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15 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces

These data are from Bandopadhyay et al., "Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces". This study aims to understand the soil microbial ecology along terrestrial-aquatic interfaces of a freshwater and estuarine region and how it relates to organic matter. We analyzed soil microbial (16S rRNA gene) and organic matter (Fourier-transform ion cyclotron resonance mass spectrometry, FTICR-MS) composition from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. This dataset includes 16S rRNA gene amplicon data (only processed file types included here) and organic matter composition from FTICR-MS data (raw and processed files included here) from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie and Chesapeake Bay regions. These sites are part of the COMPASS-FME project (https://compass.pnnl.gov/FME/COMPASSFME). File formats and software needed to access files: 16S rRNA gene amplicon data: These files follow the format reported here https://ess-dive.gitbook.io/amplicon-sequencing-reporting-format#updates-in-v1.0.1. As per this format, there are four file types reported: 1. Taxon tables (also called sequence-by-sample or OTU (operational taxonomic unit)/ESV (exact sequence variant) tables) : available in a .txt file format and accessible using TextEdit or MS Excel. 2. Representative sequences (also called consensus sequences) : available in a .fasta format and accessible using TextEdit. 3. Sequencing metadata : available in a MS Excel workbook file format and CSV file format 4. Bioinformatic metadata : available in a MS Excel workbook file format and CSV file format FTICR-MS data: 1. Raw data converted to a processed file with intensities of the peaks in the given samples : available in a MS Excel CSV file format 2. Processed file used in analyses and visualizations (appended as icr_long_) : available in a MS Excel CSV file format 3. Metadata file for ICR features (appended as icr_meta) : available in a MS Excel CSV file format

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces

Coastal soils are dynamic systems where unique microbial niches are shaped by the intensity and duration of flooding between the terrestrial and aquatic boundaries of the terrestrial-aquatic interface (TAI). We aimed to understand the soil microbial community (16S rRNA gene) along the TAIs of a freshwater versus estuarine region and how it relates to organic matter (OM, via Fourier Transform Ion Cyclotron Resonance Mass Spectrometry). We studied the TAI gradients along a transect from upland (forested), transition (stressed forest), to wetland at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. Microbial communities differed significantly by region, transect position, and site. Contrary to expectations, given their dynamic hydrologies, transitions represented midpoints in microbial richness and diversity. We identified a core microbiome conserved across all transect positions within a region, highlighting potential microbial functions most resilient to environmental change. Indicator taxa unique to each transect position defined specific niches shaped by soil biogeochemistry. Co-expression networks of feature-level β-nearest-taxon indices revealed positive relationships in bacterial and OM feature contributions to community assembly. Our study provides critical insights into microbial communities at the forefront of hydrological changes in coastal areas that connect the land to lakes and oceans and remain vulnerable to changing weather patterns.

coastal ecosystems↗
DOE OSTI2026

Soil nitrogen mineralization rates, nutrient stocks, stable isotopes, and water volumetric measurements across terrestrial-aquatic interfaces from three wetlands at the Tanglewood Biological Station, Alabama

This dataset supports a broader study investigating wetland hydrologic and biogeochemical responses to inundation events. Soil samples were collected across four sampling events along terrestrial-aquatic gradients at three wetland sites located within the Tanglewood Biological Station in Alabama from April 2024 to June 2025. The contents in this data package include soil in-situ nitrogen mineralization rates (measurements of net nitrification, net ammonification, and net mineralization), nutrient stocks (total carbon, total nitrogen, and organic matter), stable isotopes (carbon and nitrogen), and water volumetric measurements (water-filled pore space). Water level data related to each wetland location can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/2530253 (Kirker et al., 2024), related water geochemistry data can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3001967 (Forbes et al., 2025), and related surface water sediment chemistry data can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3377325 (Molina Serpas et al., 2026). In addition to this readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) file-level metadata; (2) data dictionary; (3) field metadata and international generic sample numbers (IGSNs); (4) readme; (5) the field protocol; and (6) a subfolder with sample data. The sample data subfolder contains (1) net nitrification rate, (2) net ammonification rate, (3) areal net mineralization rate, (4) percent organic matter, (5) water-filled pore space, (6) total carbon content, (7) total nitrogen content, (8) stable carbon isotope (delta carbon-13), and (9) stable nitrogen isotope (delta nitrogen-15), and (10) methods codes. All files are .csv or .pdf.

