. We have been studying these with synchrotron Scanning X-ray Fluorescent Microscopy (SXFM) since 2003, beginning at CHESS. Otoliths take up trace elements throughout life, and the visual annual zonations put a time-stamp on key life history events. Thus, we can use strontium to track migration histories and manganese to document hypoxia exposure events. We can combine this information with biological data such as fish size and body condition to document environmental impacts.
In addition to otoliths, the community is now studying trace elemental chemistry of eye lenses of fishes as a complement to otoliths. At CHESS we discovered that mercury is readily taken up in lenses as the fish grow, providing lifetime chronologies of this toxic substance. Moreover, because lenses are made of crystallin proteins, we can also analyze light stable isotopic composition over time, to interpret such things as provenance and trophic status through time. It is now possible, for example to take the lens of an adult predatory fish and determine its size and age when it became piscivorous (preyed on other fish).
We provide examples here of trace elemental SXFM mapping conducted at CHESS and the Australian Synchrotron, and also mappings made with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), which can quantify elements not possible with SXFM due to interferences. Both methods have pro’s and con’s. A possible forefront is in-situ characterization of key proteins, such as reproductive and stress proteins, in both lenses and otoliths.

Speaker: Karin Limburg (SUNY College of Environmental Science and Forestry)

3:45 PM Break- coffee and tour logistics

4:00 PM Walk to CHESS for tours

Tours of CHESS

NOTE: Please wear closed toe shoes for the CHESS tour. The tour will involve walking from Bradfield to Wilson Lab (~10 minutes), stairs, and duck-unders.

Banquet dinner

Thu, August 6

8:30 AM Breakfast (provided)

15 Announcements

Plants under stimuli (environmental stress, nanoparticles, pathogens)

Chair: Jose A. Hernandez-Viezcas

16 Toward Live Elemental Imaging of Anoxia Responses in Plants

Oxygen deprivation triggers rapid physiological and biochemical changes in plants, including alterations in ion homeostasis and nutrient redistribution. However, most elemental imaging approaches require harvested tissues and therefore provide only static snapshots of these dynamic processes. We are developing experimental approaches for live synchrotron-based elemental imaging of intact plants during anoxia and recovery. Our goal is to directly visualize temporal changes in elemental distribution, with particular emphasis on calcium and other elements implicated in low-oxygen signaling and stress adaptation. Initial studies focus on maintaining plant viability during imaging, integrating controlled oxygen environments with X-ray fluorescence measurements, and assessing the feasibility of repeated imaging through time. We will present our experimental design, technical challenges, and preliminary observations as a foundation for future studies examining elemental dynamics during plant responses to oxygen deprivation.

Speaker: Kendal Hirschi

17 Exploring plant-environment interactions through multimodal imaging at SSRL

Plants’ responses to external stimuli are highly complex coordinated events that depend on the plant species, genotype, and developmental stage, as well as the strength and duration of the stimuli. In addition, the responses occur on a scale ranging from molecular to organismal level, often resulting in emergent properties that require data with a clear spatial component. Attempts to analyze imaging data with spatial information across platforms face challenges such as incompatible sample preparation methods, incompatible data resolution and type, resulting in difficulties in data alignment. The Stanford Synchrotron Radiation Light Source at SLAC National Accelerator Laboratory is developing a multimodal imaging pipeline that allows for correlative imaging of samples across X-ray fluorescence, Fourier transformed infrared and brightfield image capture. In addition, as part of the multi-institute AIMS-LEAF (AI-driven Multimodal Science for Linking gEnotype to Phenotype) program, we aim to integrate AI/ML with multiscale multimodal imaging and sequencing data to predict heat stress tolerance in Arabidopsis thaliana. The project will connect genotype to phenotype across treatment conditions and developmental stages for the creation of a more accurate model of plant heat stress response. Development of multimodal imaging pipeline in this project can provide high resolution spatial information of the fluxes in plant ion homeostasis and changes in biochemistry in response to heat stress across platforms, allowing alignment of specialized tissue and cell types. The simultaneous collection of RNA from the adjacent tissue / organs is used to link the fluxes observed to gene expression, which will improve the model for systemic plant abiotic stress response and may produce novel insights in stress tolerance mechanisms.

Speaker: Shuxiao Zhang (SLAC National Laboratory)

18 Meeting at the Gate: The Role of Root Barriers in Microbe-Induced Resistance

Beneficial root–microbe interactions enhance plant growth and stress resilience, including the establishment of a primed immune state known as Induced Systemic Resistance (ISR). Although ISR is typically assayed through leaf responses, its establishment begins in roots, where the cues that gate successful systemic protection remain poorly understood.

Iron (Fe) is a key element for ISR establishment and sits at the intersection of nutrition and immunity. As an essential cofactor for core metabolic processes, Fe is actively contested by hosts and microbes, and its limitation can itself activate components of the ISR transcriptional program.

Here, we asked how labile Fe pools and root barrier dynamics interact, from root microbial colonization to ISR competence. Using Trichoderma as a model beneficial fungus, we investigate the genetic regulation of Trichoderma-mediated ISR against foliar challenge in both Arabidopsis and tomato. We specifically focus on the convergence of ISR and Fe-dependent responses. During colonization, a dynamic remodeling of root apoplastic barriers is accompanied by redistribution of Fe pools across tissues, indicating coordinated changes in barrier state and Fe partitioning. Our results indicate that beneficial microbes reprogram root barrier properties and Fe homeostasis to create the spatial and chemical context necessary for systemic immune competence, linking nutritional immunity, cell wall dynamics, and microbe-mediated defense across species.

