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Biological Carbon Sequestration for Climate and Soil Health

The United States recently launched the Net Zero World Initiative on decarbonization. As temperatures and sea levels rise, strong action is needed to mitigate high atmospheric CO 2 levels. In response to this need, a joint workshop between the US Department of Energy’s Oak Ridge National Laboratory (ORNL) and Lawrence Berkeley National Laboratory (LBNL) was convened to assess the challenges and opportunities within biological carbon (C) capture. The virtual workshop on Biological Carbon Sequestration for Climate and Soil Health focused on three aspects of biological C capture research: natural systems, engineered systems, and modeling. For this workshop, the scope of natural systems included unmanaged (e.g., grasslands, wetlands, natural forests) and managed (e.g., agricultural lands, commercial forests, forest biofuels) ecosystems. The engineered systems group covered topics in genetically modified plants and microbes, synthetic microbiomes, and altered plant–microbe interactions for enhancing C capture, storage, and utilization. The modeling group focused on computational tools and data collection to predict and assess the effectiveness of new biocarbon sequestration advances. Participant expertise included plant and microbial systems biology, synthetic biology, soil biogeochemistry, and techno-economic analysis. Together, participants outlined key scientific advances in support of biological C capture and storage. Among the major findings of the meeting were the need to better measure C flux within natural, agricultural, and fabricated ecosystems for experimentation; better understand the role of soil composition, plant roots, and the rhizosphere (i.e., the soil surrounding the plant root) in the underground storage of organic C; and design plant–microbe systems for maximal C storage.

54 ENVIRONMENTAL SCIENCES↗

Understanding the Physics Representation of Deep Learning Models in Environmental Applications

Deep learning (DL) models have been popular in earth and environmental modeling and analysis, which exhibit huge potential in capturing and reconstructing the non-linearity of relevant environmental processes. They are extensively used as analytical tools or emulators for multiple domains (atmosphere, land surface, ocean, and biogeochemistry). Despite their success, their internal working mechanism remains largely unknown. Such a lack of knowledge hinders the identification of physically consistent models that are fully adaptive to non-stationary climate, as well as the development of physics-informed machine learning such as physics-informed neural network (PINN). To establish preliminary knowledge and framework of such physics representation evaluation, this project focuses on an improved understanding of DL models in the environmental applications. DL models are increasingly applied to environmental modeling and prediction. However, they have been evaluated mostly from a performance perspective, and there is a gap in understanding how they represent the known physics internally. Such knowledge is especially critical when applying DL models under climate change conditions, where new inputs are likely outside the ranges of the training datasets. In this project, we reveal how the known physical processes are represented within DL models from both statistical and mechanistic perspectives. Leveraging the traditional model evaluations that focus more on the accuracies of predictions, we establish a framework that examines both the accuracy and physics representation of DL models. This analysis framework can identify DL models that make the correct predictions based on correct physics, thus enhancing the existing explainable artificial intelligence (explainable-AI) portfolio. It lays a foundation for developing novel metrics to evaluate the emerging DL models in environmental applications. This knowledge also informs the development of physics-informed DL models by revealing the direct connections between the known physical processes and specific model components or structures.

54 ENVIRONMENTAL SCIENCES↗

Illuminating the pathways to carbon liberation: a systems approach to characterizing the consequential unknowns of carbon transformation and loss from thawing permafrost peatlands (Final Report)

