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Model scripts associated with “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale”

NOTE: The manuscript associated with this data package is currently in review. The data/scripts may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final scripts and additional metadata. This data package is associated with the publication “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale” submitted to Environmental Science & Technology (Zheng et al. 2026). The project combines mechanistic process modeling with knowledge-guided machine learning (KGML) to evaluate how organic matter chemistry, microbial biomass, and physical substrate accessibility regulate realized respiration rates across river corridors. All data used in this paper have been previously published and can be accessed at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719 (Goldman et al., 2020). This data package contains 3 R-markdown (Rmd) preprocessing scripts for the previously published data and subsequent modelling workflows. The full workflow with input and output data can be found in the associated GitHub repository at https://github.com/jianqiuz/KGML-WHONDRS.

Biogeochemistry↗

Snow Depth Datasets for Snodgrass Catchment, Colorado, Water Year 2022-2023

This data package presents snow depths data from distributed temperature probes at 18 locations near Snodgrass catchment, Colorado. These data show that snow melt-out dates are approximately one or two weeks later under evergreen forests compared to other vegetation types even at the same elevation. These data were collected to understand how snowmelt heterogeneity impacts headwater hydrology, including streamflow and groundwater levels. They were also used to compare with process-based model simulations of snow depth to evaluate whether the model accurately represents snowmelt dynamics and their effects on headwater hydrology. Snow_DTPs_locations.csv includes all probes locations and their associated elevation and vegetation types. Snow_Depth_Snodgrass_WY2022_2023.csv includes processed snow depths datasets for Water Year (WY) 2022 and 2023. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. Several probes have recordings for WY 2021.

54 ENVIRONMENTAL SCIENCES↗

Specific conductivity and salinity of the Parker River, PIE LTER, Plum Island Sound MA, August-November 2022

This dataset contains specific conductivity and calculated salinity data of Parker River water at a tidal brackish wetland dominated by Typha angustifolia at the upper estuary of the Plum Island Sound in Newbury, Massachusetts (MA) within the Plum Island Ecosystems Long Term Ecological Research site (PIE LTER). Measurements were taken to evaluate temporal changes in surface water salinity in high frequency to characterize boundary conditions of soil and plant responses to changes in salinity. A PVC pipe was installed in a low elevation spot in the creek bank so that the bottom of the pipe sat on the sediment surface allowing flushing with water during flooding. Raw measurements were collected using an Onset HOBO U24-002 Saltwater Conductivity/Salinity data logger. The specific conductance and salinity measurements were corrected and calculated respectively using Onset’s HOBOware software and reference specific conductivity measurements taken in tandem with the first and last points recorded by the HOBO sensor. These reference measurements were taken using a HACH HQ14D Portable Conductivity Meter. Because of the installation design, only data one hour before and after high tide are used. Metadata files Typha_ctd_salinity_dd.csv and Typha_ctd_salinity_flmd.csv contain detailed information on data variables, sampling and QA/QC methods, and site location.

54 ENVIRONMENTAL SCIENCES↗

Specific conductivity and salinity of the Parker River, PIE LTER, Plum Island Sound MA, March-November 2023

This dataset contains specific conductivity and calculated salinity data of Parker River water at a tidal brackish wetland dominated by Typha angustifolia at the upper estuary of the Plum Island Sound in Newbury, Massachusetts (MA) within the Plum Island Ecosystems Long Term Ecological Research site (PIE LTER). Measurements were taken to evaluate temporal changes in surface water salinity in high frequency to characterize boundary conditions of soil and plant responses to changes in salinity. A PVC pipe was installed in a low elevation spot in the creek bank so that the bottom of the pipe sat on the sediment surface allowing flushing with water during flooding. Raw measurements were collected using an Onset HOBO U24-002 Saltwater Conductivity/Salinity data logger. The specific conductance and salinity measurements were corrected and calculated respectively using Onset’s HOBOware software and reference specific conductivity measurements taken in tandem with the first and last points recorded by the HOBO sensor. These reference measurements were taken using a HACH HQ14D Portable Conductivity Meter. Because of the installation design, only data one hour before and after high tide are used. Metadata files Typha_ctd_salinity_dd.csv and Typha_ctd_salinity_flmd.csv contain detailed information on data variables, sampling and QA/QC methods, and site location.

