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DOE OSTI2024

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

59 BASIC BIOLOGICAL 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 OSTI2022

Using atmospheric observations to quantify annual biogenic carbon dioxide fluxes on the Alaska North Slope

The continued warming of the Arctic could release vast stores of carbon into the atmosphere from high-latitude ecosystems, especially from thawing permafrost. Increasing uptake of carbon dioxide (CO 2 ) by vegetation during longer growing seasons may partially offset such release of carbon. However, evidence of significant net annual release of carbon from site-level observations and model simulations across tundra ecosystems has been inconclusive. To address this knowledge gap, we combined top-down observations of atmospheric CO 2 concentration enhancements from aircraft and a tall tower, which integrate ecosystem exchange over large regions, with bottom-up observed CO 2 fluxes from tundra environments and found that the Alaska North Slope is not a consistent net source nor net sink of CO 2 to the atmosphere (ranging from ₋6 to +6 Tg C yr -1 for 2012–2017). Our analysis suggests that significant biogenic CO 2 fluxes from unfrozen terrestrial soils, and likely inland waters, during the early cold season (September–December) are major factors in determining the net annual carbon balance of the North Slope, implying strong sensitivity to the rapidly warming freeze-up period. At the regional level, we find no evidence of the previously reported large late-cold-season (January–April) CO 2 emissions to the atmosphere during the study period. Despite the importance of the cold-season CO 2 emissions to the annual total, the interannual variability in the net CO 2 flux is driven by the variability in growing season fluxes. During the growing season, the regional net CO 2 flux is also highly sensitive to the distribution of tundra vegetation types throughout the North Slope. This study shows that quantification and characterization of year-round CO 2 fluxes from the heterogeneous terrestrial and aquatic ecosystems in the Arctic using both site-level and atmospheric observations are important to accurately project the Earth system response to future warming.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Seasonal drivers of dissolved oxygen across a tidal creek–marsh interface revealed by machine learning

Abstract Dissolved oxygen (DO) is a key biogeochemical control in coastal systems, and its concentration and drivers vary markedly through time and space. This makes it difficult to accurately represent coastal DO and associated biogeochemical processes in models, limiting our ability to predict how these systems will respond to global change. We obtained high‐frequency (5‐min) in situ measurements of DO collected at three locations across the interface of a tidal creek and coastal marsh in the Pacific Northwest, USA. Random Forest machine learning models quantified the importance of three categories of environmental drivers (Aquatic, Climatic, and Terrestrial) of DO variability across the creek–marsh interface. We selected two 4‐month datasets representing Summer and Winter seasonal periods to test two hypotheses on the dominant drivers of DO at the coastal interface. We found that the Terrestrial driver—characterized by long periods of anaerobic conditions and episodic pulses in DO after floods—was most important during the Winter, whereas the Aquatic driver—characterized by variability over tidal, diel, and lunar cycles—was most important during the Summer. We explored how future climate change scenarios could alter the drivers of DO variability using a cumulative sums driver–response framework. Our results suggest that under climate change, Aquatic and Climatic drivers may increase in importance during the Summer, potentially linked to changing metabolic regimes and sea level, with Terrestrial driver importance potentially increasing during the Winter. Our approach highlights useful methods for understanding the spatiotemporal complexity of oxygen across coastal interfaces and quantifying the relative importance of distinct environmental drivers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

scMicrobe PTA: near complete genomes from single bacterial cells

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil ® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the Is PETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as Is PETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Radiological Impact of 2023 Operations at the Savannah River Site