Speaker: Valeria Castaldi (Yale University)

19 Foliar application of Nanoscale Iron and Manganese Micronutrients in full life cycle of Soybean (Glycine Max) [virtual]

Iron (Fe) and manganese (Mn) are essential micronutrients for soybean growth, playing critical roles in chlorophyll biosynthesis, photosynthesis, enzyme activation, and antioxidant defense. However, limited availability of these nutrients in soil often reduces the effectiveness of conventional fertilizers. Foliar application provides a direct and efficient route for nutrient delivery, while nano fertilizers have emerged as promising alternatives due to their high surface area, enhanced plant uptake, and controlled nutrient release. This study investigates the foliar application of Mn₃O₄, Fe₃O₄, and MnFe₂O₄ nanoparticles (15–30 nm) throughout the complete life cycle of soybean plants. The nanoparticles were comprehensively characterized using X-ray diffraction (XRD), dynamic light scattering (DLS), UV–Visible spectroscopy, Fourier-transform infrared spectroscopy (FTIR), and synchrotron-based X-ray techniques at the Cornell High Energy Synchrotron Source (CHESS) to confirm their physicochemical properties and in plant distribution. Plant physiological performance was evaluated using SPAD chlorophyll measurements and LI-COR gas exchange analysis, while elemental uptake was quantified by elemental analysis. The effects of nanoparticle treatments on chlorophyll content, photosynthesis, stomatal conductance, protein accumulation, elemental uptake, and antioxidant enzyme activities (SOD, APX, and CAT) were compared with conventional Fe and Mn salts. This integrated physiological, biochemical, elemental, and synchrotron imaging approach provides a comprehensive evaluation of Fe- and Mn-based nano fertilizers as sustainable strategies to enhance soybean productivity, nutritional quality, and resilience to environmental stress.

Speaker: Sharif Uddin Ahmed (UNIVERSITY OF TEXAS AT EL PASO)

10:45 AM Group photo

11:00 AM Coffee break

Plants and critical minerals

Chair: Vibha Kalra

20 The Microbe-Mineral Atlas and Biomining Critical Elements [virtual]

Creation of a new sustainable energy infrastructure, carbon sequestration, advanced electronic and computer technologies, and advanced defense technologies all mean that the demand for metals is increasingly rapidly. But traditional mining technology can be highly environmentally damaging. This means that the supply chains for many critical metals and semiconductors stretch through unstable parts of the world, leaving them vulnerable to disruption and exploitation.

Biomining with Acidithiobacillus species already supplies about 20% of the world’s copper and 5% of its gold through an iron-specific redox process. However, there are no industrially-used microbes for any of the 30 or 40 other critical elements. This means that we will need to build microbes to enable bioprocesses to mine these elements with synthetic biology. However, we do not understand the basic science of how microbes interact with metals and minerals sufficiently to guide this engineering.

My lab has characterized the genome of the mineral-dissolving microbe Gluconobacter oxydans and discovered the genetic systems that enable it to mine rare earth elements. We have used this new knowledge to create a roadmap for engineering G. oxydans that has already improved biomining of REE by up to 1,200%. Furthermore, we engineered the hyper-engineerable microbe Vibrio natriegens to separate adjacent heavy lanthanides, leap-frogging solvent extractions.

However, this still leaves over 20 other critical elements that we need build microbes for. To build the basic knowledge for this, my lab has started the Microbe-Mineral Atlas to catalog metal and mineral-interacting microbes from around the US, and hopefully the world.

Finally, I will discuss some of the barriers that our current model of technology transfer poses to development of new technologies, what we have done to solve this problem, and some recent successes in starting REEgen for biomining rare earth elements, and Forage Evolution to develop hyper-engineerable microbes.

Speaker: Buz Barstow (Cornell University)

21 Advances in Simultaneous Reduction and Nitriding of Iron Oxides using Ammonia by Harnessing Operando Cross-Scale X-Ray Scattering Measurements [virtual]

Ammonia is the molecular foundation of the global food system, supplying the nitrogen fertilizer that sustains roughly half the world's population — yet its synthesis consumes an estimated 1–2% of global energy. Iron nitrides are earth-abundant materials central to greening this nitrogen economy: candidate catalysts for nitrogen reduction and ammonia synthesis, ammonia decomposition for hydrogen storage, and rare-earth-free magnets. Each function demands phase-selective control over iron nitride formation, requiring a mechanistic understanding of how iron oxides are simultaneously reduced and nitrided.

Departing from multi-step reduction using carbonaceous resources followed by nitriding, we develop a single-step pathway using ammonia as both reducing and nitriding agent — cheaper to transport than hydrogen and uniquely enabling simultaneous reduction and nitriding to tailor metallic versus nitride products in one step. Using Fe₂O₃ as a case study, we apply operando USAXS/SAXS/WAXS to resolve these poorly understood coupled kinetics from sub-nanometer to micrometer scales, tracking phase evolution alongside morphology relevant to scale-up.

Reducing Fe₂O₃ in ammonia at 500–800 °C reveals a temperature-independent pathway but a temperature-dependent product. Reduction proceeds Fe₂O₃ → Fe₃O₄ → FeO; FeO is then reduced and nitrided to Fe₄N, which decomposes to Fe. Temperature tunes the reduction–nitriding balance: incomplete reduction with mixed Fe/Fe₄N/Fe₃N at 500 °C, single-phase Fe₄N at 600 °C, a Fe/Fe₄N mixture at 700 °C, and pure Fe at 800 °C. USAXS shows agglomeration only at 600–800 °C, with the smoothest surfaces for single-phase products.

