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At least 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Corrinoids as model nutrients to probe microbial interactions in a soil ecosystem

Earth’s soils are habitats for microbial communities that drive biogeochemical cycling, plant growth, and carbon storage and persistence. The thousands of microbial species living in soil form an intricate web of interactions involving the exchange of molecules produced by different microbes. Understanding in detail how these molecular exchanges occur and how they shape microbial communities may lead to new methods to improve soil health, bioremediation efforts, and better understanding of biogeochemical processes. The overall goal of this research is to gain a deeper knowledge of the microbial interactions that drive soil community structure. However, the high functional and genomic diversity in soil microbiomes has posed a challenge for current microbiology methods to achieve this goal. This research leverages a model group of key metabolites related to cobalamin (vitamin B 12 ), known as corrinoids, to investigate microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Effects of Surface Water Fluctuations and Sediment Movement on Hyporheic Zone Biogeochemistry and Microbial Communities

The hyporheic zone (HZ) is the region beneath and adjacent to streams, rivers, and riverine estuaries where the bidirectional exchange of groundwater (GW) and surface water (SW) occurs. The HZ is an integral component of watersheds, a biologically-active zone providing critical control of SW quality and aquatic life. Much prior work has investigated microbially-mediated biogeochemical reactions in the HZ, mainly from a steady-state perspective. Yet key unique aspects of the HZ include 1) proximity to SW fluctuations (e.g., storms, dam operations) which cyclically drive DOC and DO into the bed and banks creating biogeochemical “hot moments,” and 2) continually shifting surface sediment. Both of these controls should substantially influence microbial communities, yet remain poorly understood, and a mechanistic predictive framework does not exist.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

MR13A-3183: Microbial and Geochemical Characterization of Groundwater: Implications for Underground Hydrogen Storage Leakage

Underground hydrogen storage (UHS) in geological formations is a key element of the clean energy transition as it enables the decarbonization of the transportation and industrial sectors by decoupling hydrogen production and storage. UHS has many benefits, including low cost, much wider availability, large storage capacity, well-established infrastructure, and increased safety because of geological sealing capabilities. However, the impact of hydrogen (H2) biogeochemical interactions in the presence of subsurface microorganisms is largely neglected from UHS perspectives. These interactions might affect the effectiveness of storage and can even cause H2 to leak into the shallow aquifers. Leakage of H2 into groundwater can change the geochemistry and induce several microbial-driven processes. Microorganisms, such as sulfate-reducers, are naturally abundant in groundwater and consume H2 to produce hydrogen sulfide (H2S), which can contaminate the freshwater drinking groundwater and cause damage to infrastructure. Hydrogen leakage can also trigger microbial reactions responsible for metal mobility, which can impact the water quality. However, the kinetics of these reactions and the temporal impact of hydrogen leakage in groundwater are still unknown. Therefore, a time series hydrogen-groundwater interaction experiment was conducted, and the changes in fluid chemistry and headspace gas composition will be analyzed along with DNA sequencing results to understand the extent and kinetics of biogeochemical reactions that occur if hydrogen leaks into groundwater. In the experiments, Ultra High Purity (UHP) hydrogen gas will be injected into glass vials with groundwater samples, for a designated time period. For each glass-sealed vial, 16S rRNA gene sequencing, IC, ICP-MS, and GC-TCD will be performed. The experiments provide insights into plausible impacts of hydrogen leakage into shallow drinking water aquifers.

Clark, Allison [West Virginia University (WVU)]↗
DOE OSTI2025

Evaluating the Influence of Plants on Hydrologic Cycling: Quantifying and Validating the Role of Plant Processes and Stomatal Conductance (Final Report)