54 ENVIRONMENTAL SCIENCES↗

High-resolution leaf area index maps generated from unoccupied aerial system, Teller Mile 27, Seward Peninsula, Alaska

Leaf area index (LAI), a measure of the amount of one-side leaf area per ground unit, is an important indicator of plant carbon, energy, and water cycle. In the heterogeneous Arctic landscapes, it has been challenging to accurately measure LAI across species and space needed for Earth system model validation. Here, we use multispectral unoccupied aerial systems (UASs) to scale up and map leaf area index (LAI) , in a low-Arctic tundra landscape on the Seward Peninsula, Alaska. We linked previous published LAI measurements with high-resolution, UAS-collected multispectral data collected over the region of Next Generation Ecosystem Experiments in the Arctic (NGEE Arctic)’s Teller Mile Maker 27 site in 2022 to develop random forest (RF) machine learning models to predict and map LAI. 100 RF models were developed to account for uncertainties in ground LAI plot measurements and process scaling. This dataset includes a raster (*.tif) map of the mean LAI value of the 100 RF models, a raster (*.tif) map of the standard deviation of the RF-modeled LAI data, and a user guide (*.pdf).

54 ENVIRONMENTAL SCIENCES↗

Investigating Resiliency of Transportation Network under Targeted and Potential Climate Change Disruptions

Ensuring robustness and resilience in intermodal transportation systems is essential for the continuity and reliability of global logistics. These systems are vulnerable to various disruptions, including natural disasters and technical failures. Despite significant research on freight transportation resilience, investigating the robustness of the system after targeted and climate-change-driven disruption remains a crucial challenge. Drawing on network science methodologies, this study models the interdependencies within the rail and water transport networks and simulates different disruption scenarios to evaluate system responses. Here, we use the data from the U.S. Department of Energy Volpe Center for network topology and tonnage projections. The proposed framework quantifies deliberate, stochastic, and climate-driven infrastructure failure, using higher resolution downscaled multiple Earth System Models’ simulations from Coupled Model Intercomparison Project Phase version 6. We show that the disruptions of a few nodes could have a larger impact on the total tonnage of freight transport than on network topology. For example, the removal of targeted 20 nodes can bring the total tonnage carrying capacity to 30% with about 75% of the rail freight network intact. This research advances the theoretical understanding of transportation resilience and provides practical applications for infrastructure managers and policymakers. By implementing these strategies, stakeholders and policymakers can better prepare for and respond to unexpected disruptions, ensuring sustained operational efficiency in transportation networks.

Climate Change Disruptions↗

Matilda v1.0: An R package for probabilistic climate projections using a reduced complexity climate model

A primary advantage to using reduced complexity climate models (RCMs) has been their ability to quickly conduct probabilistic climate projections, a key component of uncertainty quantification in many impact studies and multisector systems. Providing frameworks for such analyses has been a target of several RCMs used in studies of the future co-evolution of the human and Earth systems. In this paper, we present Matilda, an open-science R software package that facilitates probabilistic climate projection analysis, implemented here using the Hector simple climate model in a seamless and easily applied framework. The primary goal of Matilda is to provide the user with a turn-key method to build parameter sets from literature-based prior distributions, run Hector iteratively to produce perturbed parameter ensembles (PPEs), weight ensembles for realism against observed historical climate data, and compute probabilistic projections for different climate variables. This workflow gives the user the ability to explore viable parameter space and propagate uncertainty to model ensembles with just a few lines of code. The package provides significant freedom to select different scoring criteria and algorithms to weight ensemble members, as well as the flexibility to implement custom criteria. Additionally, the architecture of the package simplifies the process of building and analyzing PPEs without requiring significant programming expertise, to accommodate diverse use cases. We present a case study that provides illustrative results of a probabilistic analysis of mean global surface temperature as an example of the software application.

54 ENVIRONMENTAL SCIENCES↗

Walker Branch Watershed: Daily Stream Metabolism and Organic Carbon Spiraling Metrics in the West Fork of Walker Branch, Tennessee, USA, 2004-2010

This dataset contains daily metabolism estimates of gross primary production (GPP), ecosystem respiration (ER), and net ecosystem production (NEP), in addition to organic carbon spiraling length (SOC) and mineralization velocity (VfOC) estimates at the West Fork of Walker Branch, a small headwater stream, in the Walker Branch Watershed, Tennessee, USA. Observations were made from 2004-2010 (2004-01-01 to 2010-12-31). These data were generated to assess seasonal and interannual variability in metabolism and organic carbon spiraling and to explore potential driver variables, as analyses of intra- and interannual variability in metabolism and organic carbon spiraling are currently limited, leaving knowledge gaps in the driving mechanisms of and future changes to stream metabolism and carbon processing under climate change. Additionally, measurements of discharge (Q), stream width, stream- and canopy-level photosynthetically active radiation (PAR), water temperature, and precipitation from this time frame are included. This dataset contains one data file in comma separated (*.csv) format.

