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DOE OSTI2025

Combining Observations and Models: A Review of the CARDAMOM Framework for Data‐Constrained Terrestrial Ecosystem Modeling

The rapid increase in the volume and variety of terrestrial biosphere observations (i.e., remote sensing data and in situ measurements) offers a unique opportunity to derive ecological insights, refine process‐based models, and improve forecasting for decision support. However, despite their potential, ecological observations have primarily been used to benchmark process‐based models, as many past and current models lack the capability to directly integrate observations and their associated uncertainties for parameterization. In contrast, data assimilation frameworks such as the CARbon DAta MOdel fraMework (CARDAMOM) and its suite of process‐based models, known as the Data Assimilation Linked Ecosystem Carbon Model (DALEC), are specifically designed for model‐data fusion. This review, motivated by a recent CARDAMOM community workshop, examines the development and applications of CARDAMOM, with an emphasis on its role in advancing ecosystem process understanding. CARDAMOM employs a Bayesian approach, using a Markov Chain Monte Carlo algorithm to enable data‐driven calibration of DALEC parameters and initial states (i.e., carbon pool sizes) through observation operators. CARDAMOM's unique ability to retrieve localized model process parameters from diverse datasets—ranging from in situ measurements to global satellite observations—makes it a highly flexible tool for analyzing spatially variable ecosystem responses to environmental change. However, assimilating these data also presents challenges, including data quality issues that propagate into model skill, as well as trade‐offs between model complexity, parameter equifinality, and predictive performance. We discuss potential solutions to these challenges, such as reducing parameter equifinality by incorporating new observations. This review also offers community recommendations for incorporating emerging datasets, integrating machine learning techniques, strengthening collaboration with remote sensing, field, and modeling communities, and expanding CARDAMOM's relevance for localized ecosystem monitoring and decision‐making. CARDAMOM enables a deep, mechanistic understanding of terrestrial ecosystem dynamics that cannot be achieved through empirical analyses of observational datasets or weakly constrained models alone.

Bayesian inference↗

DOE OSTI2023

The Roles of Tidal Marshes in the Estuarine Biochemical Processes: A Numerical Modeling Study

Observations suggest that the existence of tidal marsh can alter the oxygen and nutrient dynamics in adjacent water bodies, but assessing the impacts of large tidal marshes on an estuary is challenging. In this study, we use a modeling approach to investigate the roles of tidal marshes on the estuarine biochemical processes. The marsh model, which simulates the ecological functions of marshes at seasonal and annual time-scales, is embedded inside an unstructured-grid three-dimensional hydrodynamic and eutrophication model (SCHISM-ICM). This modeling system simulates the growth and metabolism of the tidal marshes and links biological processes to nutrient dynamics in the water column and sediment. This model dynamically simulates nutrient recycling and physical transport of the materials between marshes and open water through wetting-drying processes. This coupled model system is validated and successfully applied to the York River Estuary. Model results suggest that tidal marshes influence the local diurnal dissolved oxygen (DO) cycle by exporting dissolved organic carbon and high sediment oxygen demand in the marsh system through the tidal exchange. The high deposition rates of organics and diurnal DO cycle enhance the sediment release of phosphorus. On the other hand, marshes tend to decrease dissolved inorganic nitrogen in the water column by settling particulate nutrients and enhancing the denitrification process. The study demonstrates that tidal marshes exert substantial impacts on the estuarine biochemical processes. The developed tidal marsh model enhances eutrophication modeling and advances the understanding of the feedback effects between marsh biogeochemistry and estuarine eutrophication processes on a systemic scale.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Propagule Pressure in Microbial Introductions

The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. The dataset filed here includes the experimemtal datafile, and a RMarkdown file that includes all the code used in in both the modeling and anaylsis.

agriculture↗

DOE OSTI2024

Landscape fragmentation overturns classical metapopulation thinking

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally (“residents”) were often more resilient to fragmentation than long-ranging “migrants.” This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Predictive links between microbial communities and biological oxygen utilization in the Arctic Ocean

