SEARCH · Engineering Papers

Results for “microbial scale”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 361 records · Page 20

All sources NASA NTRS DOE OSTI

DOE OSTI2026

High yield production of 3-hydroxypropionic acid using Issatchenkia orientalis

Biomanufacturing provides a more sustainable alternative to fossil-based chemical manufacturing. 3-Hydroxypropionic acid (3HP) is a top Department of Energy value-added chemical and precursor to bioplastics, yet cost-effective microbial production remains elusive. Here, we establish the acid-tolerant yeast Issatchenkia orientalis as a robust host for low-pH 3HP biosynthesis. Genome-scale modeling identifies the β-alanine pathway as optimal, offering the highest theoretical yield and lowest oxygen requirement. Thermodynamic analysis confirms its favorability under acidic conditions. Using sequence similarity network analysis, we discover highly active aspartate 1-decarboxylase (PAND), β-alanine-pyruvate aminotransferase (BAPAT), and 3HP dehydrogenase (YDFG), which significantly improve the pathway efficiency. Next, to further elevate the production, pathway optimization through multi-copy PAND integration, byproduct elimination (knockouts of pyruvate decarboxylase and glycerol-3-phosphate dehydrogenase), and reinforcement of aspartate flux by overexpression of pyruvate carboxylase and aspartate amino transferase improves the titer to 29 g/L in shake flasks. Fed-batch fermentation at pH 4 with low-cost corn steep liquor medium further increases the production to 92 g/L with 0.7 g/g yield and 0.55 g/L/h productivity. Techno-economic analysis indicates that such performance could potentially enable a financially viable process for sustainable acrylic acid production. This work establishes I. orientalis as a next-generation platform for cost-effective 3HP production and paves the way toward industrial commercialization.

Biotechnology↗

NASA NTRS1992

Aquatic biofilms and their responses to disinfection and invading species

The control of microbial contamination is a primary concern in the development of a water reclamation system for long-duration manned space flights. This paper describes bench-scale experiments, using both static and recycling water systems, investigating the interaction of bacterial species in the development of a biofilm and their response to the introduction of a disinfectant or of additional species. The results showed that iodine concentrations as high as 15 to 20 mg/l I2 are necessary to completely disinfect a stable biofilm. When S. aueus and E. coli were introduced into a system containing natural mixed culture biofilms, their colonization in the biofilms increased their survival time, from 3 to 5 days as unattached cells to over 60 days when protected in the biofilms. While iodine concentrations of 0.5 to 1 mg/l were enough to eliminate these organisms from the bulk water, concentrations higher than 4.0 mg/l were necessary to completely eliminate these organisms from the biofilm.

Smithers, G. A.↗

NASA NTRS2025

Laminae as Structural Biosignatures in NASA’s Life Detection Knowledge Base

Laminae are millimeter-scale features in rocks created by physiochemical processes that can be influenced by the presence and activities of communities of organisms that occur as biofilms and microbial mats. The structure and composition of laminae reflect the processes involved in their formation and can be preserved in the rock record over geologic time, however diagenetic and metamorphic alteration can lead to the loss of primary information and confusion over the interpretation of their origins. As potential records of ancient life, laminae can preserve evidence of microbial activity over billions of years of Earth’s history. On planetary bodies beyond Earth, laminae in sedimentary rocks are the most common sedimentary structure and represent significant features of interest that can record habitable conditions (e.g., the presence of liquid water) at the time of their formation. Here we review the significance of laminae as targets for astrobiological exploration. We discuss common mechanisms by which laminae form in natural environments on Earth, present arguments and evidence for laminae as biosignatures, and describe how such information is incorporated into the NASA Life Detection Knowledge Base.

Astrobiology↗

DOE OSTI2023

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research

Abstract As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how “microbiomes within microbiomes” affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

Abstract Background Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus . Results Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota. Conclusions The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.

Sparagon, Wesley J. (ORCID:0000000296274174)↗

DOE OSTI2023

Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils

The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.

16S rRNA gene amplicon Illumina sequencing↗

DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q3

Microbiome data is complex, spanning information from microbial genomes within diverse communities, protein and metabolite readouts, and contextual information (metadata) captured from the environments from which these samples were collected. While the variety and scale of microbiome data generation has dramatically expanded over the past twenty years, infrastructure to support data management, sharing, and access has lagged. New ways to improve interoperability across existing resources and advancing community standards are necessary to support how researchers create, use, and reuse data. The National Microbiome Data Collaborative (NMDC) aims to advance a microbiome data sharing network through infrastructure, data standards, and community building.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Energy-Efficient Microbial Electrochemical Lignin and Alkaline Hydroxide Recovery from DMR Black Liquor

