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48 records · Page 3

ESS-DIVE Reporting Format for Hydrologic Monitoring Data and Metadata

The ESS-DIVE Reporting Format (RF) for Hydrologic Monitoring Data and Metadata was designed for water level, temperature, electrical conductivity, specific conductance, dissolved oxygen, and pH measured in situ using sensors deployed in water bodies. It can also be applied to a broader suite of variables beyond its original scope. The RF is intended to provide clear and easy guidance to data generators aiming to upload consistent findable, accessible, interoperable, and reusable (FAIR) datasets. The RF includes instructions (pdf), a term guide (csv), templates (csv and xlsx), and a list of recommended vocabulary (csv) to equip the data generator with all of the tools needed to successfully apply the RF. There is also a crosswalk to some key data resources and standards (csv). Users should cite this dataset when using the RF but are encouraged to access the RF files on GitHub (https://github.com/ess-dive-community/essdive-hydrologic-monitoring) where the RF documentation is maintained and updated on the ESS-DIVE Community Space GitHub. Questions and suggestions for improvement can be submitted as GitHub issues.

54 ENVIRONMENTAL SCIENCES↗

Data for A Generalized Platform for Artificial Intelligence-powered Autonomous Protein Engineering

Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we report a generally applicable platform for autonomous enzyme engineering that integrates machine learning and large language models with biofoundry automation to eliminate the need for human intervention, judgement, and domain expertise. Requiring only an input protein sequence and a quantifiable way to measure fitness, this automated platform can be applied to engineer a wide array of proteins. As a proof of concept, we engineer Arabidopsis thaliana halide methyltransferase (AtHMT) for a 90-foldimprovement in substrate preference and 16-fold improvement in ethyl-transferase activity, along with developing a Yersinia mollaretii phytase (YmPhytase) variant with 26-fold improvement in activity at neutral pH. This is accomplished in four rounds over 4 weeks, while requiring construction and characterization of fewer than 500 variants for each enzyme. This platform for autonomous experimentation paves the way for rapid advancements across diverse industries, from medicine and biotechnology to renewable energy and sustainable chemistry.

AI/ML↗

Two Ligands of Interest in Recovering Uranium from the Oceans: The Correct Formation Constants of the Uranyl(VI) Cation with 2,2'-Bipyridyl-6,6'-dicarboxylic Acid and 1,10-Phenanthroline-2,9-dicarboxylic Acid

The ligands BDA (2,2'-bipyridyl-6,6'-dicarboxylic acid) and PDA (1,10-phenanthroline-2,9-dicarboxylic acid) are of interest as functional group types for ion-exchange materials for extracting uranium from the oceans, reported in a previous paper for PDA Lashley, M. A. ( Inorg. Chem. 2016 55 10818 10829). Yang, Y. ( Inorg. Chem. 2019, 58, 6064 6074) have published what they claim to be a more accurate result for the formation of the UO 2 2+ /PDA complex of log K 1 = 22.84 compared with our reported value of log K 1 = 16.5, as well as log K 1 = 21.52 for the BDA complex. The determination of log K 1 for the PDA and BDA complexes with the UO 2 2+ cation was carried out by Yang et al. using a competition reaction between DTPA (diethylenetriamine pentaacetic acid) and BDA or PDA, monitoring the absorbance due to the BDA and PDA ligands. This competition method using absorbance versus pH titrations was developed for determining the formation constants of the complexes of several polypyridyl ligands plus PDA complexes of metal ions, which were too stable for log K determination by competition with protons. A key feature of such titrations is that in the competition reaction, the displacement of the pyridyl donor ligand (e.g., PDA) by the competing ligand (e.g., DTPA), the absorbance spectrum of the displaced pyridyl donor ligand should be observed. Competing ligands used to date have been EDTA (ethylenediamine tetraacetic acid), DTPA, or the hydroxide ion. In the study of Yang et al., no such displaced PDA or BDA was apparent in the absorbance spectra in their titrations so that their reported log K 1 values have no validity. Their log K 1 values are so much higher than log K 1 for the uranyl DTPA complex (~13.6) that DTPA could not possibly displace BDA or PDA from the uranyl cation, and a competition reaction could not possibly occur. Here, we report the correct value of log K 1 = 15.4 (ionic strength = zero) for the uranyl BDA complex, to illustrate the correct determination of such a constant by a competition reaction between BDA and hydroxide, showing how the characteristic absorbance spectrum for a BDA complex, here the UO 2 2+ complex, disappears, and the distinctive absorbance spectrum of the free nonprotonated BDA ligand appears as the pH is increased, and BDA is displaced by the hydroxide ion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electrochemical Acid Sequestration to Ease Ocean Acidification (EASE-OA) - CRADA 600 (Abstract)