This report presents the environmental dose assessment methods and the estimated potential doses to the public from 2023 Savannah River Site (SRS) air and liquid radioactive releases. Also documented are potential doses from special-case exposure scenarios, such as the consumption of wildlife or goat milk. Dose to the Offsite Representative Person The 2023 dose to the offsite representative person from SRS liquid releases was 0.14 mrem and from SRS air releases it was 0.016 mrem. To show compliance with the U. S. Department of Energy (DOE) all pathway dose standard of 100 mrem/yr, SRS conservatively adds these two doses for a total representative person dose of 0.16 mrem which is 0.16% of the DOE standard. Sportsman Doses Onsite Hunter: SRS conducts annual hunts to control onsite deer and feral hog populations. The estimated dose from consuming harvested deer or hog meat is determined for every onsite hunter. During 2023, the maximum potential dose an onsite hunter received was 9.42 mrem, or 9.42% of DOE’s 100 mrem/yr all pathway dose standard. Creek Mouth Fisherman: SRS estimated the maximum potential dose from fish consumption at 0.17 mrem from bass collected at the mouth of Lower Three Runs. This dose is 0.17% of the DOE standard. SRS bases this hypothetical dose on the low probability scenario that, during 2023, a fisherman consumed 24 kg (53 lbs) of bass caught exclusively from the mouth of Lower Three Runs. Release of Material Containing Residual Radioactivity SRS did not release any real property (land or buildings) in 2023. SRS unconditionally released a total of 13,324 items of personal property (such as tools) from radiological areas in 2023. Most of these items did not leave the Site. However, all of these items required no additional radiological controls post-survey as they met DOE Order 458.1 release criteria. Radiation Dose to Aquatic and Terrestrial Biota SRS conducts screening evaluations of plant and animal doses for aquatic and terrestrial ecosystems. For 2023, all SRS aquatic system locations passed the initial (Level 1) screenings and no further assessments were required at those locations. For the land-based systems evaluation, SRS performed initial screenings using concentration data from the five onsite radiological soil sampling locations. Typically, SRS collects and analyzes only one soil sample per year from each location. For 2023, all land-based locations passed their initial (Level 1) pathway screenings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H 2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Climate Change Risks to Freshwater Subsistence Fisheries in Arctic Alaska: Insights and Uncertainty from Broad Whitefish Coregonus nasus

Arctic freshwater ecosystems and fish populations are largely shaped by seasonal and long-term watershed hydrology. In this paper, we hypothesize how changing air temperature and precipitation will alter freeze and thaw processes, hydrology, and instream habitat to assess potential indirect effects, such as the change to the foraging and behavioral ecology, on Arctic fishes, using Broad Whitefish Coregonus nasus as an indicator species. Climate change is expected to continue to alter hydrologic pathways, flow regimes, and, therefore, habitat suitability, connectivity, and availability for fishes. Warming and lengthening of the growing season will likely increase fish growth rates; however, the exceedance of threshold stream temperatures will likely increase physiological stress and alter life histories. We expect these changes to have mixed effects on Arctic subsistence fishes and fisheries. Management and conservation approaches focused on preserving the processes that create heterogeneity in aquatic habitats, genes, and communities will help maintain the resilience of Broad Whitefish and other important subsistence fisheries. Long-term effects are uncertain, so filling scientific knowledge gaps, such as identifying important habitats or increasing knowledge of abiotic variables in priority watersheds, is key to understanding and potentially mitigating likely impacts to Arctic fishes in a rapidly changing landscape.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Carbon Dioxide Fluxes to the Atmosphere From Waters Within Flooded Forests in the Amazon Basin

Aquatic habitats in the lowland Amazon emit large quantities of carbon dioxide (CO 2 ). However, information on CO 2 fluxes from seasonally flooded forests that constitute 80% of the surface area of aquatic environments in the lowland Amazon basin is sparse. We provide the first multi-year measurements of CO 2 exchanges within flooded forests of the central Amazon basin. Our approach combines measurement of dissolved CO 2 concentrations and fluxes between the water and atmosphere and ecological data. Although the rates of CO 2 emission by flooded forests are lower than other aquatic habitats, such as open waters in rivers and lakes, the combination of high CO 2 concentrations and a large area results in an appreciable regional out gassing of carbon dioxide from flooded forests. These fluxes can represent about half of the net primary production of flooded forests in the central Amazon basin.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Use Attainability Analysis Aquatic Life Uses for Perennial Reach of Sandia Canyon [Slides]