The IsoGenie3 Project delivered new systems-level insights into carbon cycling in thawing permafrost landscapes, with an emphasis on methane and carbon dioxide emissions. From >200 samples from the site collected over a decade, co-analyzed for geochemistry and microbiology, the team recovered ~1,500 assembled microbial genomes and ~1,900 viral population genomes, revealing appreciable genetic novelty - from a new highly abundant bacterial phylum, to novel methane consumers and their activities, to rampant viral novelty. IsoGenie3 linked these organisms to carbon compound transformations (which define the cycling of organic matter in soils, and the loss of the greenhouse gases carbon dioxide and methane), and saw that the microbes at each stage of permafrost thaw had different genetic potential to degrade categories of compounds, expressed that genetic potential differently, and actually transformed carbon compounds into greenhouse gases in different ways. IsoGenie 3 identified that some of the thaw-stage differences were due to plant-microbiome relationships; the plant species across the thaw gradient contributed different carbon compounds into the soil, and hosted distinct microbiota (differing among parts of plants as well as species). Lastly, microbes in the saturated post-thaw conditions appeared likely to contribute to the mobilization and toxification of mercury released during thaw. In parallel with ongoing field sampling and analysis, hypotheses arising from field observations were tested via lab incubation experiments. When communities are taken out of their native habitats, they behave differently, and the team first rigorously quantified the magnitude of this effect on microbiome composition and functional capacity, organic matter composition, and gas production; overall the main system processes were maintained in the lab incubations under the conditions tested. Further, the microbial data could inform geochemical reaction network models of those processes. Then, the team ran experiments with additions of compounds, varying temperature, and “live” vs. “dead” peat (the latter having been gamma irradiated, with a few additional variants to control for methodological artifacts). From these, we (a) determined the importance of plant-derived soluble phenolic compounds in bogs’ extraordinary recalcitrance of organic matter, and carbon gas emissions skewed to carbon dioxide; (b) proposed an abiotic ‘tanning’ mechanism, which could contribute to Sphagnum’s inhibitory effect on anaerobic decomposition through alteration of N availability. IsoGenie3 illuminated longer-term and landscape-scale interactions of permafrost thaw and carbon cycling, advancing knowledge of the drivers of methane dynamics not only across in the permafrost-associated peatland (where hydrology and plant communities dictate microbiomes) but also their interconnected lakes (where sediment carbon quality and resident microbiota are determined by position within lake, and lake features). By leveraging observations of site methane dynamics extending well before this project, the team was able to construct a 44-year portrait of the interplay of permafrost thaw, hydrology, vegetation dynamics, and carbon gas emissions, and the doubling of the fully-thawed fens over this time. From the detailed study of this focal site, IsoGenie3 also aimed to improve model representation of these kinds of sites and processes. To improve predictions of methane transformations, we incorporated acetate and isotope dynamics into the ‘DNDC’ biogeochemistry model. In addition, recovered genomes were grouped into ‘functional groups’, i.e. the genomes that perform a specific function of interest, then used to parameterize maximum growth rate and optimum growth temperature (via signatures in their sequence composition) for the BioCrunch model. The BioCrunch model was then in turn used to test the impact of increasing functional resolution of the microbes, on the carbon gas emissions. Lastly for modeling, the ecosys model was parameterized from the microbial and other data, and used to evaluate drivers of e.g. change in methane emissions. Finally, this project also led to the development of a range of new methods and tools, a new metric of organic matter decomposability, as well as a graph-database solution to multidisciplinary data storage and querying. This project’s ongoing analyses at our focal site also contributed to broader advancements in understanding elements of genetic plasticity and methane metabolism, climate change microbiology and community assembly, global peatland geochemistry and Arctic lakes’ roles in climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗

High-throughput physiochemical and biogeochemical characterization for coastal soils and waters

Coastal environments span large biogeochemical gradients and provide critical ecosystem services worldwide, thereby having a disproportionately larger influence on global biogeochemical cycles and greenhouse gas fluxes than their geographical extent suggests. Despite this, cohesive quantitative tools to understand and describe these environments, including scalable, standardized field and laboratory methodologies are lacking. In this work, we advanced the streamlining and standardizing of quantitative approaches to measure and understand coastal physiochemical properties and biogeochemical processes across systems and scales. Outcomes of this work includes workflows for multiple complementary and in-line analyses, from basic physiochemical datasets to targeted molecular approaches and proof of concept through manipulation and analysis of coastal soils and waters with varying salinity, minerology, and biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

Department of Energy’s Atmospheric System Research (ASR) Program’s Workshop on the Future of Atmospheric Large Eddy Simulation (LES): Workshop Report