54 ENVIRONMENTAL SCIENCES↗

Characterizing and communicating uncertainty: lessons from NASA’s Carbon Monitoring System

Navigating uncertainty is a critical challenge in all fields of science, especially when translating knowledge into real-world policies or management decisions. However, the wide variance in concepts and definitions of uncertainty across scientific fields hinders effective communication. As a microcosm of diverse fields within Earth Science, NASA’s Carbon Monitoring System (CMS) provides a useful crucible in which to identify cross-cutting concepts of uncertainty. The CMS convened the Uncertainty Working Group (UWG), a group of specialists across disciplines, to evaluate and synthesize efforts to characterize uncertainty in CMS projects. This paper represents efforts by the UWG to build a heuristic framework designed to evaluate data products and communicate uncertainty to both scientific and non-scientific end users. We consider four pillars of uncertainty: origins, severity, stochasticity versus incomplete knowledge, and spatial and temporal autocorrelation. Using a common vocabulary and a generalized workflow, the framework introduces a graphical heuristic accompanied by a narrative, exemplified through contrasting case studies. Envisioned as a versatile tool, this framework provides clarity in reporting uncertainty, guiding users and tempering expectations. Beyond CMS, it stands as a simple yet powerful means to communicate uncertainty across diverse scientific communities.

54 ENVIRONMENTAL SCIENCES↗

Data from: "Reply to ‘The challenge of defining effectively-no-snow’"

This repository contains the data and code associated with the paper titled "Reply to ‘The challenge of defining effectively-no-snow’" published in Nature Reviews Earth and Environment, 2026. In this reply, we argue that the 10th percentile of peak SWE (Snow Water Equivalent), which we propose in the original article, can be used as intended given it's a standardized, impact-based benchmark for comparing snow conditions across regions, not as a literal measure of snow absence. We present new evidence with SNOwpack TELemetry (SNOTEL) data showing that years meeting the threshold are overwhelmingly associated with subsequent drought (given United States Drought Monitor conditions), supporting its hydrologic and societal relevance. We conclude that while the distinction between "effectively no snow" and "zero snow" should be clearly communicated, the original definition remains appropriate for assessing impacts on snow-dependent water systems. The file code_nree_ML_reply_2026.Rmd contains the main processing scripts which analyze the SNOTEL data. Data from the US Drought Monitor was downloaded at: https://usdmdataservices using the Get Drought Severity Statistics By Area Percent' option, saved to the *_HUC4_delineated.csv files (Hydrologic Unit Code), which are labeled accordingly. 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.

EARTH SCIENCE > TERRESTRIAL HYDROSPHERE > SNOW/ICE↗

CROCUS Air Quality Data at Argonne National Laboratory Prairie Site

The AQT (Vaisala AQT530) instrument provides observations on meteorological conditions, including particulate matter (PM2.5, PM10), gas species concentrations (NO, NO2, O3, CO), and environment temperature and moisture. These measurements are critical for understanding air quality. These measurements are useful for understanding changes in aerosol properties, air quality research, and comparing to model experiments especially in urban environments. These measurements are collected at the Argonne Testbed for Multiscale Observational Science (ATMOS), a prairie field site at Argonne National Laboratory in Lemont, Illinois. Data is available in the netCDF data format, we encourage data users review documentation through Project Pythia to understand how to work with netCDF data https://foundations.projectpythia.org/core/data-formats/netcdf-cf.html. Each file contains one day's worth of data (24 hours, starting at 0000 UTC). The data is aggregated into daily frequency to make it easier to process multiple days, and compress the higher-resolution fields. File naming convention includes the project (CROCUS), location (atmos), data level (raw, a1), date (year, month, day), and hour (0000).