The following information will be presented during the February 23, 2022 Accord Pueblos Technical Meeting. The purpose of the study is to determine if natural thermal conditions are preventing the attainment of Coldwater Aquatic Life Use in the perennial reach of the upper Sandia Canyon Assessment Unit (Sandia AU). The New Mexico Water Quality Standards allow for a change in the designated use if a Use Attainability Analysis (UAA) demonstrates that the use is not attainable due to one or more of six factors listed in 40 CFR 131.10(g), including naturally occurring pollutant concentrations. The Sandia AU is located in a perennial reach of upper Sandia Canyon between Sigma Canyon and NPDES Outfall 001. The classified Segment 20.6.4.126 NMAC comprises perennial waters within Los Alamos National Laboratory boundaries and includes the Sandia AU. Persistent surface flows originate from NPDES permitted effluent releases. These releases have occurred since the early 1950’s and continue today. The UAA examines several lines of evidence. NMED’s Air-Water Temperature Correlation (AWTC) model is used for identifying appropriate stream classifications and attainable aquatic life use subcategories. The model correlates between July average air temperatures (ATEMP) and maximum weekly average stream temperatures. Air temperatures are obtained from PRISM and LANL Meteorological Towers and used to derive ATEMP. Thermographs were placed in the Sandia AU to obtain measured stream temperatures during summer months when stream temperatures are the highest. Measured data is used with AWTC modeled data to determine if the Sandia AU is meeting its natural air temperature driven thermal condition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Modeling exports of dissolved organic carbon from landscapes: a review of challenges and opportunities

Inland waters receive large quantities of dissolved organic carbon (DOC) from soils and act as conduits for the lateral transport of this terrestrially derived carbon, ultimately storing, mineralizing, or delivering it to oceans. The lateral DOC flux plays a crucial role in the global carbon cycle, and numerous models have been developed to estimate the DOC export from different landscapes. We reviewed 34 published models and compared their characteristics to identify challenges in model applications and opportunities for future model development. We classified these models into three types: indicator-driven, hydrology-forced, and process-based DOC export simulation models. They differ mainly in their environmental inputs, simulation approaches for soil DOC production, leaching from soils to inland waters, and transit through inland waters. It is essential to consider landscape characteristics, climate conditions, available data, and research questions when selecting the most appropriate model. Given the substantial assumptions associated with these models, sufficient measurements are required to benchmark estimates. Accurate accounting of terrestrially derived DOC export to oceans requires incorporating the DOC produced in aquatic ecosystems and deposited with rainwater; otherwise, global export estimates may be overestimated by 40.7%. Additionally, improving the representation of mineralization and burial processes in inland waters allows for more accurate accounting of carbon sequestration through land ecosystems. When all the inland water processes are ignored or assuming DOC leaching is equivalent to DOC export, the loss of soil carbon through this lateral flux could be underestimated by 43.9%.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Environmental Impacts of Closed-Loop Pumped Storage Hydropower

The goal of this report is to help license applicants, resource agencies, and other members of the hydropower community involved in closed-loop pumped storage hydropower permitting and licensing process, focus the scope of environmental reviews, and more quickly identify impacts with project nexus and potential mitigation measures for these impacts. Pumped storage hydropower (PSH) is an energy storage technology that uses energy to pump water up from a lower reservoir to an upper reservoir where water is stored until electricity is needed and the water is released to a lower reservoir passing through turbines. Closed-loop PSH—PSH that is not continuously connected to a naturally flowing water feature—is one of the lowest greenhouse gas emitting energy storage technologies and is therefore a critical part of the transition to renewable energy (Simon et al. 2023). Proposals for closed-loop PSH facilities in the United States currently account for more than 40% of original licenses and 99% of potential generation capacity in the Federal Energy Regulatory Commission (FERC) hydropower licensing pipeline (Johnson et al. 2023). While closed-loop PSH facilities can have lower environmental impacts than open-loop PSH facilities, no closed-loop facilities have been constructed in the United States to enable direct accounting of project impacts and efficacy of mitigations. Many proposals for closed-loop PSH submitted to FERC are abandoned early in the permitting and licensing process prior to license applications and environmental assessments, so there is little documentation describing potential project impacts and proposed mitigations. The newness of closed-loop PSH proposals in the United States may mean that tribal, federal, and state agencies with authorities for cultural and natural resources protection and management involved in the FERC licensing process may not have experience with closed-loop PSH regulation. Moreover, many proposed closed-loop PSH facilities are in areas that do not have high concentrations of conventional hydropower, so these agencies may also be unfamiliar with the FERC hydropower licensing process. The goal of this report is to help license applicants, resource agencies, and other members of the hydropower community focus the scope of environmental review for the closed-loop PSH development, licensing, and federal authorization process enabling quicker identification of potential impacts, mitigations, and situations where mitigation may not be possible. We found that environmental impacts of closed-loop PSH are highly site-specific, and generalizations about the types of environmental impacts across closed-loop PSH projects are difficult to make. Environmental impacts of closed-loop PSH are like those for open-loop PSH with a few exceptions including water sourcing, which can lead to delays and contention due to potential complexities with water rights, impacts to aquatic resources, and greenhouse gas emission potential. Cultural resource impacts were commonly reported in National Environmental Policy Act (NEPA) documents reviewed and discussed in interviews, but in many cases such impacts cannot be mitigated.