The PNNL team will coordinate logistics involved with setting up the field trial on the PNNL Sequim campus in collaboration with Ebb Carbon. Facilities on the PNNL Sequim campus are capable of pumping raw or filtered seawater from Sequim Bay at a rate ~45,000 L hr -1 , which can accommodate the 4000 L hr -1 requirement of the 200 ton CO2 yr-1 Ebb Carbon marine carbon dioxide removal (mCDR) system. The primary tasks for the PNNL team are 1) laying out appropriate indoor and outdoor spaces for installing the Ebb Carbon’s mCDR system, 2) facilitating Ebb Carbon’s access to the PNNL’s seawater intake on the PNNL Sequim campus, 3) conducting mesocosm experiments within the PNNL Sequim campus laboratories to test how the brine and base discharged from the Ebb Carbon system affect marine life, and 4) facilitating Ebb Carbon access to the PNNL Sequim installation site and aiding in maintenance as needed. In addition to these tasks, the PNNL team will provide surface water quality data (e.g., salinity, temperature, pH, dissolved O2) from a monitoring station located on the pier to contextualize starting conditions of the seawater used in the mCDR process. Finally, the PNNL team will also consult with Ebb Carbon on strategies for improving overall system performance and next steps for further scaling and/or monitoring the effectiveness of the mCDR system.

54 ENVIRONMENTAL SCIENCES↗

Mixing and dilution controls on marine CO 2 removal using alkalinity enhancement

Marine CO 2 removal (CDR) using enhanced-alkalinity seawater discharge was simulated in the estuarine waters of the Salish Sea, Washington, US. The high-alkalinity seawater would be generated using bipolar membrane electrodialysis technology to remove acid and the alkaline stream returned to the sea. Response of the receiving waters was evaluated using a shoreline resolving hydrodynamic model with biogeochemistry, and carbonate chemistry. Two sites, and two deployment scales, each with enhanced TA of 2997 mmol m -3 and a pH of 9 were simulated. The effects on air-sea CO 2 flux and pH in the near-field as well as over the larger estuary wide domain were assessed. The large-scale deployment (addition of 164 Mmoles TA yr -1 ) in a small embayment (Sequim Bay, 12.5 km 2 ) resulted in removal of 2066 T of CO 2 (45% of total simulated) at rate of 3756 mmol m -2 yr -1 , higher than the 63 mmol m -2 yr -1 required globally to remove 1.0 GT CO 2 yr -1 . It also reduced acidity in the bay, ΔpH ≈ +0.1 pH units, an amount comparable to the historic impacts of anthropogenic acidification in the Salish Sea. The mixing and dilution of added TA with distance from the source results in reduced CDR rates such that comparable amount 2176 T CO 2 yr -1 was removed over >1000 fold larger area of the rest of the model domain. There is the potential for more removal occurring beyond the region modeled. The CDR from reduction of outgassing between October and May accounts for as much as 90% of total CDR simulated. Of the total, only 375 T CO 2 yr -1 (8%) was from the open shelf portion of the model domain. With shallow depths limiting vertical mixing, nearshore estuarine waters may provide a more rapid removal of CO 2 using alkalinity enhancement relative to deeper oceanic sites.