13-C↗
DOE OSTI2025

Particulate organic matter (POM) transport and transformation at the terrestrial-aquatic interface (Final Report)

This project investigates the input, transport, and degradation of particulate organic matter (POM) in near-surface riverbed sediments at the Hanford 300 Area of the Columbia River, a dynamic, regulated river system influenced by upstream dam operations. Riverbed sediments are biogeochemical hot spots where organic carbon inputs stimulate intense microbial activity, affecting nutrient cycling and redox transformations in the hyporheic zone (HZ). While dissolved organic matter (DOM) cycling has been studied extensively, little is known about the infiltration and transformation of POM—particularly under variable flow regimes common in large, regulated rivers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Efficiently resolving the terrestrial-aquatic interface in E3SM with sub-grid methods to improve coastal simulations (Final Technical Report)

The broad goal of this project was to extend the capabilities of MPAS‐Ocean, the ocean component of DOE’s Energy Exascale Earth System Model (E3SM), to better resolve the hydrodynamics of the terrestrial‐aquatic interface without significantly increasing computing resource requirements. Specifically, our goal was to better resolve the small-scale features across the terrestrial‐aquatic interface which includes the low lying coastal floodplain and a dendritic network of hydraulically efficient channels connected to estuarine systems and back bays, barrier islands and high energy inlets. The processes driving flow across the terrestrial‐aquatic interface include upland and floodplain hydrology, tides, wind and atmospheric pressure (including coastally generated storm surge across continental shelves and within estuaries and bays), wind waves and water temperature and salinity gradients.

58 GEOSCIENCES↗
DOE OSTI2026

EXCHANGE Campaign Degradation (ECD): Understanding Decomposition Dynamics Across Mid-Atlantic and Great Lakes Coastal Ecosystems

The EXploration of Coastal Hydrobiogeochemistry Across a Network of Gradients and Experiments (EXCHANGE) Degradation Experiment (EXCHANGE-D) is an in situ experiment designed to assess organic matter decomposition rates across coastal terrestrial-aquatic interfaces (TAIs), from coastal uplands through transition zones to wetlands. Through a network of partner scientists and coastal sites, we are testing how environmental gradients shape decomposition and carbon dynamics across terrestrial-aquatic interfaces. Using standardized tea bag substrates deployed across a network of diverse coastal sites, we compare decomposition rates at different fresh- and salt-water TAIs to develop transferable knowledge that improves the representation of organic matter degradation in coastal ecosystem models. For more information, please see https://compass.pnnl.gov/FME/EXCHANGE. This is Version 1 of the data package, which includes: ecd_README.pdf flmd.csv dd.csv ecd_soil_weom_L2.csv ecd_soil_ph_conductivity_L2.csv ecd_soil_gwc_L2.csv ecd_soil_teabag_degradation_L2.csv ecd_readme.pdf

coastal soils↗
DOE OSTI2025

Data for Machado-Silva et al. (2024), "Short-Term Groundwater Level Fluctuations Drive Subsurface Redox Variability"

This dataset contains the analytical data reported in Machado-Silva et al. (2024) as part of the COMPASS-FME project, which seeks to advance a scalable, predictive understanding of the fundamental biogeochemical processes, ecological structure, and ecosystem dynamics that distinguish coastal terrestrial-aquatic interfaces from the purely terrestrial or aquatic systems to which they are coupled. The dataset consists of water quality parameters as well as redox potential, water content, and electrical conductivity. These data were collected in 2022 in Crane Creek (CRC), Portage River (PTR), and Old Woman Creek (OWC). Each of these sites included uplands (UP), transitions (TR), wetland-transition edge (WTE), and wetland (W) zones. The sites represent replicates of the Lake Erie terrestrial-aquatic interface under fluctuating water levels and are located in well-preserved areas with natural or restored marsh and forest cover.This dataset consists of a single data file (Machado_Silva_et_al_2024_EST_data.csv) that is in comma-separated value (CSV) format. No special software is required to read it.This dataset uses the ESS-DIVE Hydrologic Monitoring Reporting Format 1.0.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Using probability distribution function as a scaling approach to incorporate soil heterogeneity into biogeochemical models for greenhouse gas predictions (Final Technical Report)