This work shows the iron product can be tailored by composition and morphology, establishing operando cross-scale scattering for scale-up of ammonia-based reduction–nitriding. Both materials and method feed back into sustainable-nitrogen technologies: the iron nitrides here are catalyst candidates for greening ammonia — and therefore fertilizer — production, while the scattering approach transfers to nitrogen speciation and metal cycling in soils and plants.

Speaker: Greeshma Gadikota (Columbia University)

12:15 PM Lunch (provided)

22 Discussion of operations

Speaker: Joel Brock

Plants and food safety and nutritional quality

Chair: Olena Vatamaniuk

23 Synchrotron XRF-based analyses of minerals distribution in tef (Eragrostis tef) seeds and transgenic Arabidopsis and rice expressing tef Iron-responsive genes [virtual]

Tef (Eragrostis tef) is the most important cereal crop in the Horn of Africa, especially in Ethiopia and Eritrea, where it has been a staple for over 6000 years. Tef is a nutrient-dense crop containing high levels of micro (Fe, Mn, Zn) and macro (Ca, Mg) nutrients. However, the spatial distribution of mineral nutrients in tef seeds has never been analyzed before. By using the synchrotron-XRF microscopy, we determined the mineral distribution in seeds of various tef genotypes. Our findings showed that micronutrients are predominantly localized in tef seed embryos while macronutrients (Ca, K) are localized in both the seed coat and embryo. We also identified homolog of the iron-regulated transporters1 in tef (EtIRT1) and nicotianamine synthase2 (EtNAS2) genes via transcriptome analysis. Heterologous expression of the EtIRT1 and EtNAS2 in transgenic Arabidopsis increased Fe accumulation in the biomass and seeds in plants expressing both EtIRT1 and EtNAS2, while in rice, EtIRT1 expression increased Fe accumulation in the biomass only. We observed increased accumulation of micronutrients in transgenic Arabidopsis expressing the tef gene. In Arabidopsis seeds, Fe is preferentially localized in the vascular tissues of the hypocotyl and the cotyledons while Mn and Zn are localized in the cotyledon, and Cu is more concentrated in the embryo. Whereas in rice seeds, Fe, Mn and Zn are preferentially localized in the embryo with no marked difference between the wildtype and EtIRT1 expressing lines. This study reports the spatial distribution of minerals nutrients in seeds of the orphan crop tef for the first time, offering valuable information for future biofortification strategies.

Speaker: Ayalew Osena (University of North Carolina Greensboro)

24 A novel μXRF based approach to mapping Fe Absorption across the small intestine (Gallus gallus)

Iron deficiency remains the most prevalent micronutrient deficiency globally, affecting over 2 billion people, driven largely by reliance on cereal staple foods that are inherently low in bioavailable Fe. Biofortification, the enhancement of a crop’s endogenous nutrient content and bioavailability, is increasingly recognized as an effective strategy to combat Fe deficiency. While much research has focused on increasing total Fe content in cereal crops, an alternative approach targets the bioavailability of Fe already present in the grain. Nicotianamine (NA), a Fe chelator ubiquitous in cereal grains, has emerged as a key target for this strategy. Our group, in collaboration with the University of Melbourne, has demonstrated that NA-biofortified wheat enhances Fe bioavailability in vitro and in vivo (Gallus gallus) models. While poorly understood, the mechanism underlying this effect is hypothesized to involve an alternative intestinal absorption pathway. It is hypothesized that NA binds Fe to form a stable NA-Fe chelate which bypasses classical Fe(II) uptake via metal transporters in the duodenum, and therefore absorbed more distally via amino acid transporters in the jejunum. Under this framework, NA mediated uptake provides a “physiological safety net” where Fe that escapes proximal absorption is readily chelated by dietary NA and absorbed further along the intestine; thereby enhancing its bioavailability. Spatially resolving the distribution of Fe across the small intestine using μXRF would provide novel and direct evidence for the relevance of this pathway, specifically allowing the investigation of whether the addition of NA to Fe(II) shifts the pattern of Fe more distally. However, the techniques and considerations required to map Fe across the entirety of an animal’s small intestine via μXRF have not been established. This preliminary study therefore aimed to develop and validate these techniques as a necessary foundation for subsequent experiments investigating the mechanistic basis of NA-enhanced Fe bioavailability.

Speaker: Eliot Dugan (Cornell University)

25 The atomic- and molecular underpinnings by which exposure to the anthropogenic exposome impacts food quality.

Perfluorodecanoic acid (PFDA) ingestion is associated with liver, immune, developmental, and reproductive effects. Nevertheless, the molecular mechanisms underlying PFDA toxicity remain poorly understood. For example, despite its established presence in human milk, cow milk, and infant formula, its molecular interactions with constituent proteins and their consequences require further study. Here, we report the outcomes associated with the interaction between PFDA and α-lactalbumin (ALAC), a calcium-binding whey protein essential for nutrition and lactose production. Absorbance and Trp fluorescence data reveal PFDA-dependent changes consistent with interactions that perturb the native disposition of the optically active chromophores. Deconvolution of the amide I region of PFDA: protein IR spectra suggest dose-dependent distortions of PFDA in helical and sheet topologies. Ca2+-binding kinetics suggest that the “forever” chemical compromised metal-ion binding to the protein in a dose-dependent manner, reflecting impaired metal-dependent structural stabilization from the molten-globule-like apo-state to the native and biologically active holo-state. Molecular dynamics simulations identified two preferential PFDA binding regions enriched in hydrophobic and positively charged residues and showed that local rearrangements in ALAC’s unstructured N-terminus coils can generate tightly bound PFDA states with favorable interaction energies. Combined, these results reveal a coherent molecular mechanism in which PFDA anchors to the ALAC surface, disrupts secondary structure organization, and weakens Ca2+ binding. Considering ALAC’s role in early infant nutrition and human health, these findings provide a mechanistic insight into how PFAS exposure may compromise protein function in the postnatal environment.