Plants can exert strong controls on water cycling, both locally and across the globe. The impacts are driven by how plants control the exchange of water and energy between the land and the atmosphere, which in turn are influenced by how plants photosynthesize and grow (e.g. biogeochemical cycling). Our team has shown previously that plant responses to increasing CO 2 in the atmosphere can influence the water cycle through changes in rainfall and the amount of water on land with implications for drought. Plant responses can also alter both average and extreme flow of water in rivers, with implications for freshwater availability and flood frequency. Although the impact of plant responses on water cycling has been demonstrated to exist, significant uncertainty remains in our understanding of the magnitude and form of the plant responses themselves, as well as their ultimate impact on water availability for people and ecosystems. In this project we worked to quantify the role of plant processes in regulating water cycling (e.g., precipitation, evapotranspiration, runoff, droughts, etc.). We addressed the following objectives: quantify the control of physiological vs. radiative effects on water cycling across many coupled models in idealized and realistic scenarios, as well as to quantify how our assumptions about leaf-level processes (e.g. coupling between stomatal conductance and photosynthesis), and organism-level processes (e.g. leaf area response to high CO 2 ) contributed to uncertainties and biases in water cycling. We focused on the impact of these processes on water cycling to assess the sensitivities of precipitation, evapotranspiration, and runoff to model assumptions about plant processes at the leaf, organism, and community level. As part of this project we used measurements of stable carbon isotopes to generate observationally based estimates of plant functioning during the historical period. This work is directly relevant to DOE’s primary scientific research questions in the RGMA topic area (b) on Biogeochemical processes, feedbacks, and interactions in the Earth system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Identifying Hot Spots and Hot Moments of Metabolic Activity in Salt Marsh Sediments through BONCAT-FISH Microscale Mapping (Final Technical Report)

Understanding the biogeography and timing of microbial metabolic activity is a key priority for microbial ecologists. With such knowledge, the cumulative biogeochemical contributions of microbial communities become more predictable, and our ability to both understand the effects of environmental change on microbial activity and build synthetic communities with desired functions will increase substantially. In this project, we advanced this broad, ambitious goal in two substantial ways: we developed a multiplexed Fluorescence In Situ Hybridization (FISH) approach that links microbial identity with metabolic function, and we established a novel Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT) technique that can resolve the timing of anabolic activity, providing new resolution of when microbial constituents are growing. We deployed both of these techniques in multiple environmental settings to demonstrate their versatility. At the Little Sippewissett Salt Marsh, we combined a novel dual-BONCAT technique with fluorescence activated cell sorting to determine which population of cells was metabolically active during the day and which was active during the night. We found that Methylobacterium was active during daylight hours, potentially feeding on carbon-rich molecules released from plant roots. Sulfur-cycling microbes dominate the population active during the dark night-time hours. Overall, the work conducted under the auspices of this project developed two promising new techniques for identifying the “hot spots” and “hot moments” of microbial activity in complex communities with taxonomic and functional resolution. We focused largely on a salt marsh sediment context, but are confident that microbial ecologists seeking to understand the microbial role in biogeochemical cycles in a wide range of settings will find our newly developed techniques useful in future work.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Cell to Ecosystem: Understanding Methane and Associated Nutrient Cycling by Sediment Hosted Syntrophic Consortia and Their Viral Predators

The anaerobic oxidation of methane (AOM) is a significant worldwide microbial process in anoxic lake and ocean sediments, responsible for sequestering up to 80% of this greenhouse gas. Often considered a metabolism on the edge of thermodynamic probability, the impact of ANaerobic MEthane-oxidizing ‘ANME’ archaea on carbon and nutrient cycling in sediment ecosystems is far reaching. They not only serve as a sink for methane coupled to diverse electron acceptors, but also catalyze the transformation of many important nutrients including nitrogen, phosphate, and iron. While information about the potential mechanisms supporting metabolism in AOM is now available, remarkably little has been learned about their nutritional requirements, their dependencies on bacterial partners, and consequentially their ultimate impact on nutrient transformation and bioavailability within sedimentary ecosystems, and beyond. Further, the role of viruses within sediment ecosystems represents an essential but vastly understudied aspect of the transformation of carbon and nutrients by AOM. Viruses are now widely appreciated as central players in biogeochemical cycles across diverse ecosystems. These nanoscale predators have been shown to enhance the turnover of essential nutrients, thus stimulating microbial growth and environmental viruses themselves may constitute an important reservoir of nitrogen and phosphorous. Little is known about the role of viruses in methane-impacted sedimentary ecosystems, however prior genomic and microscopy evidence suggests that AOM consortia are susceptible to phage infection. The overarching scientific goal of this multi-disciplinary research proposal is to build on these recent discoveries and expand our understanding of interactions and fundamental activities involved in cycling of carbon and nutrients by syntrophic methanotrophic archaeal-bacterial consortia and associated viruses in anoxic sedimentary environments. Our three specific objectives are to 1) Quantify energy and nutrient exchange (e.g. N, P, Fe and vitamins) within AOM consortia and between ANME-bacterial partners; 2) Identify virus-host interactions associated with AOM and assess C and N transfer through viruses in methane-impacted sediment ecosystems; 3) Model energy and nutrient exchange in AOM consortia and viral-host interactions (i.e. viral activity), and their environmental distribution patterns. Our experimental emphasis cuts across scales that are important for understanding microbial and viral interactions and activities within their habitats, as well as community wide biogeochemical transformations. These research goals will be accomplished through the application of novel molecular techniques targeting DNA, RNA, proteins, and metabolites combined with a unique multi-modal analytical imaging pipeline. We will then model the ecophysiological capabilities of diverse sediment-hosted methanotrophic consortia to develop a more comprehensive understanding of the energetic and nutritional interactions between different AOM partner couplings that occur in sediments.