13 HYDRO ENERGY↗
DOE OSTI2020

Costs of mitigating the environmental impacts of hydropower projects in the United States

Developers are required to mitigate the environmental impacts of hydropower projects in the United States (U.S.) but there is very little accessible information on the associated costs. This work compiles and analyses a dataset of environmental impacts mitigation costs for 182 hydropower projects based on documents obtained from the U.S. Federal Energy Regulatory Commission (FERC). The analysis shows that environmental costs vary wildly across hydropower project classes and mitigation measures, even when normalized by plant capacity. Capital costs per kilowatt are generally higher for relicensed conventional hydropower plants, and lower for new and relicensed pumped storage hydropower plants, relative to other project classes. Smaller plants tend to spend a higher share of total project costs on mitigating environmental impacts than larger plants, and measures related to Aquatic Species, Project Operations, and Recreation have the highest capital cost per kilowatt. These findings mean that environmental costs could become a key decision variable for new hydropower developments in the U.S. due to the small scale of most of the remaining potential and the increasing stringency of environmental requirements. Therefore, technologies to reduce the environmental impacts and costs of hydropower would be important for future project developments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13 C-Tracer Analysis

Nitrospira spp. are globally abundant nitrifying bacteria in soil and aquatic ecosystems and in wastewater treatment plants, where they control the oxidation of nitrite to nitrate. Despite their critical contribution to nitrogen cycling across diverse environments, detailed understanding of their metabolic network and prediction of their function under different environmental conditions remains a major challenge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Trace Metal Dynamics and Limitations on Biogeochemical Cycling in Wetland Soils and Hyporheic Zones

Biogeochemical cycling in subsurface aquatic systems is driven by anaerobic microbial processes that employ metalloenzymes. Pure culture studies reveal that low availability of trace metals may inhibit methanogenesis, mercury methylation, and reduction of N 2 O to N 2 during denitrification. However, whether such limitations occur in natural subsurface aquatic systems is currently unclear. This project sought to establish mechanistic links between trace metal availability and biogeochemical transformations in subsurface systems. Integrated field and laboratory studies of trace metal availability and biogeochemical processes were conducted in riparian wetlands in the Tims Branch watershed at the Savannah River Site, marsh wetlands at Argonne National Laboratory, and the streambed of East Fork Poplar Creek at Oak Ridge National Laboratory, with supplemental work with wetland soils from sites in Missouri and Florida.

54 ENVIRONMENTAL SCIENCES↗
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

First observation of potential phoresy between Planorbarius metidjensis and Ancylus fluviatilis (Gastropoda: Planorbidae) in Algeria

Phoresy, an ecological phenomenon in which one organism attaches itself to another for dispersal, has been observed in various species. In this study, we describe the potential occurrence of phoresy between Ancylus fluviatilis and Planorbarius metidjensis in Algerian freshwater. Through field observations, we provide evidence to suggest that P. metidjensis may serve as a transport host for A. fluviatilis, facilitating its movement within aquatic ecosystems. Additionally, juvenile P. metidjensis were observed attached to adults of the same species, which may be a case of intraspecific phoresy. This interaction has implications for understanding the ecology and dispersal mechanisms of freshwater molluscs.

59 BASIC BIOLOGICAL SCIENCES↗