Speaker: Mahesh Narayan (The University of Texas at El Paso)

26 Keeping Babies Safe from Farm to Table: Food and Plant Science’s Role in Baby Food Manufacturing

Environmental and chemical contaminants were brought to the attention of baby food manufacturers in the late 2010s when an article was published about heavy metal concentrations found in different jar and tub baby foods. Over the last decade, parents have become increasingly concerned about what contaminants might be found in the food they are feeding their children. The quality team at Beech-Nut understands the concerns of our customers, so we have spent the last decade furthering our understanding of how different crops take up heavy metals from their environment. As we compile additional data over the years, it has become clear that this is a multifaceted issue that requires a broader understanding of farming practices, plant physiology, and processing procedures.

Speaker: Amber Morey-Lanza (Beech-Nut Nutrition)

27 Characterizing Impact of Heat Stress on Rice Nutritional Quality and Safety

Plant response to environmental stresses varies with time and does not uniformly manifest across the entire plant or even specific organs. However, in most cases the phenotypic responses are measured at a single time point and lack spatial resolution. In rice, a staple food for more than half the humans, this phenomenon is evident as the grains develop on the panicle. We have developed a non-destructive 3D imaging approach to capture the dynamic panicle level stress responses over a time course with high spatial resolution. We have applied this technique to rice panicles from diverse accessions to measure their response to heat stress. This has enabled us to identify multiple loci regulating heat stress response by combining digital traits with genome-wide association analysis. Functional characterization of the identified genes is providing mechanistic insights into heat-sensitive pathways that determine the grain nutritional quality in context of variation in high temperature responses. These findings will be discussed in context of human health and food safety.

Speaker: Harkamal Walia

Poster session

28 Chemical biomarker analysis of Desmophyllum dianthus corals in New York Bight Submarine Canyons

Submarine canyons found along the continental shelf of the New York Bight (NYB) are highly dynamic, interconnected ecosystems that serve as critical deep-sea biodiversity hotspots. These deep-sea habitats are increasingly vulnerable to anthropogenic stressors, including commercial fishing, coastal pollution, ocean acidification, and hypoxia. Direct, continuous observation of these remote environments remains a significant challenge. However, chronometric structures, like the skeletons of the long-lived, azooxanthellate coral Desmophyllum dianthus, could provide a valuable long-term record of deep-sea environmental conditions. This study aims to quantify temporal patterns of anthropogenic contamination, ocean acidification, and hypoxia within NYB submarine canyons by analyzing microchemical biomarkers in D. dianthus coral skeletons. Coral specimens were collected from the Hudson Canyon during a NOAA research cruise conducted in September 2025. Utilizing synchrotron-based X-ray fluorescence imaging or laser ablation inductively coupled plasma mass spectrometry, multiple elemental analytes (e.g., B, Mn, Cu, Zn, Pb, U) can be mapped across skeletal growth axes. These trace element-to-calcium ratios can contribute to establishing proxies for pH, dissolved oxygen, and heavy metal accumulation. This study will establish crucial pre-industrial baselines for NYB submarine canyon ecosystems. Ultimately, linking coastal urban development to offshore benthic impacts will improve our understanding of deep-sea ecology and inform robust conservation strategies for these vulnerable habitats.

29 Exploring the Role of ACA8 and ACA10 in Ion Homeostasis

The mechanisms by which plants coordinate intracellular calcium (Ca²⁺) signaling with extracellular Ca²⁺ availability, ion homeostasis, and nutrient compartmentalization remain an open question. In Arabidopsis, ACA8 and ACA10 are two major plasma membrane-localized autoinhibited Ca²⁺-ATPases that mediate Ca²⁺ efflux from the cytosol and altered ACA8 and ACA10 activities leads to changes in intracellular Ca²⁺ levels. Here, we investigate whether these cytosolic Ca²⁺ level changes caused by knockout mutations or overexpression of ACA8 and ACA10 affect extracellular Ca²⁺ reservoirs and the balance of other micronutrient ions. Using synchrotron X-ray fluorescence microscopy (SXRF) and inductively coupled plasma mass spectrometry (ICP-MS), we mapped spatial ion distribution and quantified elemental abundance across leaf tissues. We found increased Ca²⁺ abundance in both aca8 aca10 and ACA8-overexpression, as well as opposite changes in iron abundance between the two genetic backgrounds. These observations suggest that perturbed Ca²⁺ homeostasis may be accompanied by broader changes in the balance of micronutrients including iron, which is closely linked to plant stress and immune responses. Together, this study provides preliminary insight into the role of intracellular Ca²⁺ status in modulating extracellular ion homeostasis and stress adaptation.

30 Identification and characterization of putative mitochondrial copper transporters in Arabidopsis

Copper (Cu) is an important micronutrient essential for plant growth, development, and reproductive success. In recent years, significant progress has been made toward elucidating the mechanisms of copper uptake and transport in plants. However, many gaps remain in the intracellular trafficking of Cu. In mitochondria, Cu is indispensable for mitochondrial respiration as a cofactor of electron transport chain for ATP production, but the mitochondrial copper import and export in plants is poorly understood. Here, we investigate a putative mitochondrial Cu transporter family (PHT3) in Arabidopsis and explore its function, expression, and subcellular localization. We found that PHT3;1 is expressed in the rosette leaves and flowers, PHT3;2 is predominantly expressed in mature leaves, whereas PHT3;3 is highly expressed in the flowers. Importantly, heterogenous expression of the PHT3 family members partially complemented copper-related growth defect of the yeast pic2Δ mutant, which lacks the mitochondrial Pi/Cu transporter Pic2. These findings suggest that the Arabidopsis PHT3 family is involved in mitochondrial Cu transport. To understand the physiological function of the PHT3 family in planta, we generated Arabidopsis pht3s triple mutant, which exhibited significantly delayed flowering. Our future work will leverage the advanced X-ray fluorescence imaging capabilities at CHESS to investigate Cu distribution in the pht3s mutant and further define the role of PHT3 in mitochondrial Cu homeostasis.