Large-eddy simulation (LES) is used as a tool to understand physical processes such as turbulence, aerosols, clouds, precipitation, radiation, the interactions among all these, and their interactions with the underlying surface. Over the next 10 years, LES will drive fundamental progress in open scientific questions in these areas as LES is increasingly used to gain understanding of complex interacting physical processes involving atmospheric turbulence. This growth will be driven both by scientific demand and the expansion of computational resources needed to conduct LES, and the form that the growth takes will largely be determined by how computational resources are leveraged for scientific gain. In particular, we suggest that computational resources are likely to be leveraged in two separate but not necessarily distinct ways. On one hand, growth in computational resources will allow LES to be made more routine, that is, performed more frequently, while on the other hand, the computational expense (measured in total floating point operations) afforded to individual LES will expand dramatically, allowing simulations to increase in both domain size and resolution as well as physical detail. Current U.S. Department of Energy (DOE) projects such as LES ARM Symbiotic Simulation and Observation Activity (LASSO) are leading the way in conducting routine LES, building large, public databases that are accessible for data science, sensitivity studies, and training for machine learning. LES will also become more routine as it becomes more accessible for individual researchers to address their scientific questions of interest. Scientific questions addressed by LES over the next 10 years are likely to include cloud organization and aggregation; aerosol cloud interactions and atmospheric chemistry (including geo-engineering); urban-scale LES; atmospheric extreme events, ranging from small-scale severe weather to wildfires; and ocean-wave-atmosphere interactions. Further LES-related research will likely grow significantly in areas related to societal impact studies of air quality and extreme weather events, applications to renewable energy forecasting and resource assessment, and aid in decision-making processes. The growth in the use of LES in atmospheric science research will drive the need for better physical process representations (e.g., cloud aerosol microphysics, radiation, and atmospheric chemistry) at the scales resolved by LES. To date, many of the process representations used by LES have been taken directly from coarser-resolution models. Promising methods for LES process representations include superdroplet and quadrature methods for microphysics, 3D approaches for radiation, and better representation of chemistry and aerosol processes. At LES resolution, land-atmosphere interactions for complex terrains, land cover/types, biogeochemistry, and plant canopy models are needed as an improvement beyond traditional and widely used Monin-Obuhkov similarity theory.

54 ENVIRONMENTAL SCIENCES↗

Functional-type modeling approach and data-driven parameterization of methane emissions in wetlands (Final Technical Science Report)

Our goals are to improve understanding and quantitative representation of the multiple processes that affect methane emissions at a high (patch level, vertically detailed) spatial resolution, and translate this understanding to improved modeling capability of coastal wetland fluxes using the E3SM Land Model (ELM v1) wetland CH4 biogeochemistry module. We propose an experimental approach to identify and parameterize uncertainties in ELM. Understanding of methane emissions can be improved along three conceptual axes: (i) horizontal (ecohydrological patch resolution), (ii) vertical (through the depth of the soil column), and (iii) process level (e.g., resolving microbial pathways, vegetation specific transport pathways). Along each of the three axes, we will characterize, quantify, and model, the key ecological, hydrological, and meteorological controls of methane (CH4) flux heterogeneity in four model coastal wetlands.

54 ENVIRONMENTAL SCIENCES↗

Targeted Biomining and Machine Learning Approaches in Critical Minerals Revealed by a Biogeochemical Survey of a Coal Mine Drainage Remediation System

Abandoned coal mine drainage (AMD) remediation systems in Pennsylvania can concentrate critical minerals and materials (CMM) at levels comparable to mining-grade ores. Remediation systems have varying engineering features and are open to the environment, resulting in diverse microbial colonization and seasonal climate influences that may impact CMM speciation. The location of CMMs, the types of bacterial communities tolerant of these pollutant conditions, and the influence of localized climate on CMM rich remediation systems are not well characterized. Through a one-year spatiotemporal survey of biogeochemistry at a remediation system, we have initiated the process to address these questions. Rare Earth Elements (REE) ranged 180-1,200 ppm and greater than 1,500 bacterial ASVs were classified via 16S sequencing. Analyses indicate biogeochemical differences are heavily influenced by engineering features. Additionally, REE precipitants correlate strongly with the elements Al, Cu, Zn, Be, and U. Unearthing these trends has refined our line of inquiry to explore biological mining opportunities more closely with these metals. Furthermore, we created a Machine Learning Model for predicting AMD REE content, with 89% accuracy, using the data from this study and several others. Further training data is required to create a more reputable model. Recently, global research efforts have prioritized modeling work or the use of the few historical surveys to design experiments. Through our data, we challenge this approach, emphasizing the importance of expanding fundamental survey efforts prior to advanced product design and experimentation.

