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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Soil viruses: Understudied agents of soil ecology

Over the past couple decades there has been intense exploration of the soil microbiome using modern sequencing and bioinformatics approaches. These studies have revealed a vast diversity of microorganisms across a variety of habitats (Thompson et al., 2017) and how differences in the environment, for example with climate change, influence the soil microbial community composition (Jansson and Hofmockel, 2020). The focus of these studies has primarily been on microbial cellular organisms, including bacteria, archaea and fungi. By contrast, in depth study of soil viruses has been largely neglected, until recently. There are several reasons that soil viruses are less studied, including difficulties with extraction of viruses from soil particles, difficulties with classification of soil viruses based on microscopic imaging, and reliance on the small proportion of microbial hosts that can be cultivated. Now that comprehensive soil metagenomes are available the current trend has been to survey the metagenomes for viral sequences. This approach has revealed that soil viruses are incredibly abundant, highly diverse, and largely uncharacterized (Paez-Espino et al., 2016). This so-called ‘viral dark matter’ presents an incredible research opportunity for the future. Here I will highlight some of these potential research avenues based on what is known to date.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Carbon dioxide, water vapor and methane soil efflux (soil respiration) in a Pinus palustris root exclusion in Georgetown, SC

This dataset contains processed data from a combination of survey flux chambers and long-term automated flux chambers. Soil flux measurements were conducted from June 2023 through December 2025 in a mature longleaf pine forest in Georgetown, SC. Soil respiration measurements were conducted approximately biweekly for two and a half years, before and after a root exclusion that took place on May 5, 2024. Processed, QAQC’d data for the treatment (root exclusion) and control (roots intact) before and after the root exclusion can be found in the file: 1_DATA_ESS_DOE_HR_RS_HB2_QAQC_Survey_Data_20260223.csv. Two multiday deployments were also conducted prior to the root exclusion using long-term automated chambers to continuously monitor greenhouse gas soil efflux. Processed, QAQC’d data for both long-term deployments can be found in the file: 2_DATA_ESS_DOE_HR_RS_HB2_QAQC_Longterm_Data_20260209.csv. Raw and working data files (.json, .81x, & .82z format) from LI-COR equipment are included for reference and can be accessed using SoilFluxPro software. CSV metadata files describe the raw data and modifications made using SoilFluxPro v5 and Matlab R2024b, as well as formatting and units for processed CSVs. Matlab code is included for reading in the processed CSVs, with sample figures comparing treatment and control. This research was performed as part of the project: “Improving models of stand and watershed carbon and water fluxes with more accurate representations of soil-plant-water dynamics in southern pine ecosystems”, which examines in part the effects hydraulic redistribution on soil efflux of carbon dioxide, water vapor and methane, as well as soil moisture and temperature in a southern pine ecosystem with sandy soils and high water table.

CARBON DIOXIDE FLUX↗
DOE OSTI2026

Carbon dioxide, water vapor and methane soil efflux (soil respiration) in a Pinus palustris restoration site in Georgetown, SC

This dataset contains processed data from a combination of survey flux chambers and long-term automated flux chambers. Biweekly soil flux measurements were conducted from June 2023 through December 2025 at a longleaf pine restoration site in Georgetown, SC. Processed, QAQC’d data can be found in the file: 1_DATA_ESS_DOE_HR_RS_HB3_QAQC_Survey_Data_20260223.csv. Raw and working data files (.json, & .81x format) from LI-COR equipment are included for reference and can be accessed using SoilFluxPro software. CSV metadata files describe the raw data and modifications made using SoilFluxPro v5 and Matlab R2024b, as well as formatting and units for processed CSVs. Matlab code is included for reading in the processed CSVs. This research was performed as part of the project: “Improving models of stand and watershed carbon and water fluxes with more accurate representations of soil-plant-water dynamics in southern pine ecosystems”, which examines in part the effects hydraulic redistribution on soil efflux of carbon dioxide, water vapor and methane, as well as soil moisture and temperature in a southern pine ecosystem with sandy soils and high water table.