54 ENVIRONMENTAL SCIENCES↗

Land Use Change Alters Soil Organic Carbon: Constrained Global Patterns and Predictors

Abstract Land use change (LUC) alters the global carbon (C) stock, but our estimation of the alteration remains uncertain and is a major impediment to predicting the global C cycle. The uncertainty is partly due to the limited number and geographical bias of observations, and limited exploration of its predictors. Here we generated a comprehensive global database of 5,980 observations from 790 articles. The number of sites evaluated is at least seven times larger than in previous meta‐analyses. Our constrained estimates of different LUC's effects on soil organic C (SOC) and their variations across global climates reveal underestimation/overestimation in previous estimates. Converting forests and grasslands to croplands reduced SOC by 24.5% ± 1.53% (−11.03 ± 1.06 Mg ha −1 ) and 22.7% ± 1.22% (−8.09 ± 0.67 Mg ha −1 ), while 28.0% ± 1.56% (4.46 ± 0.42 Mg ha −1 ) and 33.5% ± 1.68% (5.8 ± 0.38 Mg ha −1 ) increases, respectively, were obtained in the reverse processes. Converting forests to grasslands decreased SOC by 2.1% ± 1.22% (−1.13 ± 0.44 Mg ha −1 ), while the reverse process increased SOC by 18.6% ± 1.73% (3.31 ± 0.51 Mg ha −1 ). Modeled relative importance of 10 drivers of LUC's impact on SOC revealed that higher initial SOC (iSOC) does not solely determine SOC loss in SOC‐negative LUC scenarios as previously proposed. Across four decades, reconverting croplands to forests and grasslands recovered only 49.5% (6.1 ± 0.51 Mg ha −1 ) and 75.3% (7.0 ± 0.38 Mg ha −1 ) of the iSOC, respectively, indicating the need for protecting C‐rich ecosystems. Our global data set advances information on LUC's effect on SOC and can be valuable to constrain Earth system models to reliably estimate global SOC stocks and plan climate change mitigation strategies.

Environmental Sciences & Ecology↗

CROCUS Weather Data at Argonne National Laboratory Prairie Site

Vaisala WXT sensor is an all-in-one weather instrument that provides 6 of the most important weather parameters: barometric pressure, temperature, relative humidity, rainfall, wind speed and direction. Temperature, pressure, relative humidity, and rainfall are sampled at 1 second frequency, while wind speed/direction is measured at ten per second (10Hz) frequency. These measurements are useful for looking at characterizing local weather, identifying unique weather events, and studying local turbulence, especially given the high temporal resolution of the wind measurements. These measurements are collected at the Argonne Testbed for Multiscale Observational Science (ATMOS), a prairie field site at Argonne National Laboratory in Lemont, Illinois. Data is available in the netCDF data format, we encourage data users review documentation through Project Pythia to understand how to work with netCDF data https://foundations.projectpythia.org/core/data-formats/netcdf-cf.html. The data is aggregated into daily frequency to make it easier to process multiple days, and compress the higher-resolution fields. Each file contains one day's worth of data (24 hours, starting at 0000 UTC). File naming convention includes the project (CROCUS), location (atmos), data level (raw, a1), date (year, month, day), and hour (0000).

54 ENVIRONMENTAL SCIENCES↗

2024 Atmospheric Radiation Measurement (ARM) Annual Report

This report provides an overview of the Atmospheric Radiation Measurement (ARM) user facility and a sample of achievements for fiscal year 2024 (FY2024). Strong collaborations between nine DOE national laboratories enable ARM to successfully operate in remote locations around the world. This unique partnership supports the DOE mission to provide for the energy security of the nation. Without the support of the following laboratories, ARM would not be the state-of-the-art facility that it is today. ARM is a multi-laboratory, U.S. Department of Energy (DOE) Office of Science user facility and a key contributor to national and international atmospheric and climate research efforts. ARM offers scientists cutting-edge, ground-based observatories, aerial observation capabilities, and high-performance computing. ARM’s capabilities have enabled more than 30 years of continuous measurements of cloud and aerosol properties and their effects on Earth’s energy balance.

54 ENVIRONMENTAL SCIENCES↗

GNSS-based Vegetation Optical Depth, Tree Sway, and Evapotranspiration data from the Niwot Ridge Subalpine Forest (US-NR1) AmeriFlux site