Microbial metabolism influences rates of net community production (NCP), exerting a direct biological control on marine oxygen and carbon fluxes. In the Arctic, it is increasingly important to understand and quantify this process, as ecological and oceanographic conditions shift due to changing climate. Here, we describe potential ecological links between pelagic microbial diversity and an NCP precursor, biological oxygen utilization, using machine learning and paired observations of community structure and metabolic activity from a seasonally and spatially variable transect of the Arctic Ocean (2019–2020 MOSAiC Expedition). Community structure was determined using 16S (prokaryotic) and 18S (eukaryotic) rRNA gene amplicon sequencing, and metabolic activity was derived from ΔO 2 /Ar. Using self-organizing maps, we identified clear successional patterns in observed microbial community structure that were seasonally driven in the upper ocean and vertically stratified with depth. Metabolic activity was also stratified, with a primarily net heterotrophic water column (median −1.5% biological oxygen saturation), excepting periodic oxygen supersaturation (maximum: 13.6%) within the mixed layer. Using DNA sequences as predictor variables, we then constructed a random forest regression model that reliably reconstructed biological oxygen concentrations (root mean squared error = 4.14 μmol kg −1 ). Top predictors from this model were from heterotrophic (bacteria) or potentially mixotrophic (dinoflagellate) taxa. These analyses highlight biologically driven diagnostic tools that can be used to expand biogeochemical datasets and improve the microbial perspectives and metabolisms represented in ecological models of net productivity and carbon flux in a changing Arctic Ocean.

Chamberlain, Emelia J. [Univ. of San Diego, San Di↗

DOE OSTI2026

Dominant Controls on Preferential Flow and Their Implications for Future Soil Water Fluxes

Abstract Soil water flow, particularly preferential flow (PF), is a critical control on hydrological and biogeochemical processes, including groundwater recharge, contaminant transport, and carbon cycling. However, it remains challenging to predict PF occurrence across large environmental gradients. Here, we developed a deep learning (DL) model to estimate event‐scale soil water flow velocity and the probability of PF occurrence using high‐frequency soil moisture and precipitation data from 33 sites across the National Ecological Observatory Network. The model demonstrated high skill in predicting the binary occurrence of PF (91% F1‐score; 85% accuracy) but the performance was limited in predicting soil water velocity ( R 2 = 0.31). We found that precipitation characteristics (duration, volume, and intensity) were the most important predictors for soil water velocity. Among the non‐precipitation event variables, sand content showed relatively high predictive skill, though differences among non‐event climate variables were generally modest. Lower sand content was associated with increased predicted soil water velocity, a finding that highlights the role of soil structure in producing more non‐uniform flow, which contrasts with traditional uniform flow models. Projecting a reduced DL model under both moderate and high‐emissions future climate scenarios (2060–2099 Representative Concentration Pathways 4.5 and 8.5), we found ∼7.3% increase under RCP4.5 and ∼15% under RCP8.5 of soil water velocities compared to the historical simulation, while modeled likelihood of PF changed little. These findings suggest climate change is not making PF more frequent, but it is making existing PF pathways more efficient with important consequences for associated nutrient and contaminant transport under climate change. Plain Language Summary Water movement in soil is critical for water quality. While often modeled as a uniform flow process, in reality water moves rapidly through cracks and burrows in what is called “preferential flow” (PF), which limits natural filtration and can transport pollutants. We developed a deep learning model, trained on data from 33 U.S. sites, to predict when and how fast this PF occurs based on precipitation, soil, and climate data. The model showed that precipitation characteristics (duration, intensity, volume) were the most important predictors of PF. Lower soil sand content/higher clay content was associated with faster water flow, likely due to clay soils forming aggregates and cracks that water moves through rather than infiltrating uniformly. Further analyses based on climate projections suggest that the speed at which PF occurs will become more rapid under future climate scenarios compared to historical simulation. This highlights the need to represent PF in soil water models when assessing future water quality. Key Points The effect of precipitation peak intensity on soil water velocities declined with increasing precipitation intensity Antecedent soil moisture failed to predict preferential flow (PF), contrasting the high predictive power of sand content Climate predictions suggest that soil water velocities through PF paths will increase ∼15% by 2099