CARBON DIOXIDE FLUX↗
DOE OSTI2020

Time-domain reflectometer survey across the East River Watershed, Colorado

Lawrence Berkeley National Laboratory (LBNL) collected near-surface point-measurements of soil temperature (file variable TDR_T(C)), volumetric water content (file variable TDR_SM(VWC%)), and soil electrical conductivity (file variable TDR_EC(mS/m)) using a time-domain reflectometer (TDR) at a depth of 25 cm. The survey aimed to characterize the spatial heterogeneity of near-surface hydrological properties at the hillslope scale considering sites with different aspects and elevation within the watershed. The East River is part of the Watershed Function Scientific Focus Area (WFSFA) located in the Upper Colorado River Basin, United States. These data were collected in early July 2019 over four hillslope sites: Pumphouse (north-east facing slope), Bradley (west and east-facing slopes), and Snodgrass (east-facing slope) within the East River watershed. Part of this survey was used to investigate soil-plant interactions at the hillslope scale in Jashvina et al. 2020.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Comprehensive Baseline Environmental Monitoring of an Interim Legacy Waste Store in Arid Zone Australia - 20062

Radionuclide containing soil and rubble from the clean-up of a former uranium, thorium and rare earth minerals processing research facility carried out in the early 50's and 60's is currently stored at the Woomera Test Range in South Australia awaiting final disposal. Prior to developing a final disposal pathway commensurate with waste acceptance criteria, a comprehensive baseline environmental monitoring has been carried out to establish the background radiation levels. The survey included in situ gamma scanning of the surface soil ({sup 238}U, {sup 232}Th, {sup 40}K), a laboratory analysis of 86 soil samples (from 0-20 cm depth), which involved XRF measurements (U, Th, and rare earth metals) and spectroscopic analysis ({sup 238}U, {sup 232}Th, {sup 226}Ra and daughter nuclides). A time series of radon concentration measurements in air was established, while soil radon ({sup 222}Rn) and thoron ({sup 220}Rn) flux measurements were undertaken at 18 different locations. The 2018 comprehensive baseline survey demonstrated radiation levels in the immediate vicinity of the Woomera interim waste store are typical background values of soil and rock. No contamination was detected. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Subtask 1.3 – Integrated Carbon Capture and Storage for North Dakota Ethanol Production