03 NATURAL GAS↗
DOE OSTI2025

Root genetics in the field to understand drought adaptation and carbon sequestration (Final Scientific/Technical Report)

For all crop plants, roots play a critical role in growth. Roots anchor the plants, and are the primary site of nutrient and water uptake. Roots are also the main source of C to soil in the form of root tissues and exudates, and thus greatly influence SOM stocks. To perform these functions, primary roots extend into soil, producing a network of branching roots of characteristic form, known as its root system architecture (RSA). RSA varies among species, and among varieties within a species that are adapted to different environments. Root traits are major targets for the second green revolution because of their potential to improve crop productivity, increase drought tolerance and nutrient acquisition, and increase C capture of soil. Improving the quality of roots in maize will be particularly valuable, since this crop is planted on over 92 million acres annually in the US. The future sustainability of agricultural systems relies on their ability to enhance soil organic matter (SOM) storage and reduce GHG emissions, while maintaining or enhancing productivity. This program had two components, Sensors and Models. For the first component, we designed and built a high-throughput phenotyping platform for root pulling of maize plants. This eliminated the physical labor of manually pulling up plants and reduced the number of personnel required down to one. The standardized pulling mechanism allowed recording force curves during the pulling process, providing additional information. We validated that the maximum force for pulling the root system was well-correlated with the root system mass and provided root crowns for further RSA analysis. These root crowns identified significant correlations with 2D root area and root depth, along with 3D root volume, total root length and number of root tips. We then used this system for field-based studies in maize on the genetics of root system architecture and its relation to nitrogen-use efficiency (NUE), including using lines relevant to the Corteva breeding program. Varieties were also evaluated at Corteva sites in the cornbelt and Danforth farm in Missouri, to establish responses across sites. From these studies we have identified genetic loci associated with root traits and created mutant lines for these loci and correlations of root traits with NUE. For the Models component, we worked to incorporate root and soil characteristics into the MEMS 2.0 soil and ecosystem biogeochemical model. Existing soil C models, such as Century, are unable to represent specific root trait interactions with the soil environment and therefore to accurately forecast the potential C sequestration benefits of root breeding under different climatic and soil type conditions. We have developed the MEMS 2.0 ecosystem biogeochemical model to improve quantification of farm-scale soil carbon and greenhouse gas emissions. The new knowledge and large datasets produced by this project will be used to develop and drive an innovative model capable of forecasting the impacts on soil C stocks and nutrient dynamics. An innovation was to use the empirical data from the field studies (in 1, above) to model genetic variation in nitrogen use efficiencies and soil C input. Our work demonstrated that maize root-derived C rapidly replaces existing soil C and after 3 years of continuous maize, up to 20% of soil organic C in the topsoil (0-15cm) and 3% in the subsoil (15-30cm) was contributed by maize. However, this contribution did not entirely represent a net increase. Root C contribution to soil was affected by maize genetics. We have analyzed soils derived from the CSU field trials for C and N stocks, in the different soil physical fractions represented by the MEMS model, using both physical fractionation with elemental analyses, and Fourier transformed infrared spectroscopy. Data will be used to link crop nitrogen use efficiencies with soil C sequestration and provide data to bridge the field trials with the model development, for verification of model predictions. The project had a number of successful outcomes: we have used the new phenotyping platform to identify new genetic loci that can enhance root phenotypes; we have partnered with multiple maize seed companies phenotype varieties in their breeding programs; we have developed the MEMS model that can help inform industry on the potential for carbon sequestration in the agricultural sector, and which is now available at the CSU Soil Carbon Solutions Center for use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Integration and Quantitative Comparison of Up-Scaled Molecular Observation Network Data with Existing Soil Databases