critical minerals↗

CAMAS 2025: Continuing to Advance Arctic Marine Science

The Consortium for the Advancement of Marine Arctic Science (CAMAS) held its second annual Workshop and Early-Career School in Seattle, WA, on April 15-18, 2025. The workshop attracted 74 participants, including a dozen scientists from Europe (8) and Asia (4). The goal of CAMAS is to facilitate and enhance international collaboration on marine Arctic science, in order to advance the understanding and model representation of key marine Arctic processes that contribute to the rapid changes in the Arctic Earth system. These rapid changes have profound impacts on operations in the Arctic, including those associated with the national and energy security of the United States. The Early-Career School started the event on Tuesday April 15. Thirty-three early-career scientists (postdocs and students) gathered for lectures and discussions on topics like high-resolution Arctic Ocean and sea ice modeling; biogeochemistry of the Arctic; Machine Learning for Arctic Earth system modeling; and an Arctic perspective on geo-engineering.

54 ENVIRONMENTAL SCIENCES↗

NitroNet: Smart System to Quantify Nitrous Oxide Emissions

Agricultural croplands are the largest anthropogenic source of nitrous oxide (N 2 O), the third most important greenhouse gas. Emissions are characterized by “hot spots” and “hot moments”, meaning emissions are highly heterogeneous in space and time. Emissions are driven by nitrification and denitrification processes which depend upon complex factors such as soil characteristics (type, compaction, pH, moisture, topography), management practices (fertilizer type and application, tillage, crop type, field history, irrigation), biogeochemistry (organic carbon, microbial composition), and meteorology (precipitation, temperature, and wind). For these reasons, quantifying cropland emissions by either measurements or modeling is extremely challenging with large uncertainties.

09 BIOMASS FUELS↗

The GREEN ‘omics of Nutrient Feedbacks to Soil Warming

The GREEN ‘omics of Nutrient Feedbacks in Soil project advanced the DOE Biological and Environmental Research (BER) mission by developing and applying isotope-enabled ’omics tools to understand how soil microbes regulate carbon and nutrient cycling. Guided by the Growth Rate, growth Efficiency, and stoichiometry of Essential Nutrients (GREEN ’omics) framework, the project aimed to build a predictive, systems-level understanding of microbial traits that control ecosystem biogeochemistry. In a collaboration among Northern Arizona University (lead), West Virginia University, Lawrence Livermore National Laboratory, and Pacific Northwest National Laboratory, we combined quantitative stable isotope probing (qSIP), Chip-SIP, NanoSIMS, and genome-resolved metagenomics across long-term experiments in Arctic, boreal, temperate, and tropical ecosystems. The project produced three key outcomes: 1) We showed that community-weighted temperature sensitivities of bacterial growth (Q10) can predict ecosystem-scale soil respiration responses across diverse soils. 2) We provided the first in situ evidence for density-dependent population dynamics in soil bacteria and demonstrated that nutrient additions intensify competition, concentrating carbon use into fewer taxa. 3) We improved and extended isotope-enabled ’omics methods by quantifying qSIP measurement error to guide experimental design and coupling SIP with genome-resolved metagenomics to reveal cross-kingdom interactions among bacteria, fungi, and viruses. Together, these results show that a small number of microbial traits and taxa exert disproportionate control over soil carbon and nutrient cycling, providing critical data and methods to improve representation of microbial processes in Earth system models.