The Energy & Environmental Research Center (EERC), in partnership with Red Trail Energy, LLC (RTE), a North Dakota ethanol producer; the North Dakota Industrial Commission (NDIC) Renewable Energy Program (REP); and the U.S. Department of Energy (DOE), conducted a feasibility and implementation study for a commercial carbon capture and storage (CCS) effort. This subtask provided technical support and developed recommended practices of how small-scale industrial CO2 emitters (<1,000,000 tonnes of CO2 emitted annually) may economically deploy CCS. The 64-million-gallon dry mill RTE ethanol facility, emitting an average 180,000 tonnes of CO2 annually, was the subject of the case study. The positive outcome of this research, which shows technical and economic potential for ethanol–CCS in North Dakota, has resulted in RTE acquiring an approved Permit to Drill on December 2, 2019, for a stratigraphic test well in early 2020, a necessary step toward a North Dakota CO2 Storage Facility Permit (SFP) for the RTE CCS effort. Outcomes include 1) validating the Broom Creek Formation as a regional target for CCS, 2) determining the full carbon life cycle of an industrial fuel production facility with CCS, 3) developing a field implementation plan (FIP) for small-scale CCS, and 4) determining the validity and pathway for using CCS to meet low-carbon fuel (LCF) standards. The technical team included the EERC, RTE, Trimeric Corporation, Schlumberger Carbon Services, and Computer Modelling Group (CMG). Findings from activities conducted November 2016 – May 2020 are summarized as follows. Several key steps have been accomplished toward validating the Broom Creek Formation as a CO2 injection and storage target at the RTE CCS site, including verification of the presence and structure of sandstone layers that may comprise the potential CO2 storage reservoir and the several thousand feet of overlying confining zone. Work included site characterization using existing data, interpretation of seismic data within the study area, and geologic modeling simulation of CO2 injection. Interpreted results estimate 3000 feet of confining zone between the Broom Creek Formation (storage target) and the lowermost underground source of drinking water (e.g., the Fox Hills Formation). The thickness of the Broom Creek injection target varies 230–420 ft within the survey area. Results were used to inform the location of a stratigraphic test well and associated characterization test program. No impediments were identified within the targeted CO2 storage complex that would prevent the project from moving forward. A stratigraphic test well is the next step to validate these results and to acquire remaining data necessary to develop a North Dakota CO2 SFP application. The EERC generated full carbon life cycle estimates for CCS integration with the RTE ethanol facility. Results indicated that an average 40% reduction in CO2 emissions is possible through CCS implementation. Approximately half of the carbon in the overall life cycle for a dry mill ethanol plant is generated through the fermentation process and emitted to the atmosphere; this is the CO2 stream targeted for CCS. The remaining carbon is attributed to corn feedstock farming (diesel, fertilizer), energy for fuel processing (natural gas, electricity), and transportation (diesel) of the fuel product. Life cycle carbon estimates are also affected by the anticipated energy consumption of a potential capture facility, which depend on the type of CO2 product generated. For example, a 30%–40% net CO2 emission reduction is estimated if a liquefied CO2 facility were incorporated compared to a 40%–50% net CO2 reduction if a supercritical “injection-grade” CO2 product is generated; i.e., more energy is required to further refine the CO2 stream, affecting the full carbon life cycle estimates. A CCS FIP was developed and initiated at the RTE CCS site, resulting in the development of several guidance documents: a CO2 Capture Process Design Package, a North Dakota CO2 geologic Storage Permits Template, and a Public Outreach Package for CCS in North Dakota. General FIP components include CO2 capture system, pipeline and well designs; monitoring, verification, and accounting (MVA) plans; geologic characterization and testing programs; and permitting and outreach plans. Vendor bids were also acquired for the CO2 liquefaction facility. Near-surface characterization (groundwater and soil gas sampling) and geologic characterization (seismic survey) were initiated to inform development of a UIC Class VI-compliant MVA plan compliant with a North Dakota CO2 SFP. Designs (well and geologic testing) were completed for a stratigraphic test well compliant with a North Dakota CO2 SFP. In addition, the outreach plan was executed, including community open houses, meetings with city/county/state officials, and development of public materials. Although other entities continued to mature incentive programs in 2019–2020, California and the Internal Revenue Service (IRS) currently provide the most advanced economic opportunities for CCS integrated with fuel production. The California Low-Carbon Fuel Standard (LCFS) adopted a CCS Protocol in January 2019, allowing submittal of a design-based pathway (DBP) application for an approved temporary (not certified) carbon intensity value for a fully engineered facility. An ethanol–CCS DBP application to the California LCFS Program (officially approved February 28, 2020) was developed to show that the RTE CCS effort meets LCFS requirements. The approved DBP provides confidence to advance the project and supports potential investments. Other entities continue to mature incentive programs. The IRS issued guidance in February 2020 that addresses the definition of beginning of construction and revenue procedure on partnerships for the Enhancement of Carbon Dioxide Sequestration Credit (a.k.a. Section 45Q) CCS tax credit program; the IRS anticipates issuing further guidance on issues such as secure geologic storage, utilization qualifications, and recapture of claimed credits. Maturing incentive programs coupled with workable permitting regulations provide confidence to advance CCS projects in North Dakota and support financial investment to proceed with designing, constructing, and implementing CCS projects at small-scale fuel production facilities. The largest hurdles for CCS implementation at small-scale industrial systems are often business/economic-related (i.e., not technical). Market uncertainty already exists for agriculture-based alternative fuels such as corn ethanol, for which production has increased by ~33%, and prices have correspondingly lowered since 2015. Passing the Section 45Q tax credit program improves economic feasibility for CCS but may require external investors for a small business to achieve maximum benefits. Public–private partnerships with NDIC and DOE have resulted in foundational technical and regulatory knowledge, growing stakeholder confidence, and a pathway to implementation that enables similar industrial CCS projects in the region to advance. This subtask was funded through the EERC–DOE Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by NDIC and RTE. The authors would also like to thank CMG, ESRI, IHS, Neuralog, and Schlumberger for allowing the use of their software packages in support of this work.