MONet provides novel soil molecular data to the research community for understanding biogeochemical processes and complementing other soil datasets. This study assesses MONet's ability to replicate known soil patterns via a comparative analysis of soil respiration (Rs), pH, and clay content against benchmark datasets. Results show moderate agreement for pH and clay content, highlighting MONet's strengths in capturing soil biogeochemical variation in underrepresented regions like urban areas. Rs data are marked by the appropriate trends relative to other datasets, but direct comparison is impractical due to methodological differences in underlying data. Strategic sampling is recommended to improve MONet's coverage and eventual utility in bridging molecular observations with global datasets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

From tides to seasons: How cyclic tidal drivers and plant physiology interact to affect carbon cycling at the terrestrial-estuarine boundary (Final technical report)

Coastal ecosystems are among the most biologically and biogeochemically active and diverse systems on Earth. Because they act as important linkages between terrestrial ecosystems and the open ocean, their incorporation in Earth system models (ESMs) is critical to predict coastal and global responses to environmental changes. However, they vary greatly in the magnitude of tides and the volume and timing of freshwater input from land, making it challenging to model the major biogeochemical reactions that control productivity and greenhouse gas emissions across coastal terrestrial aquatic interfaces (TAIs). Our overall objective was to improve mechanistic process understanding and modeling of tidal wetland hydro-biogeochemistry in coastal TAIs. We established a new flux tower site (Ameriflux US-PLo) in the oligohaline part of the Parker River to continuously monitor ecosystem-scale carbon fluxes under temporally varying salinity conditions. The site is co-located with long-term monitoring plots of the Plum Island Ecosystems LTER project. We installed wells and redox sensors in the marsh interior and creek bank, established biomass monitoring plots and deployed novel optode sensors in both locations. We used this data to parameterize plant-mediated transport in PFLOTRAN and tested the impact of soil heterogeneity on porewater constituents and gas fluxes. We collected observations of root oxygen release with a novel planar optode system in the field. Flux data collected during the measurement period encompasses a large variation in salinity ranging from drought to record precipitation years. We developed a method to extract functional relationships from the flux data using artificial neural networks, identifying salinity thresholds for CH 4 fluxes. Finally, we are using the coupled ELM-PFLOTRAN model to test the impact of antecedent hydrological conditions on the salinity-CH 4 flux relationship. This grant contributed to the professional development of one postdoc, three research assistants and one graduate student. The sensor data has been shared with external collaborators.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Cytochrome Nanowire XRD