Li, Bonan↗

DOE OSTI2025

MSD CoP Webinar: "Generative agents: A new frontier for representing human actors and their behavior in MSD models"

Context: This webinar was hosted by the MultiSector Dynamics Community of Practice (MSD CoP; https://multisectordynamics.org). Talk #1: Behavioral Generative Agents for Energy Operations Presenter: Dr. Cong Chen (Thayer School of Engineering, Dartmouth College) Abstract: Accurately modeling consumer behavior in energy operations remains challenging due to inherent uncertainties, behavioral complexities, and limited empirical data. This talk introduces a novel approach leveraging generative agents--artificial agents powered by large language models--to realistically simulate customer decision-making in dynamic energy operations. Talk #2: Simulating multiple human perspectives in socio-ecological systems using large language models Presenter: Dr. Yongchao Zeng (Institute of Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU) of the Karlsruhe Institute of Technology in Germany) Abstract: Understanding socio-ecological systems requires insights from diverse stakeholder perspectives. This talk describes a novel simulation system called HoPeS (Human-oriented Perspective Shifting). HoPeS enables model users to not only explore simulated socio-ecological systems (SESs) from a third-person observer's perspective but also take any of the simulated stakeholder roles, like playing an RPG game. By shifting multiple perspectives, model users can reflect and integrate the situated knowledge learned through the participatory simulation, approximating a more holistic and less biased understanding of SESs. Moderators: Jim Yoon (MSD CoP Human Systems Modeling Working Group Co-Chair); Stefano Galelli (MSD CoP Using AI to Enhance MSD Research Working Group Co-Chair); Patrick M. Reed (MSD CoP Facilitation Team) This webinar was held on: November 13th, 2025 from 12-1 PM EST.

Artificial Intelligence↗

DOE OSTI2025

Hydropower and environmental flow management: System-level trade-offs at Glen Canyon Dam

The research focuses on the Colorado River Basin, specifically examining the Glen Canyon Dam (GCD) and its influence on surrounding aquatic ecosystems. This area is crucial due to its role in hydropower production and its impact on downstream environments, including the Grand Canyon National Park. This study explores the integration of environmental factors into hydro dispatch modeling at GCD to tackle ecological challenges posed by the invasive smallmouth bass (SMB). Utilizing the GTMax SL and SERM models, the research assesses the effects of SMB control experiments on hydropower generation, economic value, and grid stability. The study examines the financial and economic impacts of bypass flows designed to release colder water to prevent SMB spawning, which can significantly reduce hydropower output and increase costs. The research identifies that declining reservoir levels and rising water temperatures in Lake Powell have facilitated SMB spawning, posing a threat to native fish populations like the endangered humpback chub. The findings highlight the importance of adaptive management strategies to balance ecological preservation with hydropower generation amid long-term weather-related challenges. The study underscores the need for comprehensive assessments of flow options to prevent SMB establishment below GCD, considering the broader implications for sediment dynamics and ecological interactions.

Ecological impact assessment↗

DOE OSTI2026

BRCore: an R package implementing flexible selection of core taxa using contribution to Bray-Curtis dissimilarity and neutral model fitting

Identifying core taxa in microbial ecology highlights groups likely to participate in a broad range of potential ecological interactions. Here, we present BRCore, an R package to identify core taxa using abundance-occupancy distributions and beta-diversity contributions across ecological niches, and predict stochastic and deterministic taxa.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Riders’ perceptions towards transit bus electrification: Evidence from Salt Lake City, Utah

While battery electric buses (BEBs) can lead to energy savings and reduced emissions, BEB adoption is developing slowly. Although BEBs offer quieter operations, better acceleration, and no smell of diesel or gas fumes, little focus has been placed on the user’s perspective. Here, this study investigates bus riders’ preferences toward BEBs. To achieve these objectives, a survey was designed and administered to solicit riders’ typical travel behaviors and patterns as well as preferences and opinions about BEBs’ performance in terms of emissions and noise. Statistical analysis showed that several factors influence rider perceptions towards transit bus electrification that include trip purpose, attitudes towards environmental issues and environmental impacts of BEBs, and certain non-instrumental ride factors such as ride comfort and social image. A better understanding of the importance of electrification to transit riders can help transit service providers adjust their marketing decisions and their systemwide operations to accommodate preferences towards BEBs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