Speakers: Olena Vatamaniuk (Cornell University), Xing Liu

31 Imaging Elements in Fish “Hard Parts” To Make Discoveries About Their Secret Lives

Fish bodies contain numerous sclerochronological structures that have been used for routine age determination (from annual increment deposition) and increasingly, to study elemental and isotopic composition for life history interpretation. The most widely used structures are otoliths (literally, ear-stones), made of aragonite (CaCO3) precipitated on a protein framework, that are part of the hearing/balance system in modern fishes. We have been studying these with synchrotron Scanning X-ray Fluorescent Microscopy (SXFM) since 2003, beginning at CHESS. Otoliths take up trace elements throughout life, and the visual annual zonations put a time-stamp on key life history events. Thus, we can use strontium to track migration histories and manganese to document hypoxia exposure events. We can combine this information with biological data such as fish size and body condition to document environmental impacts.
In addition to otoliths, the community is now studying trace elemental chemistry of eye lenses of fishes as a complement to otoliths. At CHESS we discovered that mercury is readily taken up in lenses as the fish grow, providing lifetime chronologies of this toxic substance. Moreover, because lenses are made of crystallin proteins, we can also analyze light stable isotopic composition over time, to interpret such things as provenance and trophic status through time. It is now possible, for example to take the lens of an adult predatory fish and determine its size and age when it became piscivorous (preyed on other fish).
We provide examples here of trace elemental SXFM mapping conducted at CHESS and the Australian Synchrotron, and also mappings made with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), which can quantify elements not possible with SXFM due to interferences. Both methods have pro’s and con’s. A possible forefront is in-situ characterization of key proteins, such as reproductive and stress proteins, in both lenses and otoliths.

32 Investigating the Role of Copper in Arabidopsis thaliana Reproduction Using X-ray Fluorescence (XRF) Microscopy

It has been known for decades that micronutrient copper is essential for plant growth, development, fertility, and seed yield. However, which plant reproductive organs require copper, how copper is delivered to these structures, and how it acts to ensure fertility is not entirely understood. In this poster I will present my research findings as well as some previous investigations done in the Vatamaniuk Lab derived from Synchrotron x-ray fluorescence microscopy (2D-SXRF) at the nanoscale, 3D and 2D confocal synchrotron x-ray fluorescence microscopy (2D and 3D C-SXRF), Scanning electron microscopy (SEM), Confocal microscopy, Fluorescence/DIC microscopy, etc. These techniques allowed to identify surface alterations, highlight developmental issues, and track the spatial distribution of copper in the floral organs of the model plant Arabidopsis thaliana. I will also briefly mention the role of two transcription factors, CITF1 and SPL7, in controlling copper uptake, delivery to the specific sites in flowers and the impact of these transcription factors on the development of the male and female gametophytes. Our new findings broaden our knowledge of copper's function in plant reproduction and raise the possibility that it may play a signaling role in the development of reproductive organs.

33 Meeting at the Gate: The Role of Root Barriers in Microbe-Induced Resistance

Beneficial root–microbe interactions enhance plant growth and stress resilience, including the establishment of a primed immune state known as Induced Systemic Resistance (ISR). Although ISR is typically assayed through leaf responses, its establishment begins in roots, where the cues that gate successful systemic protection remain poorly understood.

Iron (Fe) is a key element for ISR establishment and sits at the intersection of nutrition and immunity. As an essential cofactor for core metabolic processes, Fe is actively contested by hosts and microbes, and its limitation can itself activate components of the ISR transcriptional program.

Here, we asked how labile Fe pools and root barrier dynamics interact, from root microbial colonization to ISR competence. Using Trichoderma as a model beneficial fungus, we investigate the genetic regulation of Trichoderma-mediated ISR against foliar challenge in both Arabidopsis and tomato. We specifically focus on the convergence of ISR and Fe-dependent responses. During colonization, a dynamic remodeling of root apoplastic barriers is accompanied by redistribution of Fe pools across tissues, indicating coordinated changes in barrier state and Fe partitioning. Our results indicate that beneficial microbes reprogram root barrier properties and Fe homeostasis to create the spatial and chemical context necessary for systemic immune competence, linking nutritional immunity, cell wall dynamics, and microbe-mediated defense across species.

34 Multimodal imaging at LiX for plant and environmental sciences

In the last few years, the LiX beamline at NSLS-II has developed capabilities for scanning imaging and tomography based on both scattering and fluorescence contrasts. This is accomplished using fly-scanning with a typical beam size of 5 microns, and simultaneous data collection on a pair of Pilatus detectors (Dectris) for small- and wide-angle X-ray scattering, as well as two two-channel silicon drift detectors (Rayspec), located on either side of the sample, for X-ray fluorescence. A software pipeline is provided to enable users to extract relevant features from the scattering data as the contrast mechanism for imaging. In addition to characteristic diffraction peaks for well-known materials (e.g. cellulose and starch), these features can also be based on components derived from machine learning algorithms. So far LiX users have published their studies on wood and growing plant stems. More active research is on-going to explore the application of scattering imaging to plant seeds, leaves, roots, as well as soil samples. Scanning imaging is time-consuming, limiting the throughput of user experiments and sometimes resulting in obvious radiation damage to the samples. We therefore have implemented a micro-tomography detector for rapid full-filed imaging of the sample based on absorption contrast, to guide subsequent X-ray scattering and fluorescence data collection. We also plan to pursue correlative imaging on the same samples using chemical imaging techniques to help interpret the scattering data to maximize the information content from multi-modal imaging data collected at LiX.