42 ENGINEERING↗
DOE OSTI2025

White Rock Canyon Riparian Monitoring

Lands at Los Alamos National Laboratory (LANL) are owned and managed by the Department of Energy, National Nuclear Security Administration (DOE/NNSA). The Laboratory’s eastern boundary is in White Rock Canyon (WRC) along the Rio Grande within Technical Areas (TAs) 70 and 33, with approximately 4 miles of property along the river (Figure 1). Feral cattle have been documented along the Rio Grande in WRC since the 1980s. Cattle activity is known to be especially harmful to riparian ecosystems, which are hubs for biodiversity and crucial habitat used by multiple endangered species in this region, including the Southwestern Willow Flycatcher and Yellow-billed Cuckoo on LANL property (Poessel 2020, Sanchez 2021). To gain a comprehensive understanding of the status of riparian ecosystems within WRC and the damage feral cattle populations are imposing, ecologists at LANL conducted a month-long vegetation monitoring project in September 2025. Riparian vegetation monitoring protocols and rapid assessments of cattle impacts were used to quantify the intensity and extent of cattle damage. The data collected will be used as a baseline for comparison following the removal of feral cattle from the canyon. Abundant cattle sign indicates current and heavy utilization of the riparian areas that were surveyed. There are multiple wallowing areas where soils are completely denuded of vegetation and highly compacted. Based on the severity and extent of impact observed in these areas, cattle use appears consistent and on-going over an extended period of years, supporting the need for removal and restoration management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Abstract Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Molecular and morphological characterization of a first report of Cactodera torreyanae Cid del Prado Vera & Subbotin, 2014 (Nematoda: Heteroderidae) from Minnesota, the United States of America

Cactodera torreyanae Cid del Prado Vera & Subbotin, 2014 cysts were discovered during a Pale Potato Cyst Nematode (PCN) survey conducted by Minnesota Department of Agriculture as part of the Animal and Plant Health Inspection Service (APHIS) efforts to survey states for the presence of PCN. The soil samples were collected from a potato field, located in Karlstad, Kittson County, Minnesota, USA. Two out of 175 vials submitted for identification to the Mycology and Nematology Genetic Diversity and Biology Laboratory (MNGDBL) contained few cysts and juveniles of C. torreyanae. Cysts were dark brown in color, lemon-shaped to elongated with distinct vulval cone. Vulva with denticles present around fenestra, cyst length to width ratio between 1.6 and 2.3 and anus distinct. The juveniles had rounded stylet knobs, some sloping slightly posteriorly. The molecular analysis included sequence and phylogenetic analysis of ITS rRNA, D2-D3 expansion segments of 28S rRNA and COI of mtDNA genes. The nematode species was identified by both morphological and molecular means as Cactodera torreyanae. To the best of our knowledge this represents the first report of Cactodera torreyanae from the United States and first report of this cyst nematode species from potato fields. Definite host plant for this nematode remains unknown.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

NGEE Arctic 2019 Alder Ground Truth Survey, Seward Peninsula AK

In July 2019 we made traveled the road system outside of Nome, AK and detailed the GPS coordinates of alder shrublands for the purpose of ground-truthing alder maps of the region. Both visual and ground-based observations were made for patches of alder shrublands greater 5x5m and larger, ideally 10x10m. Visual observations were made from the car and GPS coordinates are approximate, placed by dropping pins on georeferenced pdfs using the Avenza app. Visual observations included positive identified alder shrublands as well as thickets of non-alder shrubs. Ground Observations were made at a subset of locations where we were able to hike to alders shrubland areas. Ground observations include GPS points (made with Garmin InReach) as well as relevant features of a centrally located, representative alder shrub in the patch (max height, basal diameter of all ramets, soil depth). Aboveground biomass (weight dry mass) of the surveyed shrub was calculated based on alder-specific allometric equations in Berner et al 2015 which our team checked for accuracy for the Seward Peninsula as part of Salmon et al 2019. This dataset contains three data files, three data dictionaries, and one file-level metadata file all in*.csv format plus one *.txt README file. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Opportunities to Implement Solutions to Achieve Remedial Action Objectives in Consideration of Stakeholder Interests - 20365