Toward a coordinated understanding of hydro‐biogeochemical root functions in tropical forests for application in vegetation models

Summary Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest–climate feedbacks for these carbon‐rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine‐root strategies for soil resource exploration, (2) coupling and trade‐offs in fine‐root water vs nutrient acquisition, and (3) aboveground–belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground–belowground hydro‐nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO 2 . The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.

Plant Sciences↗

DOE OSTI2024

Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

Abstract Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12 family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Geographic source attribution of honey by strontium isotope analyses: Latvia and India measurements compared to model predictions in a feasibility study

Strontium isotope ratios ( 87 Sr/ 86 Sr) can be used to determine the geographic origin of agricultural products. Here, in this study, we measured the 87 Sr/ 86 Sr of honey samples from Richland, WA, USA, Latvia, and India, and compared the results to published 87 Sr/ 86 Sr from surrounding areas and values predicted based upon a random forest isoscape model (Bataille et al., 2020). While the 87 Sr/ 86 Sr of the honey samples compared well with previously published data, the model did not accurately predict the 87 Sr/ 86 Sr of the honey samples, demonstrating that further refinement of the model would be beneficial. Because Sr cycling in terrestrial ecosystems is complex, the 87 Sr/ 86 Sr of honey is likely to reflect several sources (e.g., nectar, surface water, dust) and may change over time. In order to accurately predict the 87 Sr/ 86 Sr of honey, models must consider local geology, ecology, and bee behavior. Additional research examining how Sr is incorporated into honey is needed to inform models.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Embracing fine-root system complexity in terrestrial ecosystem modeling

Projecting the dynamics and functioning of the biosphere requires a holistic consideration of whole-ecosystem processes. However, biases toward leaf, canopy, and soil modeling since the 1970s have constantly left fine-root systems being rudimentarily treated. As accelerated empirical advances in the last two decades establish clearly functional differentiation conferred by the hierarchical structure of fine-root orders and associations with mycorrhizal fungi, a need emerges to embrace this complexity to bridge the data-model gap in still extremely uncertain models. In this work, we propose a three-pool structure comprising transport and absorptive fine roots with mycorrhizal fungi (TAM) to model vertically resolved fine-root systems across organizational and spatial–temporal scales. Emerging from a conceptual shift away from arbitrary homogenization, TAM builds upon theoretical and empirical foundations as an effective and efficient approximation that balances realism and simplicity. A proof-of-concept demonstration of TAM in a big-leaf model both conservatively and radically shows robust impacts of differentiation within fine-root systems on simulating carbon cycling in temperate forests. Theoretical and quantitative support warrants exploiting its rich potentials across ecosystems and models to confront uncertainties and challenges for a predictive understanding of the biosphere. Echoing a broad trend of embracing ecological complexity in integrative ecosystem modeling, TAM may offer a consistent framework where modelers and empiricists can work together toward this grand goal.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Human–Earth system interactions under climate change

This special issue, titled ‘Focus on human–Earth system interactions under climate change,’ compiles cutting-edge research that deepens our understanding of the complex feedback mechanisms between anthropogenic activities and Earth system processes in the context of a changing climate (figure 1). The featured articles employ a diverse array of methodologies—including field studies, remote sensing, modeling, and socio-ecological analyses—to explore these interconnections. A unifying theme across these contributions is the imperative to bridge disciplinary divides, integrating physical Earth sciences with social sciences to fully capture the spectrum of human-Earth system interactions. Key topics addressed the impacts of human activities on natural systems, encompassing land-use change and water resource management on biogeochemistry, climate dynamics, and feedback on the climate system and socioeconomics from local to global scales under a changing climate.