54 ENVIRONMENTAL SCIENCES↗

Geochemical, Biological, and Clumped Isotopologue Evidence for Substantial Microbial Methane Production Under Carbon Limitation in Serpentinites of the Samail Ophiolite, Oman

In hyperalkaline (pH > 10) fluids that have participated in low-temperature (<150°C) serpentinization reactions, the dominant form of C is often methane (CH 4 ), but the origin of this CH 4 is uncertain. To assess CH 4 origin in serpentinite aquifers within the Samail Ophiolite, Oman, we determined fluid chemical compositions, analyzed taxonomic profiles of fluid-hosted microbial communities, and measured isotopic compositions of hydrocarbon gases. We found that 16S rRNA gene sequences affiliated with methanogens were widespread in the aquifer. We measured clumped isotopologue ( 13 CH 3 D and 12 CH 2 D 2 ) relative abundances less than equilibrium, consistent with substantial microbial CH 4 production. Furthermore, we observed an inverse relationship between dissolved inorganic C concentrations and δ 13 C CH 4 across fluids bearing microbiological evidence of methanogenic activity, suggesting that the apparent C isotope effect of microbial methanogenesis is modulated by C availability. An additional source of CH 4 is evidenced by the presence of CH 4 -bearing fluid inclusions in the Samail Ophiolite and our measurement of high δ 13 C values of ethane and propane, which are similar to those reported in studies of CH 4 -rich inclusions in rocks from the oceanic lithosphere. In addition, we observed 16S rRNA gene sequences affiliated with aerobic methanotrophs and, in lower abundance, anaerobic methanotrophs, indicating that microbial consumption of CH 4 in the ophiolite may further enrich CH 4 in 13 C. We conclude that substantial microbial CH 4 is produced under varying degrees of C limitation and mixes with abiotic CH 4 released from fluid inclusions. This study lends insight into the functioning of microbial ecosystems supported by water/rock reactions.

58 GEOSCIENCES↗

Reaction path model of the formation of abiotic immiscible hydrocarbon fluids in subducted carbonated serpentinites, Lanzo Massif (Western Italian Alps)

Fluids generated from subducted slabs participate in the cycling of deep carbon in the crust and upper mantle. In these fluids, aqueous carbon species vary in oxidation state between +IV and -IV depending on whether the fluids are oxidizing or reducing, respectively. Most studies of subduction-zone fluids have focused on oxidized carbon species. However, recent studies of natural samples have demonstrated the occurrence of deep, reducing fluids, generated in both subducted oceanic upper mantle and crustal rocks. CH 4 -H 2 -rich fluid inclusions in subducted carbonated serpentinites have demonstrated the existence of abiotic, immiscible, hydrocarbon fluids at upper mantle conditions. To investigate the formation of such immiscible hydrocarbon fluids during the evolution of subducted carbonated serpentinites, we used equilibrium constants from the Deep Earth Water model to carry out predictive chemical mass transfer modeling to simulate the alteration reactions. A novel feature of the models was the inclusion of an immiscible hydrocarbon fluid containing six components (CH 4,f , C 2 H 6,f , C 3 H 8,f , isoC 4 H 10,f , CO 2,f , H 2,f ). This feature enabled prediction of the formation of a separate immiscible fluid in equilibrium with aqueous species and minerals. We developed a predictive reaction path model of invasive H 2,f reacting with carbonated serpentinites and interstitial aqueous fluids for comparison with the natural samples from the Lanzo Massif, western Italian Alps. Over a range of temperatures and pressures, immiscible hydrocarbon fluids formed in association with altered mineral assemblages. Reaction progress caused the transformation of carbonated serpentinites and the formation of clinopyroxene, brucite, graphite, and hydrocarbon fluids, along with changes of pH, logfO 2 , and aqueous species. CH 4,f was the most abundant hydrocarbon species in all the models. The overall results at 2.0 GPa and 400 to 450 °C were consistent with the natural samples from the Lanzo Massif. Interestingly, large amounts of H 2 O formed due to oxidation of H 2 . More hydrocarbons and H 2 O formed in models with lower fluid/rock mass ratios or with more reactant H 2 . Models at different pressure and temperature conditions showed similar results with some variation in the relative stabilities of aragonite, graphite and olivine solid solution, and associated differences in mineral sequences, hydrocarbon fluids, values of aqueous species, and the final log fO 2 and pH. As a result, our models strongly support the laboratory and field evidence that reduction of carbonated serpentinites by infiltrating H 2 fluids can cause the formation of immiscible, abiotic hydrocarbon fluids in subduction zones.