The project investigated biogeochemical processes at terrestrial-aquatic interfaces (TAIs), focusing on soil microsite heterogeneity and its impact on greenhouse gas (GHG) fluxes. Using laboratory experiments, modeling, and data integration, researchers explored redox-driven microbial processes under fluctuating hydrological conditions. Key advancements included modifying the DAMM-GHG model to incorporateelectron acceptor availability and enhancing the AquaMEND model for improved microbial metabolism representation. Results highlighted microsite redox variability as a key driver of GHG fluxes, informing Earth system models. The project fostered interdisciplinary collaborations, student training, and the development of novel modeling frameworks to improve Earth'senergy budget.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

COMPASS-FME Synoptic Site Characterization

This dataset contains soil biogeochemical and physicochemical characterization data for the COMPASS-FME synoptic sites.This dataset also contains data for the paper Patel et al. 2025 "Transition zones at the changing coastal terrestrial-aquatic interface", https://doi.org/10.1029/2025JG008978.Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience unique spatial and temporal variability in biogeochemical processes, driven by wetland-to-upland gradients and hydrological fluctuations. We studied drivers of coastal soil variability (a) at regional scales and (b) across transects from upland forest to wetland, in two contrasting regions — Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity-related analytes were a key driver of soil variability, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI – however, contrary to expectations, transition soils were not consistently intermediate between upland and wetland endmembers; the non-monotonic trends of carbon, phosphorus, iron along our transects suggest that these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients provide insights into which soil processes may act as precursors to ecosystem shifts. Our comprehensive soil characterization across the coastal transects provides essential data for mechanistic modeling of ecosystem dynamics.The data are provided as processed, csv files. Raw data and processing scripts can be accessed on GitHub (https://github.com/COMPASS-DOE/cmps-soil_characterization).A note on the nomenclature: the experimental design represents three points along the coastal gradient -- upland, transition, and wetland. "wetland" is referred to as "marsh" in the corresponding paper. The two terms can be used interchangeably for the sites in this study.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data for Stetten et al. (2025), "Biogeochemical controls on iron speciation and cycling across upland to shoreline gradients in freshwater and estuarine coastal soils (Lake Erie and Chesapeake Bay, United States)"

Coastal environments are dynamic interfaces that mediate carbon and nutrient exchanges between terrestrial landscapes and open waters, but it is unclear how biogeochemical reactions, in particular iron (Fe) redox transformations, affect the understanding and prediction of coastal ecosystem functions. This dataset includes measurements from two freshwater sites in the Western and Central basins of Lake Erie (Ohio, United States) and two estuarine sites in the Chesapeake Bay (Maryland, United States); the analytical results were reported by Stetten et al. (2025) in Science of the Total Environment. It was produced as part of the COMPASS-FME project, which seeks to advance a scalable, predictive understanding of the fundamental biogeochemical processes, ecological structure, and ecosystem dynamics that distinguish coastal terrestrial-aquatic interfaces from the purely terrestrial or aquatic systems to which they are coupled. The sites were sampled in November 2022 (CRC), December 2022 (MSM), February 2023 (GCW), and March 2023 (OWC); site codes follow those used by Pennington et al. (2025).The dataset consists of the following soil data:- Solid data (Fe concentration, etc.)- Porewater data (sulfate, sulfide, etc.)- Linear combination fitting results of X-ray absorption near edge structure (XANES) spectra; i.e., quantitative results of the oxidation state of Fe, indicated as a proportion of pure Fe(III) and Fe(II) model compounds- Linear combination fitting results of EXAFS (extended X-ray absorption fine structure) spectra, indicated as proportion of of Fe-model compounds (illite, smectite, etc.)Each data type has a single file in comma-separated value (CSV) format. No special software is required to read it.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