Li, Huidong [Vanderbilt Univ., Nashville, TN (Unit↗

DOE OSTI2022

The global decline in the sensitivity of vegetation productivity to precipitation from 2001 to 2018

The sensitivity of vegetation productivity to precipitation (S ppt ) is a key metric for understanding the variations in vegetation productivity under changing precipitation and predicting future changes in ecosystem functions. However, a comprehensive assessment of S ppt over all the global land is lacking. Here, we investigated spatial patterns and temporal changes of S ppt across the global land from 2001 to 2018 with multiple streams of satellite observations. We found consistent spatial patterns of S ppt with different satellite products: S ppt was highest in dry regions while low in humid regions. Grassland and shrubland showed the highest S ppt , and evergreen needle-leaf forest and wetland showed the lowest. Temporally, S ppt showed a generally declining trend over the past two decades (p < .05), yet with clear spatial heterogeneities. The decline in S ppt was especially noticeable in North America and Europe, likely due to the increase in precipitation. In central Russia and Australia, however, S ppt showed an increasing trend. Biome-wise, most ecosystem types exhibited significant decrease in S ppt , while grassland, evergreen broadleaf forest, and mixed forest showed slight increases or non-significant changes in S ppt . Our finding of the overall decline in S ppt implies a potential stabilization mechanism for ecosystem productivity under climate change. However, the revealed S ppt increase for some regions and ecosystem types, in particular global grasslands, suggests that grasslands might be increasingly vulnerable to climatic variability with continuing global climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Electromagnetic Induction (EMI) Data, 2024, Trail Creek, Colorado

This dataset contains Electromagnetic Induction (EMI) data collected at Trail Creek, Colorado, in 2024. EMI surveys were conducted to investigate the spatial distribution of electrical conductivity in the subsurface, providing insights into soil moisture and subsurface geological features. The surveys were performed along multiple transects to capture variations in conductivity influenced by changes in soil composition, moisture content, and underlying geological structures. This dataset complements other geophysical data collected in the region, including Electrical Resistivity Tomography (ERT) and Terrestrial LiDAR Scanning (TLS), providing a detailed understanding of the subsurface and its impact on surface vegetation and hydrological processes. The data are valuable for environmental geophysics, ecological research, and hydrological modeling in mountainous ecosystems. The files include: - data.zip: the raw EMI data (.csv) - inversion.zip: the inverted resistivity model (.csv and .kml) - kriging.zip: the kriging resistivity model (.csv, .tif, .kmz) - flmd.csv: file level metadata file describing all files within this dataset - dd.csv: data dictionary file describing the column headers within CSV files This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

CMD Mini-Explorer↗

DOE OSTI2023

Determining the biogeochemical transformations of organic matter composition in rivers using molecular signatures

Inland waters are hotspots for biogeochemical activity, but the environmental and biological factors that govern the transformation of organic matter (OM) flowing through them are still poorly constrained. Here we evaluate data from a crowdsourced sampling campaign led by the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to investigate broad continental-scale trends in OM composition compared to localized events that influence biogeochemical transformations. Samples from two different OM compartments, sediments and surface water, were collected from 97 streams throughout the Northern Hemisphere and analyzed to identify differences in biogeochemical processes involved in OM transformations. By using dimensional reduction techniques, we identified that putative biogeochemical transformations and microbial respiration rates vary across sediment and surface water along river continua independent of latitude (18°N–68°N). In contrast, we reveal small- and large-scale patterns in OM composition related to local (sediment vs. water column) and reach (stream order, latitude) characteristics. These patterns lay the foundation to modeling the linkage between ecological processes and biogeochemical signals. We further showed how spatial, physical, and biogeochemical factors influence the reactivity of the two OM pools in local reaches yet find emergent broad-scale patterns between OM concentrations and stream order. OM processing will likely change as hydrologic flow regimes shift and vertical mixing occurs on different spatial and temporal scales. As our planet continues to warm and the timing and magnitude of surface and subsurface flows shift, understanding changes in OM cycling across hydrologic systems is critical, given the unknown broad-scale responses and consequences for riverine OM.

rivers↗