54 ENVIRONMENTAL SCIENCES↗

From tides to seasons: How cyclic tidal drivers and plant physiology interact to affect carbon cycling at the terrestrial-estuarine boundary (Final technical report)

Coastal ecosystems are among the most biologically and biogeochemically active and diverse systems on Earth. Because they act as important linkages between terrestrial ecosystems and the open ocean, their incorporation in Earth system models (ESMs) is critical to predict coastal and global responses to environmental changes. However, they vary greatly in the magnitude of tides and the volume and timing of freshwater input from land, making it challenging to model the major biogeochemical reactions that control productivity and greenhouse gas emissions across coastal terrestrial aquatic interfaces (TAIs). Our overall objective was to improve mechanistic process understanding and modeling of tidal wetland hydro-biogeochemistry in coastal TAIs. We established a new flux tower site (Ameriflux US-PLo) in the oligohaline part of the Parker River to continuously monitor ecosystem-scale carbon fluxes under temporally varying salinity conditions. The site is co-located with long-term monitoring plots of the Plum Island Ecosystems LTER project. We installed wells and redox sensors in the marsh interior and creek bank, established biomass monitoring plots and deployed novel optode sensors in both locations. We used this data to parameterize plant-mediated transport in PFLOTRAN and tested the impact of soil heterogeneity on porewater constituents and gas fluxes. We collected observations of root oxygen release with a novel planar optode system in the field. Flux data collected during the measurement period encompasses a large variation in salinity ranging from drought to record precipitation years. We developed a method to extract functional relationships from the flux data using artificial neural networks, identifying salinity thresholds for CH 4 fluxes. Finally, we are using the coupled ELM-PFLOTRAN model to test the impact of antecedent hydrological conditions on the salinity-CH 4 flux relationship. This grant contributed to the professional development of one postdoc, three research assistants and one graduate student. The sensor data has been shared with external collaborators.

54 ENVIRONMENTAL SCIENCES↗

Elucidating Processes Controlling Arctic Atmospheric Aerosol Sources, Aging, and Mixing States (Final Report)

Atmospheric aerosols play critical roles in the Earth’s energy budget, directly by scattering or absorbing solar and terrestrial radiation and indirectly by serving as seeds (nuclei) for cloud droplet and ice crystal formation and by depositing on snow and ice surface, thereby changing the surface albedo. These effects are dependent on aerosol particle size and chemical composition and impact the hydrological cycle as well. This project provided single-particle size and chemical composition measurements across the entire annual cycle in the high Arctic and in the Alaskan Arctic during fall – winter, addressing the most significant gaps in Arctic aerosol observational data. These needs were based on recent rapid sea ice loss across the entire Arctic, as well as the major annual delays in sea ice freeze-up during fall in the Chukchi Sea and increased wintertime sea ice fracturing in the Beaufort Sea, both off the North Slope of Alaska. Two DOE Atmospheric Radiation Measurement (ARM) field campaigns were conducted for atmospheric aerosol sampling. The Aerosols during the Polar Utqiagvik Night (APUN – ‘snow on ground’ in Iñupiaq) ARM field campaign at Utqagivik, Alaska was conducted from Oct. 28 – Dec. 22, 2018. Aerosol sizing instrumentation and a single-particle mass spectrometer were successfully deployed for size-resolved number concentration measurements and measurements of individual particle size and chemical composition, respectively. These results show the influence of locally-produced sea spray aerosol, with high cloud-forming potential, due to delayed sea ice freeze-up in the fall. During the 2019‐2020 international Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition, daily atmospheric aerosol particles were collected aboard the German icebreaker Polarstern in the Central Arctic from Nov. 2019 – Oct. 2020. Sea salt aerosol and marine organics were observed year-round during MOSAiC with varying morphologies and sources. These findings are important because most Arctic models do not include a sea spray aerosol source, despite this source increasing with declining sea ice extent. In addition to collecting new samples and data, this project also conducted further analysis of previously collected single-particle chemical composition measurements within the North Slope of Alaska oil fields and at Utqiaġvik, AK, during Aug. – Sep. 2015 and 2016 field campaigns. This work resulted in the discovery of chemical reactions of oil field combustion emissions occurring within fog droplets across the North Slope of Alaska and forming secondary aerosol, showing the impact of Arctic oil field emissions beyond black carbon aerosol and greenhouse gases. In addition, the distribution of chemical species across the aerosol population within the oil fields was quantified, using these data and a previously development framework. We also presented the first ambient evidence of the collision of two atmospheric particles resulting in formation of an organic-coated ammonium sulfate particle of marine origin, which has implications for cloud formation with declining sea ice extent. Overall, this project has elucidated connections between seawater biogeochemistry, resource extraction activities, atmospheric composition, clouds, and the energy budget of the Arctic region. The results of this project are expected to improve weather and sea ice forecasting for security and development in the Arctic and beyond.