TEMPEST3 surface runoff water chemistry and organic matter composition

Coastal flooding, driven by storm surges and sea level rise, can mobilize organic matter (OM) via runoff, while introducing compositionally distinct OM (e.g., estuarine OM) into the system. To understand event-scale OM dynamics, we monitored source waters and surface runoff during an ecosystem-scale field manipulation experiment, TEMPEST (Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments), in June 2024. The TEMPEST experiment is part of the COMPASS-FME (Coastal Observations, Mechanisms, and Predictions Across Systems and Scales – Field, Measurements, and Experiments) project and designed to investigate biogeochemical and ecological impacts of freshwater and seawater flooding on coastal terrestrial-aquatic interface ecosystems by simulating freshwater and seawater storm events in two 2000m2 coastal upland forest plots (freshwater and brackish seawater plots). The temporal coverage of this dataset is during the TEMPESTⅢ event (June 11-13, 2024). This dataset contains: - Surface runoff discharge measured by flumes - Sensor data (specific conductivity, salinity, dissolved oxygen, and temperature) - Particle size distribution - Total suspended sediment concentrations (TSS), particulate and dissolved organic carbon (POC, DOC) concentrations, total nitrogen and total dissolved nitrogen (TN, TDN) concentrations - Bulk particulate and dissolved OM compositions (stable C and N isotopes of particulates and optical measurements of chromophoric dissolved OM) - High resolution mass spectrometry analysis data - Water isotope data All data files are plain-text CSV (comma-separated value), and no special software is required to read them.

COMPASS-FME↗
DOE OSTI2024

Understanding and modeling current and future coastal wetland methane dynamics (Final Report)

The coastal terrestrial-aquatic interface (TAI) is a highly dynamic component of the Earth system that plays a critical role in biogeochemical cycling. Due to its dynamic nature, the processes that regulate decomposition and methane (CH 4 ) emissions are of greater significance at the TAI than in upland systems. Despite this, we have limited mechanistic understanding of how climate stressors interact to regulate the electron acceptors and donors that determine decomposition pathways within TAIs, including the generation of hot spots and hot moments. Accurately modeling these processes is critical for incorporating the coastal TAI into Earth systems models, such as DOE’s E3SM. With previous DOE support, we adapted an aerobic terrestrial representation of decomposition using PFLOTRAN, a reactive flow and transport model, and added anerobic decomposition pathways, salinity, and oxygen (O 2 ) that fluctuates independently of water table level. However, because this model (PFLOTRAN TAI ) is based on decomposition rates and organic matter carbon to nitrogen ratios from terrestrial systems, its performance in TAI systems is currently limited by the lack of empirical data to properly parameterize variables. In addition, while PFLOTRAN TAI can simulate movement of O 2 into sediments, it is not currently capable of tracking the movement of CH 4 gas through plant tissues due to both current model structure and lack of available data. Our overall objective of the project was the increase our mechanistic understanding of CH 4 dynamics in response to environmental change, such that we can improve the representation of these dynamics in PFLOTRAN. We installed automated flux chambers in a new field-scale active soil warming experiment and set up marsh organs (mesocosms) to test effects of warming, flooding, and salinity. This resulted in a new dataset consisting of chamber-level CH 4 flux measurements across multiple sites, ecological conditions, and timeframes, as well as corresponding measurements on porewater chemistry, soil carbon quality, plant biomass, and redox reaction rates. Using these data, we improved PFLOTRAN TAI to more accurately model CH 4 dynamics and successfully tested our hypotheses. This grant contributed to the professional development of 3 postdocs, 4 undergraduate interns, 4 teacher interns, 17 technicians, and 15 participatory scientists. The automated chamber technology designed for this grant has also been shared with multiple new projects.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Biogeochemical controls on iron speciation and cycling across upland to shoreline gradients in freshwater and estuarine coastal soils (Lake Erie and Chesapeake Bay, United States)