A case study in the implementation of a soils excavation and removal project conducted at a Formerly Utilized Sites Remedial Action Program (FUSRAP) Maywood Superfund Site (FMSS) vicinity property; an active commercial business, in a densely populated area, with significant operational, technical and, logistical constraints that were expected to limit areas that could be remediated. The United States Army Corps of Engineers-led (USACE) team successfully navigated complex overlapping stakeholder interests to achieve a more efficient and complete removal of contaminated soils and debris while minimizing unnecessary excess costs to the Government. This paper centers on FUSRAP activities at the FMSS vicinity property located at 149-151 Maywood Avenue, Maywood, Bergen County, New Jersey. For most of its FUSRAP history, this ∼109,000 square meter (27-acre) property housed a now-demolished ∼26,000 square meter (6.5-acre) warehouse operated by Sears Logistics Services, a unit of the Sears Roebuck Company (Figure 2). Sears ended its property lease and vacated the warehouse in December 2016. Given that long history and for the purposes of this paper, the property will be referred to as the 'Sears property' or simply 'the property.' The Sears property is approximately 109,000 square meters (27-acres) and is currently zoned for commercial use. The property is bound to the north and northwest by 100 West Hunter Avenue (the Stepan Company), to the northeast by 205 Maywood Avenue, to the east by Maywood Avenue, to the south by 23 West Howcroft Road, and to the west by businesses on NJ Route 17 and the NJ Route 17 roadway. Until December 2016, the property housed a warehouse and distribution center operated by Sears Logistical Services. On-site structures were demolished by the property owner in 2017. The warehouse covered the north section of the property along the Stepan Company property line. A railroad spur from the adjacent property now known as the Maywood Interim Storage Site (MISS) ended at the northeast corner of the warehouse. Wetlands were located east of the warehouse; the rest of the property was covered with paved parking lots and grassed areas. During remediation at the property, opportunities frequently arose where the project team was able to coordinate effectively with stakeholders to sequence remediation activities to facilitate removal of otherwise inaccessible soils and identify opportunities for materials reuse when supported by residual radiological and chemical levels. Some specific opportunities include: - remediating individual truck loading dock bays to maintain tenant operations; - working along a busy highway and in a utility corridor containing a 30-inch high pressure gas main; - remediating Lodi Brook and associated wetlands requiring bypass pumping and other diversionary structures to maintain local community stormwater drainage; - protecting during remediation and supporting access to facilitate tenant/owner maintenance of critical fire protection and water supply system service lines buried in contaminated soils and necessary for safe warehouse operations; and - coordinating with stakeholders to ensure non-radiological contaminants of concern for the site (unaffiliated with FUSRAP) were addressed by the responsible party in a manner that maximized benefit to all parties while supporting an efficient overall site remediation program. Once the property was vacant and the warehouse structure and radiologically non-impacted above-grade structures were demolished, the project identified an opportunity to significantly reduce the volume of waste associated with the foundation of the former warehouse, a foundation suspected of being partially constructed in radiologically contaminated soils. The project developed and implemented supplemental radiological verification survey and sampling strategies based on radiological cross-contamination risk potential with process flow-charts and screening-level based decision points; a program that classified saw-cut sections of concrete based on observed residual surface radioactivity conditions using a combination of gamma sensitive sodium-iodide scans and beta sensitive Geiger-Muller direct measurements. The proposed approach was reviewed with stakeholders with feedback, including consideration of applicable State of New Jersey Site Remediation Program criteria and guidance before implementation. Once classified, additional sampling was performed at frequencies driven by screening. The sampling methods, stockpile sampling frequencies, criteria and, approach to data evaluation were developed in consideration of existing site cleanup standards, regional background ranges, State of New Jersey radiological remediation program guidance, and specific stakeholder input With the property remediation and survey efforts nearly completed, it is relevant to examine retrospectively the objectives, assumptions and limitations in the remedial design (i.e., what was planned) versus what was able to be accomplished through effective teaming. Benefits to other environmental remediation site programs include better understanding of how to work effectively with stakeholders to achieve win-win outcomes, and approaches to site remediation, waste minimization and materials reuse that were successful in their overall outcomes. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Bedrock architecture, soil texture, and hyporheic zone characterization combining electrical resistivity and induced polarization imaging