Microbial metabolism plays an important role in the global cycling of carbon, nutrients, and metals. Recent discovery of microorganisms sharing energy using direct electrical connections might represent a prominent strategy by which anaerobic microorganisms interact with the diversity of environments. The purpose of the proposed research is to apply these newly developed principles of electron exchange in microbial communities to the study of biogeochemical cycling in climate and subsurface systems. Previous studies revealed that soil bacteria Geobacter sulfurreducens produce conductive pili nanofilaments that facilitate long-range electron transport to extracellular electron acceptors and other cells. This discovery has already transformed our understanding of the function of microbial communities in diverse environments, making basic contributions to microbial ecology and helping to improve practical applications such as increasing current output of microbial fuel cells and enhancing the conversion of organic waste to methane. Microbial electron exchange via pili may also contribute to methane production in terrestrial environments that are major sources of atmospheric methane. However, the mechanism of electron transport through pili is not well understood. Initial studies have suggested that pili exhibit metallic-like conductivity similar to conducting polymer polyaniline. However, these studies were limited to electrical measurements. X-ray diffraction studies have suggested that aromatic amino acids tyrosine and phenylalanine are closely packed in pili. But these studies used homology modeling to predict the pilus assembly and information about the number of monomers in each pilus assembly unit and their organization are still lacking. The central hypothesis of this proposal is aromatics in pili enable intermolecular electron delocalization due to pi-stacking that can give rise to metallic-like conductivity. By analyzing pili structure using infrared scattering-scanning near field optical microscope (IR s-SNOM) and combining with solution NMR, Focused Ion Beam (FIB and computational capabilities, this work will provide comprehensive understanding of the conduction mechanism from a structure-function perspective. The specific aims are: 1) With infrared scattering scanning near field optical microscope (IR s-SNOM), image the organization and density of pilin monomers and pH-induced conformational changes in a pilus filament. 2) With solution NMR, resolve pH-induced structural changes in the pilin monomer. 3) Using Focused Ion Beam (FIB), draw electrodes on single pili to measure their conductivity. 4) With computational modeling using the NWChem, simulate the effect of environment on the electronic properties of pili as a function of pH. The proposed work will gain the nanoscale insight into the structure of the pili, as the basis for understanding interspecies electrical communications. The improved understanding will be harnessed to accelerate bioenergy production and bioremediation using pili as well as for predictive modeling of carbon cycling in diverse environments to reach the central goals of DOE-BER to develop sustainable energy sources, regulate the contaminants in the subsurface and understand the effects of greenhouse gas emissions on biosphere. The proposed studies will provide design principles for engineering of electrical interactions among these communities by manipulating the amino acid composition of pili. Moreover, these studies will identify the forces that maintain the function of these communities in the face of environmental perturbation. Therefore, these studies will help to address the need "to incorporate process understanding of biogeochemical cycling into a scalable hierarchy of predictive capabilities" specified in EMSL's Science Themes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Global Soil Virus (GSV) Atlas

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset from 2,953 soils that comprises 616,935 uncultivated virus genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents the most extensive characterization of soil viral diversity to date and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

Graham, Emily B↗
DOE OSTI2020

Validation of the Community Land Model Version 5 over the Contiguous United States (CONUS) using in-situ and remote sensing datasets

The Community Land Model (CLM) is an effective tool to simulate the biophysical and biogeochemical processes and their interactions with the atmosphere. Although CLM Version 5 (CLM5) constitutes various updates in these processes, its performance in simulating energy, water and carbon cycles over the Contiguous United States (CONUS) at scales which land surface changes and hydrometeorological and hydroclimatological applications are more locally relevant is yet to be assessed. In this study, we conducted three simulations at 0.125? during 1979-2018 over the CONUS using different configurations of CLM, namely CLM5-biogeochemistry (CLM5BGC), CLM4.5BGC, and CLM5-satellite phenology (CLM5SP). We validated and compared their simulations against multiple remote-sensed and in-situ datasets. Overall, the parametric and structural updates (e.g., carbon cost for nitrogen uptake, variable soil thickness, dry surface layer) in CLM5 improve its ability in capturing terrestrial biogeochemical dynamics. The low evapotranspiration in CLM5BGC is associated with biases in simulating vegetation phenological characteristics rather than soil water limitations. The mismatch between CLM5BGC-simulated peak leaf area index and reference data can be attributed to CLM5BGC's inability in simulating phenology of trees and grasses. The differences between CLM-simulated irrigation and reference estimates can be attributed to differences between processes represented in models and in reality, and uncertainties in input and validation datasets. Evaluation against observations at small catchments suggest that hydrologic parameters needed to be calibrated to improve simulations of runoff, especially subsurface runoff. Additional efforts are needed to incorporate spatially-distributed plant phenology and physiology parameters and regional-specific agricultural management practices (e.g., planting, harvest).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Stability of Floodplain Subsurface Microbial Communities Through Seasonal Hydrological and Geochemical Cycles