Coastal environments are dynamic interfaces that mediate carbon and nutrient exchanges between terrestrial landscapes and open waters, and understanding the biogeochemical factors controlling these exchanges, particularly iron (Fe) redox transformations, is crucial for predicting coastal ecosystem functions. Here, we investigated the mechanisms controlling Fe speciation changes across upland-to-shoreline gradients in freshwater and estuarine soils using Fe K-edge X-ray absorption spectroscopy, solid and porewater composition analysis, and 16S rRNA sequencing analysis. We show that Fe transformations depend primarily on inundation patterns. In unsaturated uplands, Fe occurs as Fe(III) oxyhydroxides, mainly goethite (9–35 %), Fe(II,III)-phyllosilicates (39–89 %), and Fe(III)-organic species (0–61 %). Soils influenced by estuarine waters exhibit porewater sulfide concentrations reaching up to 221 μM, Fe- and S-cycling bacteria, and up to 81 % pyrite (FeS 2 ), indicating that sulfur-driven redox dynamics control Fe transformations. In lacustrine wetlands, Fe(III) reduction is indicated by porewater Fe(II) concentrations increasing to 1.0–2.1 mM, and ~10–15 % of Fe as Fe(II,III)-(hydr)oxides (green rust), vivianite (Fe 3 (PO 4 ) 2 ·8H 2 O), and/or adsorbed Fe(II) species. EXAFS data also indicate reduction of structural Fe(III) to Fe(II) in phyllosilicates. The presence of Fe- and S-cycling bacteria, as well as sulfide (0–10 μM), suggests that Fe-cycling is microbially driven and potentially coupled with cryptic S-cycling. Fe(II) oxidation was indicated above/near the water table by the presence of Fe(III) oxyhydroxides (ferrihydrite, lepidocrocite). Furthermore, negligible Fe(III) or sulfate reduction was observed at some water-saturated sites located at the upland-wetland transition, likely due to oxic (sub-)surface water inputs. Overall, our results highlight the importance of considering both Fe-speciation and hydro-biogeochemical dynamics when predicting Fe-cycling at coastal interfaces.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Rising Water Levels and Vegetation Shifts Drive Substantial Reductions in Methane Emissions and Carbon Dioxide Uptake in a Great Lakes Coastal Freshwater Wetland

ABSTRACT Coastal freshwater wetlands are critical ecosystems for both local and global carbon cycles, sequestering substantial carbon while also emitting methane (CH 4 ) due to anoxic conditions. Estuarine freshwater wetlands face unique challenges from fluctuating water levels, which influence water quality, vegetation, and carbon cycling. However, the response of CH 4 fluxes and their drivers to altered hydrology and vegetation remains unclear, hindering mechanistic modeling. To address these knowledge gaps, we studied an estuarine freshwater wetland in the Great Lakes region, where rising water levels led to a vegetation shift from emergent Typha dominance in 2015–2016 to floating‐leaved species in 2020–2022. Using eddy covariance flux measurements during the peak growing season (June–September) of both periods, we observed a 60% decrease in CH 4 emissions, from 81 ± 4 g C m −2 in 2015–2016 to 31 ± 3 g C m −2 in 2020–2022. This decline was driven by two main factors: (1) higher water levels, which suppressed ebullitive fluxes via increased hydrostatic pressure and extended CH 4 residence time, enhancing oxidation potential in the water column; and (2) reduced CH 4 conductance through plants. Net carbon dioxide (CO 2 ) uptake decreased by 90%, from −267 ± 26 g C m −2 in 2015–2016 to −27 ± 49 g C m −2 in 2020–2022. Additionally, diel CH 4 flux patterns shifted, with a distinct morning peak observed in 2015–2016 but absent in 2020–2022, suggesting changes in plant‐mediated transport and a potential decoupling from photosynthesis. The dominant factors influencing CH 4 fluxes shifted from water temperature and gross primary productivity in 2015–2016 to atmospheric pressure in 2020–2022, suggesting an increased role of ebullition as a primary transport pathway. Our results demonstrate that changes in water levels and vegetation can substantially alter CH 4 and CO 2 fluxes in coastal freshwater wetlands, underscoring the critical role of hydrological shifts in driving carbon dynamics in these ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Gap-filled methane and carbon dioxide fluxes across two ecosystem states at the US-OWC AmeriFlux site (2015−2016, 2020−2022)

This dataset contains gap-filled measurements of methane flux (FCH4), net ecosystem CO2 exchange (NEE) partitioned into gross primary productivity (GPP) and ecosystem respiration (RE), as well as latent heat flux (LE) from a Great Lakes coastal freshwater wetland at the US-OWC AmeriFlux site. The dataset covers the peak growing seasons (June−September) of 2015−2016, dominated by Typha spp., and 2020−2022, characterized by floating-leaved species (lotus and water lily). These data were generated to investigate how rising water levels and vegetation shifts influence CH4 and CO2 fluxes across two distinct ecosystem states in this wetland. The dataset, provided in CSV format, includes half-hourly gap-filled flux data from June to September for 2015, 2016, 2020, 2021, and 2022. The gap-filled data refers to measurements where missing values due to instrument issues or quality control were filled using artificial neural networks (ANNs).

54 ENVIRONMENTAL SCIENCES↗