The shallow (<15 m depth) subsurface environment of a short reach along a bedrock stream was investigated with electrical resistivity and induced polarization (IP) to map details of bedrock and soil sediments. The bedrock is mostly comprised of limestone, and is generally resistive compared to the overlying soil. The soil-bedrock interface was determined through a trial and error approach using a sharp boundary feature in the inversion model. The inferred bedrock surface determined from the inversions exhibited undulating patterns with troughs and ridges. A near continuous trough ran alongside the stream within the floodplain, and is suggestive of a paleochannel among other interpretations of this feature. The structure of the electrical resistivity above the bedrock showed small-scale elongated features. The chargeability from the IP method showed larger scale features. High values of chargeability were associated with the sediments in the floodplain, and low values were associated with bedrock, stream, and soil on the elevated banks above the stream. If the chargeability is associated with membrane polarization characteristic of clayey soils, then IP seems to highlight the mere existence of clay, while the resistivity may be more discernable of the relative proportion of clay. Vegetation differences may also explain the chargeability distribution, where parts of the survey with high chargeability had dense pine with no understory making the soils more organically rich.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Morphological and Molecular Characterization of Punctodera stonei Brzeski, 1998 (Nematoda: Heteroderidae) from Virginia, USA

In August of 2021, several cysts with juveniles and eggs were discovered during a vegetation survey conducted at the Arlington National Cemetery, Virginia. Eight soil samples were collected from the rhizosphere region of the common grass (Festuca arundinacea L.) and processed at the Mycology and Nematology Genetic Diversity and Biology Laboratory (MNGDBL). Cysts were light to dark brown in color, and oval to pear-shaped without bullae in young cysts but present in older cysts and with prominent vulval cone. The juveniles had slightly concave stylet knobs projecting sometimes anteriorly, tail tapering gradually to a narrowly rounded terminus, and hyaline tail terminus conspicuous at least twice the length of stylet. The molecular analysis included the analysis of three gene sequence fragments: D2–D3 of 28S rRNA, ITS rRNA, and COI. The nematode species was identified by both morphological and molecular means as Stone's cyst nematode, Punctodera stonei. Detection of P. stonei in Virginia represents a new record of this species in the United States, and a second report after Canada in North America.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Epidemiological Investigation of a Mortality Event in a Translocated Gopher Tortoise (Gopherus polyphemus) Population in Northwest Florida

Nokuse Plantation, a 22,055 ha private conservation preserve in northwest Florida, is a recipient site for gopher tortoises translocated from development sites in Florida. Since 2006, Nokuse has received over 5,000 tortoises from multiple development sites. During 2013–2015, 52 tortoises were found sick (n = 14) or dead (n = 38) in multiple soft-release enclosures in which tortoises consistently exhibited clinical signs, with additional sick (n = 5) and dead (n = 5) tortoises presenting similarly during 2016–2017. When found alive, tortoises behaved abnormally (e.g., frequently out of burrows during cold weather, pacing along enclosure fencing), appeared emaciated, were lethargic, and had developed redness under plastron scutes. Similar numbers of male (n = 28) and female (n = 32) tortoises were recovered along with two of unidentified sex, including mainly adults (n = 59) and three subadults. Physical examination, blood analysis, and other diagnostics were indicative of starvation and dehydration. Most sick tortoises provided with supportive care recovered. Necropsy findings generally confirmed starvation, with no evidence of infectious pathogens or contaminants. There were no apparent differences in quality of habitat, plant community, or soil or water among affected and unaffected enclosures. Botanical surveys indicated adequate forage quality and quantity, with no poisonous exotic or native plants detected. No land management practices changed prior to this event. Analysis of epidemiological data and demographic factors from before and during this mortality event identified initial density of tortoises in the enclosures as exerting the strongest influence on detection of tortoise morbidity and mortality. We believe that the stress associated with mixing tortoises from different populations and at higher densities during translocation impacted an individual tortoise’s ability to obtain or absorb adequate nutrients from foraging, ultimately leading to a wasting condition consistent with starvation. Based on our findings, we recommend a maximum of 3 gopher tortoises per ha in soft-release enclosures for translocation, but further research is warranted to investigate the complexity of stress and social pressures associated with translocation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Mapping the soil microbiome functions shaping wetland methane emissions