35 Predicting Spatial Maps of Iron Redox Heterogeneity Using Multi-Energy μXRF

Woodchip samples with varying ferrihydrite surface coatings were incubated under different bulk redox conditions to investigate how iron availability and redox fluctuations affect localized redox gradients and hotspots. The spatial distribution of iron oxidation states in these samples can help identify reducing zones in the wood, with potential implications for understanding the effect of microscale redox heterogeneity on other redox-driven biogeochemical processes such as denitrification. However, resolving the spatial distribution of iron oxidation states is analytically challenging. Although XANES spectra can be used to infer iron oxidation states at individual points, they are not practical to acquire at sufficient granularity to develop two-dimensional maps of iron oxidation state and reveal spatial patterns of redox heterogeneity. Instead, we used multi-energy μXRF maps collected at five energies to register the equivalent of a five-point sparsely sampled XANES spectrum at each pixel. Using a limited number of XANES measurements from each sample, we trained a machine learning model to predict a proxy for iron oxidation state derived from the XANES spectra. The model’s features were constructed from the five-energy μXRF intensities at the pixel corresponding to each XANES measurement. The trained model was subsequently applied to the five-energy μXRF maps for all pixels to predict two-dimensional maps of iron redox-sensitive spectral variation in each sample. This approach can help extend sparse measurements into high-resolution spatial predictions, which could enable future investigation of microscale iron redox heterogeneity in complex environmental samples.

36 Refurbished ID21 beamline (ESRF): novel tools for µ-XRF and µ-XANES data acquisition and processing

The Extremely Brilliant Source (EBS) of the European Synchrotron Radiation Facility (ESRF) is the world’s premier fourth-generation high-energy synchrotron source, offering remarkable flux and coherence that have enabled an unprecedented enhancement in experimental throughput. The ID21 beamline is dedicated to micro- and nano-X ray spectroscopy, offering 2D X-ray fluorescence (XRF) mapping and X-ray absorption spectroscopy (XAS) in the tender X-ray energy range (2.1 - 10.5 keV), which can be combined to provide both 2D elemental mapping and chemical speciation at the point (0D), line (1D), and area (2D) modes. As a beamline optimised for detecting analytes from sodium (Na) to zinc (Zn), as well as the L- and M-edges of heavier elements, ID21 is employed across a wide range of research areas, particularly in environmental and life sciences studies. Following the EBS release, ID21 underwent refurbishment that included a next-generation double-crystal monochromator, enhanced beam stability, and a new X-ray scanning nanoscope (nano-SXM) with improved spatial resolution, detection limits, and acquisition capabilities down to ~ 110 x 100 nm, enabling sub-cellular analysis. The beamline also features a high level of automation, including the user-friendly Daiquiri web-based user interface for sample navigation and measurement programming, automated elemental-map fitting, and in-house workflows built on the Orange data mining framework, which provides comprehensive XANES data handling, including pre-processing (alignment and normalisation), visualisation, and selection of Principal Component Analysis clustering for subsequent linear combination fitting and/or multivariate curve resolution–alternating least squares analyses. Altogether, these features make ID21 beamline the “go-to” for spatially-resolved XRF imaging and XAS in life and environmental studies in Europe. Its robust automation and data processing capabilities allow users to handle large datasets in real time, make informed decisions during beamtime, and streamline post beamtime analysis, ultimately speeding up the acquisition to publication timeframe.

37 Uranium Bioremediation in Water Using Geobacter Sulfurreducens Electroactive Biofilm on Boron-Doped Diamond Electrode Modified with Nano Zero Valent Iron

The demand for uranium (U) has surged due to its role in nuclear energy, agriculture, mining, and military defense. This widespread use leads to uranium entering aqueous environments, raising concerns about its impact on public health and wildlife. In the United States, the tolerance limit for U in drinking water is set at 30 ug/L, with ground water exhibiting the higher concentration of U, primarily in the U(VI) oxidation state. Microorganisms, particularly bacterial like Geobacter Sulfurreducens (GS), have demonstrated the ability to efficiently remove U(VI) due to functional groups in their outer membranes. Yet, it is still unknown how effectively this system can facilitate microbial U(VI) reduction and whether a whole-cell sensor can reliably track this process. This project aims to address these uncertainties by investigating the uranium oxidation states and assessing the feasibility of a whole-cell sensor for U(VI) reduction, contributing to the development of sustainable bioremediation strategies.

38 Urea-to-Ammonia Conversion at Proteus mirabilis Modified Pt‑Ni/BDD Electrodes

The electrochemical conversion of urea rich wastewater into value added products presents a promising strategy for sustainable water treatment, energy generation, and resource recovery for long duration space missions. In this work, boron-doped diamond (BDD) electrodes sequentially modified with nickel and platinum nanoparticles were developed to investigate enhanced urea oxidation and selective ammonia production in the presence of Proteus mirabilis. Nickel was first electrodeposited onto the BDD surface to provide high catalytic activity toward urea oxidation, followed by platinum surface modification to improve electron transfer kinetics, catalytic stability, and ammonia selectivity. The bioelectrochemical system leverages the urease activity of Proteus mirabilis to hydrolyze urea while the Pt–Ni catalytic interface promotes subsequent electrooxidation of ammonia to nitrogen. Electrochemical characterization using cyclic voltammetry showed improved electrochemical surface activity compared to unmodified electrodes. The integrated Pt–Ni–BDD microbial platform demonstrates potential for simultaneous wastewater remediation, ammonia generation, and water recovery, with prospective applications in sustainable environmental treatment systems and closed-loop resource utilization for long-duration space missions.