54 ENVIRONMENTAL SCIENCES↗

Leveraging High-resolution Molecular Composition of Soil Organic Matter to Enhance Carbon Cycling Modeling

Soils store more carbon than the atmosphere and vegetation combined, yet Earth system models still struggle to predict how this vast reservoir will respond to environmental change. A central limitation is that most soil biogeochemical models represent organic matter using bulk conceptual pools or chemically homogeneous fractions, preventing direct use of rapidly expanding molecular-scale datasets. Here we develop and test a new soil decomposition framework that explicitly integrates high-resolution information on organic matter composition. First, we construct a molecularly informed litter decomposition module in which plant inputs are partitioned into five functional compound classes—carbohydrates, proteins, lignin-like aromatics, lipids, and carbonyls—using a molecular mixing model calibrated to solid-state 13 C Nuclear Magnetic Resonance (NMR) spectra. Class-specific kinetics, lignin-dependent physical protection, and substrate-driven microbial carbon use efficiency allow the module to capture metabolic tradeoffs associated with enzyme production and nutrient limitation. We then embed this litter module within a microbially explicit whole-soil model that tracks the transformation of these compound classes through particulate organic matter, dissolved organic matter, mineral-associated organic matter, and microbial biomass. High-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS) data are used to link internal pools to measurable soil organic matter fractions and to constrain key process parameters. Applications at soil-core and ecosystem scales demonstrate that the new model reproduces observed soil respiration dynamics while providing mechanistic attribution of CO 2 fluxes to specific chemical classes and pools. Compared to existing frameworks such as the Community Land Model soil biogeochemistry module and the Millennial model, our approach maintains competitive predictive skill while substantially improving interpretability and opportunities for data–model integration. This work illustrates a viable pathway for leveraging molecular-scale observations to reduce structural uncertainty in soil carbon–climate feedback projections.

54 ENVIRONMENTAL SCIENCES↗

A Computational Workflow of Elucidating Viral Impact on Mediating Microbial Response to In-situ Experimental Warming: Bridging microbial modeling to carbon and mineral modeling

Viruses are abundant in soils and shape microbial communities in ways that can potentially influence ecosystem processes, yet their contributions to carbon cycling and mineral transformations remain poorly understood. Here we present a multi-phase framework that links virus-host interactions to soil biogeochemistry by combining ecological simulations, genome- and community-scale metabolic modeling, and statistical and machine-learning analyses. We first calibrated microbial abundance profiles under explicit infection scenarios to capture how viral pressure alters community structure, then explored alternative interaction strategies, including kill-the-winner, piggyback-the-winner, and mixed lytic-lysogenic modes, through forward simulations. These ecological shifts were translated into metabolic consequences using exchange fluxes summarized into biologically meaningful categories, while integrated statistical and machine-learning screens elevated subtle but consistent signals. Application of this framework revealed that viral infections shift the balance between organic and inorganic fluxes, redirecting metabolism from diffuse organic transformations toward inorganic pools such as protons and CO 2 , directly linking viral regulation to respiration and soil carbon balance. The roll-up analysis also isolated perturbations in critical mineral ions, including magnesium, manganese, zinc, and copper, which serve as essential enzymatic cofactors. In piggyback-the-winner scenarios, uptake of these ions was strongly suppressed. Contrasting viral strategies produced distinct community structures and metabolic outcomes, from broad suppression under kill-the-winner dynamics to dramatic redistributions under high-lytic and high-gain lysogenic regimes that collapsed vulnerable microbial populations while promoting opportunists. Together, these results provide a tractable path to trace viral perturbations from host abundance shifts to metabolic flux adjustments and ecosystem-scale processes, offering a practical way to include viruses in earth system models.