58 GEOSCIENCES↗

Radical Treatment of Haloacetonitriles in Aqueous Systems: A Kinetic Study

Haloacetonitriles (HANs) are important drinking water disinfection byproducts formed through the chlorination and chloramination of amino acids. Although HAN concentrations in treated water are usually lower than trihalomethanes, they are still of major concern due to their higher cyto- and genotoxicity. HANs undergo chemical transformations by hydrolysis on the hour to week time scales; however, for possible direct water reuse situations, their active removal using advanced oxidation/reduction processes (AO/RPs) may be required. We report here our systematic kinetic study of the four major AO/RP radiolysis species, oxidizing hydroxyl (·OH) and sulfate (SO 4 −· ) radicals and reducing hydrated electron (e aq − ) and hydrogen atoms (H · ) with five HANs (mono-, di-, and trichloroacetonitriles and mono- and dibromoacetonitriles) in water measured using electron pulse radiolysis techniques. At ambient temperatures and pH 1−7, significant reactivity was found for e aq − ( k = (1−5) × 10 10 M −1 s −1 ) and H · atoms ( k = (1 − 40 × 10 7 M −1 s −1 ), but only minimal oxidation by ·OH ( k = (0.6−10) × 10 7 M −1 s −1 ) and SO 4 −· ( k = (0.2−4) × 10 6 M −1 s −1 ) occurred. These data suggest that the large-scale AO/RP treatment of these contaminants will be effective for deaerated reducing systems, where the reductive electron-induced degradation of HANs will occur.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data for Roebuck et al. (2025), "Differences in dissolved organic matter composition between rivers and estuaries is conserved across freshwater and saltwater coastal regions"

Dissolved organic matter (DOM) in coastal surface waters influences local water quality and is an important component of biogeochemical cycling in coastal systems, but the processes that alter DOM composition along lower reaches of rivers and estuarine waters are poorly understood. Roebuck et al. (2025) leveraged a spatially distributed community sampling effort in coastal ecosystems across two regions to identify broad spatial drivers of surface water DOM composition and identify transferable trends between saltwater and freshwater coastal systems. Samples were collected by community members from 47 locations within the mid-Atlantic and Great Lakes coastal regions.This dataset includes:* A selection of commonly reported absorbance and fluorescence peaks normalized to dissolved organic carbon concentrations* Parallel factor output from the EC1 fluorescence datasets* A selection of commonly reported absorbance and fluorescence peaks * Spectral indices output from matlab script for absorbance and fluorescence datasets* CO2sys calculations of pH changes under varying temperatures and a constant salinity, DIC, and alkalinity concentrationAll data files are plain-text CSV (comma separated value) and no special software is required to read them.

54 ENVIRONMENTAL SCIENCES↗

Data for: A Synoptic System for Capturing Ecosystem Control Points Across Terrestrial-Aquatic Interfaces

The investigation of how climate change and water level fluctuations impact variable and interconnected ecosystems, like the interfaces between terrestrial and aquatic environments, requires the collection and integration of many data types. We describe an integrative and autonomous environmental monitoring approach that uses environmental sensors and data loggers to monitor surface water, groundwater, soil, and vegetation changes and generate essential data for predictive models. We established the network at seven sites along the Chesapeake Bay and Lake Erie coastlines, including a large-scale flood manipulation experiment, collectively generating over three million observations per month. Such sensor networks hold great promise for tracking and comprehending environmental changes where land and water intersect. The sensor system and overall approach to sensor management that we have designed is intended to be widely accessible for research teams spanning in size from an individual investigator to large multi-institution projects. This dataset shows example data generated by the sensor network described above. Data output for data loggers connected to groundwater water quality sondes measuring dissolved oxygen, pH, oxidative redox potential (ORP), groundwater elevation, groundwater salinity and temperature, and groundwater elevation; replicate soil moisture and conductivity probes installed at 10 and 30 cm below the ground surface; rainfall and solar radiation; and mean sap flow from 8 replicate probes. Sensors are installed at upland forest (UP), wetlands (W), and transitional locations between these ecosystems (TR). Example datasets are from Goodwin Islands in the Chesapeake Bay and Portage River along the Lake Erie coastline.