39 X-ray induced damage in monocot plants at ambient temperature

X-ray-based imaging and spectroscopy are increasingly used to investigate the structure, elemental composition, and physiological processes of living plants. However, exposure to ionizing radiation can damage plant tissues and alter the biological processes being measured. The severity of these effects depends on factors including X-ray energy, photon flux, exposure duration, illuminated area, developmental stage, and tissue type. Understanding radiation-induced damage is essential for distinguishing genuine biological variation from experimental artifacts during in situ and repeated-measurement experiments, including plant-bacterial interactions, nanoparticle distribution, elemental transport or diffusion. Systematic evaluation of dose-dependent damage in plants can therefore support the development of safer experimental protocols, including reduced exposure times, optimized beam conditions, and improved experimental design. In this study, selected beam parameters (photon flux and incident energy) were systematically explored of model monocot plants (Brachypodium distachyon). The resulting effects on plant tissues were evaluated to identify exposure conditions associated with radiation-induced changes and to establish measurement strategies that minimize biological disruption. This approach aims to improve the reliability of X-ray-based plant analyses while preserving plant viability and physiological relevance.

40 XLEAP: A new beamline under construction at CHESS

A new microfocus beamline entitled XLEAP (X-rays for Life, Environmental, Agricultural, and Plant Sciences) is under construction at the Cornell High Energy Synchrotron Source (CHESS). This mid-scale research infrastructure award (USNSF-2330043) began in April 2024, procurement and construction are under way, and the facility is planned to open for user operations in 2028. During construction, graduate students and faculty from the University of Texas at El Paso are collaborating with CHESS staff and Cornell faculty on pilot experiments that develop future capabilities and workflows for XLEAP.

The science priorities for XLEAP, driven by workshops and conferences in 2020-2023 [1], include (1) fundamental mechanisms in plant sciences, such as micronutrient uptake, transport, and storage; (2) how plants respond to external stimuli such as nanoparticles, pathogens, and environmental stresses; (3) mechanisms of elemental cycling at the root-soil interface and in soil; and (4) mecha-nisms of elemental uptake and cycling in aquatic flora, seaweeds, algae, and other organisms.

XLEAP will offer spatially resolved x-ray fluorescence microscopy (2D mapping, 3D computed tomography, and 3D confocal imaging), x-ray absorption spectroscopy, and x-ray diffraction, with tunable spatial resolution from >100 µm to <1 µm, energies ranging from 3-80 keV, and high-flux or high-energy-resolution modes. XLEAP will also offer users complementary optical microscopy, plant growth, and sample preparation facilities, as well as the potential for in-situ x-ray measure-ments with custom plant growth environments directly on the beamline. We will report on the beamline design and construction status, illustrate the planned experimental modes, and describe planned support facilities in addition to the beamline itself.

References
[1] Smieska, L., Guerinot, M. L., Olson Hoal, K. E., Reid, M. C., Vatamaniuk, O. K. Metallomics, 15 (8), mfad041 (2023), 10.1093/mtomcs/mfad041

Fri, August 7

8:30 AM Breakfast (provided)

41 Announcements

Looking forward

Chair: Louisa Smieska

42 X-ray fluorescence microscopy, the next chapter: correlating elemental distributions with structural features

Biological X-ray fluorescence microscopy (XFM) has emerged as a powerful tool for investigating the spatial distribution and quantification of trace elements in biological materials. By providing precise elemental distributions with low background and increasingly high resolution, XFM now allows for the study of metals and the roles of essential and toxic elements in biological processes at the subcellular level. The advances in instrumentation, optics and detector capabilities are met with a new challenge. How can we interpret elemental maps without additional structural, molecular or functional information which XFM can rarely provide. Over the past few years, this problem has been further exacerbated by increasingly bright light sources coming online that allow for increasingly higher resolution at increasingly higher scan speed. Soon, higher resolution XFM scans will no longer equate to higher information content unless additional correlative context is provided.
Correlative approaches can integrate XFM scans with complementary techniques such as optical fluorescence microscopy, heavy metal conjugates, lanthanide DNA probes, or organelle targeting metal-nanoparticle particles. Multi- or single modal workflows allow elemental distributions to be linked with cellular ultrastructure or even protein localization for example. Here, we will present an overview on recent advances of work done in our lab as well as by other investigators. We will highlight current methodologies and applications of correlative biological XFM and discuss challenges associated with sample preparation and data integration.