Accounting for only 8% of Earth’s land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.

MAG↗
DOE OSTI2021

Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland

Microbial communities are early responders to wetland degradation, and instrumental players in the reversal of this degradation. However, our understanding of soil microbial community structure and function throughout wetland development remains incomplete. We conducted a survey across cranberry farms, young retired farms, old retired farms, flooded former farms, ecologically restored former farms, and natural reference wetlands with no history of cranberry farming. We investigated the relationship between the microbial community and soil characteristics that restoration intends to maximize, such as soil organic matter, cation exchange capacity and denitrification potential. Among the five treatments considered, flooded and restored sites had the highest prokaryote and microeukaryote community similarity to natural wetlands. In contrast, young retired sites had similar communities to farms, and old retired sites failed to develop wetland microbial communities or functions. Canonical analysis of principal coordinates revealed that soil variables, in particular potassium base saturation, sodium, and denitrification potential, explained 45% of the variation in prokaryote communities and 44% of the variation in microeukaryote communities, segregating soil samples into two clouds in ordination space: farm, old retired and young retired sites on one side and restored, flooded, and natural sites on the other. Heat trees revealed possible prokaryotic ( Gemmatimonadetes ) and microeukaryotic ( Rhizaria ) indicators of wetland development, along with a drop in the dominance of Nucletmycea in restored sites, a class that includes suspected mycorrhizal symbionts of the cranberry crop. Flooded sites showed the strongest evidence of wetland development, with triple the soil organic matter accumulation, double the cation exchange capacity, and seventy times the denitrification potential compared to farms. However, given that flooding does not promote any of the watershed or habitat benefits as ecological restoration, we suggest that flooding can be used to stimulate beneficial microbial communities and soil functions during the restoration waiting period, or when restoration is not an option.

Rubin, Rachel L. (ORCID:0000000284326811)↗
DOE OSTI2025

On the emergent scale of bedrock groundwater contribution to headwater mountain streams

We investigated the contribution of bedrock groundwater to streamflow as a function of catchment scale in a headwater stream. Synoptic surveys were conducted during hydrologically important periods of the year using multiple environmental tracers in stream water, soil water, and bedrock groundwater, along a first-order montane stream, in west-central Montana. Sampled analytes included 222 Rn, used to constrain total subsurface flux, and major and minor elements, used in end-member mixing analysis (EMMA) to identify the contributions of soil and bedrock groundwater to the stream. Partitioning between soil-derived and bedrock-derived groundwater was then analyzed as a function of the incremental and accumulated sub-catchment sizes. Radon results indicated that subsurface water contributions accounted for the majority of streamflow at all surveyed times. EMMA results revealed that the bedrock groundwater contribution to streamflow varied between 26% during peak snowmelt and 44% during late summer. Streamflow generation was dominated by soil groundwater contribution along the entire reach, but the bedrock groundwater contribution increased consistently with accumulated sub-catchment size. However, groundwater contributions were not well-correlated with incremental sub-catchment size. The scale at which increased bedrock groundwater discharge can be correlated with sub-catchment size appears to be >1 km 2 for our study. Our results are consistent with a conceptual model where streamflow is predominantly generated by a 3D subsurface nested flow system. Local subsurface heterogeneities control the stream source at local scales but begin to average out at scales >2 km 2 . Our study indicates that, while soil groundwater is the dominant source, bedrock groundwater remains an important and predictable contributor to streamflow throughout the year, even in a snow-dominated, mountainous headwater catchment.

environmental tracers↗