Riparian floodplains represent an interaction zone between the terrestrial subsurface and rivers, where regional groundwater flows, infiltration, and evapotranspiration drive mixing of water and import/export of nutrients and contaminants. These dynamics create seasonally transient redox conditions that drive biogeochemical transformations, which strongly modify groundwater quality. Microbial responses to changing hydrological conditions are perhaps the critical step connecting hydrology to geochemical transformations and groundwater quality, yet are not well understood. We aimed to address this knowledge gap by monitoring seasonal transitions at the U.S. Department of Energy legacy uranium ore processing site in Riverton, WY, through spring-summer-fall hydrological transitions. Our goal was to characterize the microbial community throughout the soil profile, down to the saturated aquifer, and observe its response to wet-dry transitions across a full season and compare to changes in geochemistry and hydrology. Next-generation sequencing was employed to identify biogeochemically-relevant microbial taxa based on the 16S rRNA gene; we found a broad diversity of microbial clades including taxa involved in sulfur and metal cycling, as well as nitrification. These data were paired with measurements of soil moisture, major nutrients and cations, and trace elements. Overall microbial community composition was dependent on soil depth or type, with seasonal effects only observed in the topsoil or subsurface aquifer. This finding indicates that microbial communities in the transiently-reduced center of the soil profile at the Riverton, WY site are remarkably stable, despite moisture and redox inversions. In addition, these communities likely impact the communities in surrounding soil horizons through export of metabolites and solutes as the water table rises and falls throughout the season.

16S rRNA↗
DOE OSTI2020

Controls on Soil Organic Matter Degradation and Subsequent Greenhouse Gas Emissions Across a Permafrost Thaw Gradient in Northern Sweden

Warming-induced permafrost thaw could enhance microbial decomposition of previously stored soil organic matter (SOM) to carbon dioxide (CO 2 ) and methane (CH 4 ), one of the most significant potential feedbacks from terrestrial ecosystems to the atmosphere in a changing climate. The environmental parameters regulating microbe-organic matter interactions and greenhouse gas (GHG) emissions in northern permafrost peatlands are however still largely unknown. The objective of this work is to understand controls on SOM degradation and its impact on porewater GHG concentrations across the Stordalen Mire, a thawing peat plateau in Northern Sweden. Here, we applied high-resolution mass spectrometry to characterize SOM molecular composition in peat soil samples from the active layers of a Sphagnum-dominated bog and rich fen sites in the Mire. Microbe-organic matter interactions and porewater GHG concentrations across the thaw gradient were controlled by aboveground vegetation and soil pH. An increasingly high abundance of reduced organic compounds experiencing greater humification rates due to enhanced microbial activity were observed with increasing thaw, in parallel with higher CH 4 and CO 2 porewater concentrations. Bog SOM however contained more Sphagnum-derived phenolics, simple carbohydrates, and organic- acids. The low degradation of bog SOM by microbial communities, the enhanced SOM transformation by potentially abiotic mechanisms, and the accumulation of simple carbohydrates in the bog sites could be attributed in part to the low pH conditions of the system associated with Sphagnum mosses. We show that Gibbs free energy of C half reactions based on C oxidation state for OM can be used as a quantifiable measure for OM decomposability and quality to enhance current biogeochemical models to predict C decomposition rates. We found a direct association between OM chemical diversity and δ 13 C-CH 4 in peat porewater; where higher substrate diversity was positively correlated with enriched δ 13 C-CH 4 in fen sites. Oxidized sulfur-containing compounds, produced by Sphagnum, were further hypothesized to control GHG emissions by acting as electron acceptors for a sulfate-reducing electron transport chain, inhibiting methanogenesis in peat bogs. These results suggest that warming-induced permafrost thaw might increase organic matter lability, in subset of sites that become wetlands, and shift biogeochemical processes toward faster decomposition with an increasing proportion of carbon released as CH 4 .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Oxidation of Dissolved Tetravalent Selenium by Birnessite: Se Isotope Fractionation and the Effects of pH and Birnessite Structure