Speaker: Martina Ralle

43 Optimising cryofixation of plant tissues for 2D X-ray microscopy: insights from the ID-21 beamline (ESRF)

Synchrotron-based X-ray fluorescence spectroscopy (SXRF) imaging is a unique tool for understanding the localisation and dynamics of chemical elements within plant tissues, e.g., leaves, roots, stems, flowers (including pollen), fruits, and seeds, down to subcellular-level resolution. Unlike cell cultures, 2D XRF imaging of plant specimens often requires thin sections and, hence, an imbibing medium to support and maintain the sample’s structural integrity during freezing, cryo-sectioning, and transport to the beamline’s instruments. Although optimal cutting temperature (OCT) compounds are widely regarded as the ‘gold standard’ imbibing medium for immunohistochemical analyses, usually performed between -20 and -40 °C, their use for fast-plunging cryofixation at much lower temperatures (ca. -150 to -180 °C) often results in fractured blocks, compromising or even preventing proper sectioning of the samples. Moreover, widely adopted cryofixation protocols include OCT-poured into plastic containers, such as microcentrifuge tubes, thereby creating additional insulation layers that can reduce the freezing speed and lead to elemental redistribution. Here, we present a simple, insulation-free setup and a sucrose-doped imbibition medium for the cryofixation of plant materials. The XRF imaging results obtained using leaves of crop and ornamental species at the ID-21 beamline of the European Synchrotron Radiation Laboratory (ESRF, Grenoble, France) revealed optimal preservation of structural integrity and elemental distribution in the leaf cross-sections, as well as a significant reduction in the block’s cracking incidence. Furthermore, no striking differences were observed between samples cryofixed directly in liquid nitrogen and those plunged into supercooled isopentane, suggesting that the use of isopentane, a toxic and difficult-to-handle compound, could be avoided without compromising data quality. Therefore, as a simpler and more efficient methodology, this approach is expected to be reproducible at other experimental stations dedicated to 2D X-ray fluorescence spectroscopy imaging of plant materials.

Speaker: Gabriel Sgarbiero Montanha (European Synchrotron Radiation Facility (ESRF))

44 XLEAP-Enabled Opportunities for Micron-Scale Confocal X-ray Fluorescence Imaging

A nearly ubiquitous challenge in conventional x-ray fluorescence (XRF) microscopy, especially for biological applications, is preparing sufficiently thin samples to obtain the best-possible spatial resolution. To make full use of the sub-micron beamsize available at XLEAP in this mode, sample thicknesses will be limited to a few microns or less. Apart from the time and skill required to prepare thin sections, this degree of thinning can damage or otherwise disrupt the morphology and/or elemental distribution that is the target of the investigation. XRF Computed Tomography (XRF-CT) provides one way around this challenge by enabling 3D elemental mapping within intact samples, but imposes a constraint on sample width.

Confocal X-ray Fluorescence (CXRF) is a well-established but less common approach to XRF microscopy that employs a secondary optic, placed between the sample and detector, to enable 3D elemental localization without constraining sample thickness or width. Moreover, a unique implementation of CXRF, developed at CHESS, enables it to be performed with a spatial resolution of close to 1 micron in largest linear dimension, which is 10-20 times better than previous implementations of this technique.

The combination of sub-micron beamsize and high intensity available at XLEAP represent an unprecedented opportunity to implement micron-scale CXRF in biology and other domains. In plant sciences in particular, this technique has already helped elucidate aspects of Copper signaling and homeostasis. Here, after reviewing the approach in more detail, we explore new scientific possibilities we believe will be enabled by the combination of this methodology and the unique capabilities of XLEAP.

Speaker: Arthur Woll (CLASSE)

10:15 AM Coffee break

Looking forward

Chair: Louisa Smieska

45 Technique-Independent Analysis Software for Biological Elemental Imaging [virtual]

Elemental imaging has become an important tool for investigating biological systems, providing spatially resolved measurements of elements in whole organisms, tissues and cells. While instrumentation continues to advance across multiple modalities including laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), X-ray fluorescence microscopy (XFM), and particle-induced X-ray emission (PIXE), and laser induced breakdown spectroscopy (LIBS), software development has largely remained focused on instrument-specific data processing. As a result, many biological researchers lack access to elemental imaging data co-registration, interpretation and statistical tools designed around the common questions asked of elemental imaging data.
We present a suite of complementary open-source software tools developed through the Biomedical National Elemental Imaging Resource (BNEIR) that support modality-independent analysis of biological elemental imaging datasets. TRACE enables co-registration of elemental maps with histological whole-slide images, facilitating tissue annotation and quantitative comparison of elemental abundance across biological structures. TRACE further supports integration with other spatially resolved datasets through a unified tissue coordinate framework.
Muad’Data provides interactive visualization and quantitative exploration of elemental maps, including region-of-interest analysis, elemental overlays, ratio imaging, and extraction of summary statistics from user-defined tissue regions. ScaleBarOn supports standardized visualization and comparison of large collections of elemental images through common scaling approaches, publication-ready figure generation, and quantitative comparison across biological replicates.

Together, these tools demonstrate an alternative software paradigm for elemental imaging in biology, emphasizing biological interpretation rather than instrument-specific data processing. We discuss future opportunities for community software development, including implementation of spatial statistics, measures of heterogeneity and clustering (e.g., Moran’s I), cross-platform data standards, and interoperable workflows that enable quantitative comparison of elemental distributions across imaging modalities. Such capabilities will be increasingly important as elemental imaging datasets grow in size, complexity, and biological relevance.

Speaker: Tracy Punshon (Dartmouth College)

46 Synthetic Biology and Programmable Plant Systems - Opening a Dialogue with Plants

Programmable plant systems are plants engineered to have new capabilities to receive and transmit signals, enabling them to report on their environment, respond to external stimuli, and interact with other organisms and sensors. Programmable plant systems are enabled by a deep understanding of plant signaling, gene function, and synthetic biology that create new connections between plants, people, microbes, and the environment. Crop species provide an important context for programmable plant systems, and transition synthetic biology from model organisms to adoption in our agricultural systems. We envisage crops being incorporated into an ‘Internet of Living Things’ with programmable plant systems being integrated with above and below ground robotics, prediction methods, architected frameworks, and AI, making agriculture smarter, more efficient, and more sustainable.

Speaker: Margaret Frank (Cornell University)

47 Closing remarks and time to complete survey

11:45 AM Boxed lunch (provided)

Optional campus walk and social time

Optional walk around campus- Beebe Lake, botanical garden, possible visit to Dairy Bar!