54 ENVIRONMENTAL SCIENCES↗

Patterns of Element Incorporation in Calcium Carbonate Biominerals Recapitulate Phylogeny for a Diverse Range of Marine Calcifiers

Elemental ratios in biogenic marine calcium carbonates are widely used in geobiology, environmental science, and paleoenvironmental reconstructions. It is generally accepted that the elemental abundance of biogenic marine carbonates reflects a combination of the abundance of that ion in seawater, the physical properties of seawater, the mineralogy of the biomineral, and the pathways and mechanisms of biomineralization. Here we report measurements of a suite of nine elemental ratios (Li/Ca, B/Ca, Na/Ca, Mg/Ca, Zn/Ca, Sr/Ca, Cd/Ca, Ba/Ca, and U/Ca) in 18 species of benthic marine invertebrates spanning a range of biogenic carbonate polymorph mineralogies (low-Mg calcite, high-Mg calcite, aragonite, mixed mineralogy) and of phyla (including Mollusca, Echinodermata, Arthropoda, Annelida, Cnidaria, Chlorophyta, and Rhodophyta) cultured at a single temperature (25°C) and a range of p CO 2 treatments (ca. 409, 606, 903, and 2856 ppm). This dataset was used to explore various controls over elemental partitioning in biogenic marine carbonates, including species-level and biomineralization-pathway-level controls, the influence of internal pH regulation compared to external pH changes, and biocalcification responses to changes in seawater carbonate chemistry. The dataset also enables exploration of broad scale phylogenetic patterns of elemental partitioning across calcifying species, exhibiting high phylogenetic signals estimated from both uni- and multivariate analyses of the elemental ratio data (univariate: λ = 0–0.889; multivariate: λ = 0.895–0.99). Comparing partial R 2 values returned from non-phylogenetic and phylogenetic regression analyses echo the importance of and show that phylogeny explains the elemental ratio data 1.4–59 times better than mineralogy in five out of nine of the elements analyzed. Therefore, the strong associations between biomineral elemental chemistry and species relatedness suggests mechanistic controls over element incorporation rooted in the evolution of biomineralization mechanisms.

58 GEOSCIENCES↗

Tendencies of Soil Microbial NO Emissions During HI‐SCALE as Predicted by a Nitrification/Denitrification Scheme

Many atmospheric chemical processes, including the formation of secondary organic aerosol (SOA), are strongly modulated by the reactions of NO and NO 2 (NO x ). Though NO x is controlled by anthropogenic emissions near urban areas, in rural areas soil microbes can be a significant contribution to NO emission globally. The relative rates of emissions of different nitrogen-containing species (e.g., NO, N 2 O, HONO, and N 2 ) are strong functions of soil properties such as temperature, moisture content, pH, and soil carbon and nitrogen pools. However, typical large-scale biogeochemical models either express these emissions simplistically, or not at all. Here we investigate the potential impact of soil NO emissions on atmospheric chemistry and SOA formation over regional and monthly time scales, specifically the 2016 spring and summer Intensive Observational Periods (IOPs) of the Holistic Interactions of Shallow Clouds, Aerosols and Land Ecosystems (HI-SCALE) field campaign. We implement the soil NO nitrification/denitrification parameterization of Rasool et al. (2019) into the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem), supplemented by a 1-km soil moisture analysis. We then simulate both IOPs over the U.S. Great Plains, evaluating against ground stations and flight data. We show that soil NO emissions can account for a large fraction of total NO x and locally increase O 3 concentrations by up to 25%, while alleviating negative biases of gases and aerosols toward observations. Soil moisture and temperature changes between IOP1 and IOP2 lead to overall differences in emissions, but with large regional variability due to heterogeneous surface characteristics.

Atmoshpheric Chemistry↗