Redox reactions control the mobility and bioavailability of selenium (Se) in biogeochemical systems, both modern and ancient. Se isotope ratio measurements (e.g., 82 Se/ 76 Se) have been developed to enhance understanding of biogeochemical transformations and transport of Se. Stable isotope ratios of many elements are known to be powerful indicators of redox reactions, and shifts in 82 Se/ 76 Se have been observed for Se reduction reactions. However, Se isotope shifts caused by naturally relevant oxidation reactions have not been published. Here, we report Se isotope fractionation factors for oxidation of Se(IV) by birnessite. Experiments were conducted at pH = 4.0 and 5.5, with two types of birnessite of contrasting composition at two concentrations of suspended birnessite. The results are consistent with a single 82 Se/ 76 Se fractionation factor, for all times during all experiments, of 0.99767 (±0.0035 2 s.d.). Expressed as ε, the fractionation is 2.33‰ (±0.08‰).

58 GEOSCIENCES↗
DOE OSTI2021

Seasonal changes in the drivers of water physico-chemistry variability of a small freshwater tidal river

Where rivers meet the sea, tides can exert a physical and chemical influence on the lower reaches of a river. How tidal dynamics in these tidal river reaches interact with upstream hydrological drivers such as storm rainfall, which ultimately determines the quantity and composition of material transferred from watersheds to estuaries, is currently unknown. We monitored a small freshwater tidal river in the Pacific Northwest, USA in high resolution over one year to evaluate the relative importance of tides versus upstream hydrological flows (i.e., base flow and precipitation events) on basic physico-chemical parameters (pH, dissolved oxygen, turbidity, specific conductivity, and temperature), and how these interactions relate to the downstream estuary. Tidal variability and diurnal cycles (i.e. solar radiation) dominated water physico-chemical variability in the summer, but the influence of these drivers was overshadowed by storm-driven sharp pulses in river physico-chemistry during the remainder of the year. Within such events, we found incidences of counterclockwise hysteresis of pH, counterclockwise hysteresis of dissolved oxygen, and clockwise hysteresis of turbidity, although systematic trends were not observed across events. The dominance of storm rainfall in the river’s physico-chemistry dynamics, and similar pulses of decreased pH observed in adjacent estuarine waters, suggest that the linkage between tidal streams and the broader system is variable throughout the year. High-frequency monitoring of tidal river biogeochemistry is therefore crucial to enable the assessment of how the relative strength of these drivers may change with future sea level rise and altered precipitation patterns to modulate biogeochemical dynamics across the land-ocean-atmosphere continuum.

aquatic↗
DOE OSTI2021

Light Regulation of Phytoplankton Growth in San Francisco Bay Studied Using a 3D Sediment Transport Model

In San Francisco Bay (SFB), light availability is largely determined by the concentration of suspended particulate matter (SPM) in the water column. SPM exhibits substantial variation with time, depth, and location. To study how SPM influences light and phytoplankton growth, we coupled a sediment transport model with a hydrodynamic model and a biogeochemical model. The coupled models were used to simulate conditions for the year of 2011 with a focus on northern SFB. For comparison, two simulations were conducted with ecosystem processes driven by SPM concentrations supplied by the sediment transport model and by applying a constant SPM concentration of 20 mg l –1 . The sediment transport model successfully reproduced the general pattern of SPM variation in northern SFB, which improved the chlorophyll-a simulation resulting from the biogeochemical model, with vertically integrated primary productivity varying greatly, from 40 g[C] m –2 year –1 over shoals to 160 g[C] m –2 year –1 in the deep channel. Primary productivity in northern SFB is influenced by euphotic zone depth ( Ze ). Our results show that Ze in shallow water regions (<2 m) is mainly determined by water depth, while Ze in deep water regions is controlled by SPM concentration. As a result, Ze has low (high) values in shallow (deep) water regions. Large (small) differences in primary productivity exist between the two simulations in deep (shallow) water regions. Furthermore, we defined a new parameter F light for “averaged light limitation” in the euphotic zone. The averaged chlorophyll-a concentration in the euphotic zone and F light share a similar distribution such that both have high (low) values in shallow (deep) water regions. Our study demonstrates that light is a critical factor in regulating the phytoplankton growth in northern SFB, and a sediment transport model improves simulation of light availability in the water column.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

59 BASIC BIOLOGICAL SCIENCES↗