54 ENVIRONMENTAL SCIENCES↗

EMSL Community Science Campaign Meeting: Critical Minerals and Materials - Rhizo Critical Campaign Breakout Session Report Summary

The “Critical Minerals Biogeochemistry in the Rhizosphere – Ultramafic Soils (Rhizo Critical)” campaign breakout (BO) session was organized to identify major knowledge gaps and fundamental research needs in rhizosphere microbiology and geochemistry that, if addressed, could transform our ability to recover critical minerals from ultramafic soil systems. We sought to identify significant challenges that must be surmounted in the pursuit of deeper science knowledge. Our ultimate goal is to understand this landscape well enough to identify and prioritize opportunities for EMSL to make the greatest impact with Environmental Transformations and Interactions (ETI) science area research campaigns focused on the biogeochemical processes controlling the behavior of critical minerals and materials in the rhizosphere. The increasing demand for critical materials and minerals (CMM) in the U.S. has heightened interest in low-grade ores with much attention on ultramafic soils, which contain valuable metals such as nickel (Ni), chromium (Cr), manganese, cobalt (Co), and copper (Lee et al., 2025; DOE CMM Report, 2023) used in advanced battery, magnet, wiring and wind turbines, and stainless steel technologies. Metal hyperaccumulating plants grown in ultramafic soils can extract economically valuable concentrations of CMMs through the process of phytomining. This technology has evolved from phytoremediation, which involves using plants to cleanse contaminated environments by removing, detoxifying, or stabilizing pollutants like metals and organic compounds. Hyperaccumulator plants are capable of storing metals in their living tissues at concentrations hundreds to thousands of times higher than those found in 'normal' plants. For instance, while the average concentration of Ni in the dry matter of plants growing in typical soils is usually less than 5 µg g?¹, Ni hyperaccumulation is defined by concentrations exceeding 1,000 µg g?¹ (Corzo Remigio et al., 2020; Reeves et al., 2018). Phytomining research has primarily focused on Ni (Rylott and van der Ent, 2025), for which the U.S. has very limited conventional mines in operation. Most soils typically contain Ni concentrations ranging from 7 to 50 mg kg-1, whereas serpentine soils exhibit significantly higher levels, with Ni content often ranging between 700 and 8,000 mg kg-1 (Sobczyk et al., 2017). While more than 500 plant species in over 50 different families have been identified as Ni hyperaccumulators (Kidd et al., 2018), Ni phytomining (and phytominng in general) remains largely untested because most studies are short-term, small-scale, and conducted under simplified or artificially enriched conditions, so they fail to capture the low metal concentrations, environmental variability, and management constraints that would be needed for a field-scale demonstration. Few hyperaccumulator species have been validated as true “metal crops,” and their biomass production, stress tolerance, and rooting characteristics are usually too poor to yield economically meaningful metal outputs. Critically, the basic mechanisms of metal uptake, transport, and sequestration, especially as shaped by belowground processes such as root exudation, rhizosphere chemistry, and root–microbe interactions that control metal mobility and bioavailability (Montreemuk et al., 2023; Kidd et al., 2018; Durand et al., 2023; Alford et al., 2010), are still only partially understood, and downstream metal recovery from biomass is rarely optimized. Because these limitations stem from gaps in fundamental knowledge rather than from a failure of the concept itself (Rylott and van der Ent, 2025; van der Ent et al., 2015), there is a strong need for basic science that dissects plant metal homeostasis, rhizosphere and microbial processes, and their integration with soil chemistry and process engineering to design more robust, scalable phytomining systems.

Ahkami, Amirhossein↗

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

Data for EMSL Project 60929 from August 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