This data package contains data and information about Global Navigation Satellite System (GNSS)-based Vegetation Optical Depth (VOD), tree sway motion, and eddy-covariance evapotranspiration (ET) data collected at the Niwot Ridge Subalpine Forest AmeriFlux site (US-NR1). The raw GNSS data were collected between May 2022 and August 2023. Other processed datasets such as tree sway motion and ET data are also included. The goal was to study the water content within a subalpine forest and, more specifically, examine the canopy evaporation process. This data archive includes all data that were used within the following Biogeosciences discussion paper that further summarizes the research objectives and conclusions:Burns, S.P., V. Humphrey, E.D. Gutmann, M.S. Raleigh, D.R. Bowling, and P.D. Blanken, 2025: Using GNSS-based vegetation optical depth, tree sway motion, and eddy-covariance to examine evaporation of canopy-intercepted rainfall in a subalpine forest. EGUsphere [preprint],https://doi.org/10.5194/egusphere-2025-1755This data archive also supplements the 30-min Lawrence Berkeley National Laboratory (LBNL) AmeriFlux dataset for US-NR1 (i.e., https://doi.org/10.17190/AMF/1246088) and updates what was in the 2020 ESS-DIVE US-NR1 archive (https://doi.org/10.15485/1671825) to include data from the years 2020-2025. More specifically, the following updates are provided: (i) five-minute statistics (means, variances, covariances) of all data measured by the US-NR1 data system between Sep 2020 and Jun 2025 in netCDF format, (ii) the electronic logbook of US-NR1 site visits, (iii) a web calendar (in HTML format) documenting activity at the site (a replica of https://urquell.colorado.edu/calendar/), (iv) photos taken at the site between years 2020 and present day (Aug 2025), and (v) several auxiliary datasets, primary related to trees near the site, soil properties, soil moisture and soil temperature, and subcanopy radiation data. The data package is setup so that the web calendar, photos, and electronic logbook can be easily accessed on a local computer using a web browser. The provided data files are in either BINEX or SBF format (for the raw GNSS data), netCDF, CSV, ASCII, or MATLAB format. To obtain a better understanding about the archive, please start by reading the following PDF which is included within the data archive:README_ESS_DIVE_USNR1_2025_readme_first.pdf.

54 ENVIRONMENTAL SCIENCES↗

Microbial community data from throughfall exclusion experiment: Metadata, SI, community composition, LefSe, and FunGuilR data tables from PARCHED Panama tropical forest soils, 2024-2025

Soil contains more carbon (C) than terrestrial vegetation and the atmosphere combined, with some of the largest terrestrial C stocks in tropical rainforests. Soil microbes decompose organic matter, playing a vital role in the storage or loss of soil C. With climate change, drought conditions are predicted to increase in many tropical regions, including both chronic drying and extended drought, potentially influencing these processes. This project explored the effects of chronic and seasonal drying on soil microbial communities across four distinct tropical forests in a long-term drying experiment. We investigated the effects of a chronic drying manipulation on soil microbial community abundance and variation across different forests and seasons. We also compared findings with previously published data from these forests after short-term drying. This project used soils from a long-term drying experiment established in 2018 across four seasonal lowland forests in Panama. Soils were collected from 0 – 10 cm depths during three seasonal periods in control and drying plots in 2024 and 2025 from a total of 32 plots (n = 4 per forest per treatment). The forests varied in baseline rainfall and soil fertility. We calculated alpha and beta diversity indices and compared taxonomic community composition. We found significant biogeographic variation in microbial diversity and taxonomy, with significant differences across the forests and significant effects of the drying treatment. Metadata and sample IDs are within Metadata_16S.csv and Metadata_ITS.csv. Relative abundance tables of every sample at every season are shown in the Excel workbooks 16S Relative Abundance.xlsx and ITS Relative Abundance.xlsx. They are then also shown in CSV files by each taxonomic level. Linear discriminant analysis effect size (LefSe) tables are shown for the full 16S and ITS datasets (n = 96), subsets for every site at every season (n = 8), and then for the forests with each plot merged by season (n = 8). FunGuildR data table of ITS data is uploaded.

Bacteria↗

ArcticShark Uncrewed Aerial System

Some studies of atmospheric processes benefit from specialized instrumented observation platforms, including towers, crewed aircraft, tethered balloon systems, and uncrewed aerial systems (UAS). The ArcticShark UAS, managed by the U.S. Department of Energy’s (DOE’s) Atmospheric Radiation Measurement (ARM) User Facility, has emerged as a vital scientific platform, providing comprehensive measurements to expand the horizons of atmospheric research and ARM data. The ArcticShark focuses on small-scale, accurate, and repetitive flight patterns over areas of scientific interest, including ARM’s ground observatories in Alabama and Oklahoma. When used in concert with data from ground-based instruments and other aerial platforms, UAS observations help deliver a complete picture of atmospheric processes, helping scientists evaluate and improve the accuracy of earth system models needed to inform energy infrastructure planning.

47 OTHER INSTRUMENTATION↗