Black liquor is a complex waste stream generated from the fast-expanding biorefinery industry, and the high management cost has been known as a major development barrier. In this work, we demonstrated a rationally designed 4-chamber microbial electrolysis process that was capable of recovering the value-added lignin, NaOH, and H2 products while removing waste organics from the Deacetylation and Mechanical Refining (DMR) black liquor, which could potentially reduce the disposal cost by up to 40%. The lab-scale MEC achieved 52% organic removal from a highly concentrated feedstock (28,960 ± 212 mg/L COD) and recovered 83.2 mM NaOH under a small voltage application (1.2 V). Lignin recovery was observed to be as high as 13.98 +/- 0.28 g/L, and 0.35 L/L/day H2 was produced with a faradaic efficiency of 93.5%. This work provided a good example on how complex liquid waste stream can be valorized via multi-functional microbial electrochemical technology, and how the traditionally unfavored pH gradient in an electrochemical reactor can be manipulated for lignin precipitation and alkaline recovery at the same time. The versatility and good performance in concurrent contaminants removal, lignin precipitation, H2 production and NaOH recovery demonstrate a good potential for microbial electrolysis in black liquor treatment.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

NASA NTRSDate not supplied

Studying Microbial Adaptation in the Laboratory: Sensor & Control Upgrades for an Experimental Evolution Biofluidics System

Experimental evolution (EE) involves iteratively exposing a microbial community to specific stressors to study its response to changes in environment over time. EE work is commonly done manually in the laboratory, but, when there are many environmental variables to measure and adjust, it is highly labor intensive, prone to human error, and challenging to scale. Single-purpose automated continuous culturing chambers exist, but implement only limited stressor types. A more general-purpose design is desirable. The BeING Lab at Ames Research Center created the prototype Automated Adaptive Directed Evolution Chamber (AADEC) to address these problems, beginning with Escherichia coli tolerance of short-wave ultraviolet (UV-C) radiation and of temperature. In newer versions, AADEC monitors microbial activity and can adjust the UV-C and temperature levels automatically. An optical density measurement is used to determine how many cells are present in the growth medium—over time, this corresponds to how many survive and reproduce. Oxidation-reduction potential provides information on consumed metabolic energy, and pH and electrical conductivity on metabolic products. Dissolved oxygen content is used to determine aerobic vs anaerobic growth. A Raspberry Pi computer processes all this data to set the UV-C stressor level. AADEC’s auxiliary systems include peristaltic pumps to change media and agitation to counteract cell settling. These actuators can also act as additional stressors. With the Raspberry Pi monitoring sensors and adjusting actuators in real time, AADEC takes measurements and controls the environment much more accurately than can be done with a manual EE implementation. The third and latest AADEC iteration is the first to simplify design and usage with circuits on PCBs and the ability to pre-program experimental protocols. Still planned is expansion to a multi-well design for the study of varying cell cultures in parallel, which will enable researchers to retain and re-inoculate cultures exhibiting the desired trait most strongly while flushing out others. AADEC’s special capabilities make it a valuable tool for studying life under multiple stressors, enabling scientists to replicate changes in climate on microbes for study in a lab setting.

Microbial Adaptation↗

DOE OSTI2025

Leveraging High-resolution Molecular Composition of Soil Organic Matter to Enhance Carbon Cycling Modeling

Soils store more carbon than the atmosphere and vegetation combined, yet Earth system models still struggle to predict how this vast reservoir will respond to environmental change. A central limitation is that most soil biogeochemical models represent organic matter using bulk conceptual pools or chemically homogeneous fractions, preventing direct use of rapidly expanding molecular-scale datasets. Here we develop and test a new soil decomposition framework that explicitly integrates high-resolution information on organic matter composition. First, we construct a molecularly informed litter decomposition module in which plant inputs are partitioned into five functional compound classes—carbohydrates, proteins, lignin-like aromatics, lipids, and carbonyls—using a molecular mixing model calibrated to solid-state 13 C Nuclear Magnetic Resonance (NMR) spectra. Class-specific kinetics, lignin-dependent physical protection, and substrate-driven microbial carbon use efficiency allow the module to capture metabolic tradeoffs associated with enzyme production and nutrient limitation. We then embed this litter module within a microbially explicit whole-soil model that tracks the transformation of these compound classes through particulate organic matter, dissolved organic matter, mineral-associated organic matter, and microbial biomass. High-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS) data are used to link internal pools to measurable soil organic matter fractions and to constrain key process parameters. Applications at soil-core and ecosystem scales demonstrate that the new model reproduces observed soil respiration dynamics while providing mechanistic attribution of CO 2 fluxes to specific chemical classes and pools. Compared to existing frameworks such as the Community Land Model soil biogeochemistry module and the Millennial model, our approach maintains competitive predictive skill while substantially improving interpretability and opportunities for data–model integration. This work illustrates a viable pathway for leveraging molecular-scale observations to reduce structural uncertainty in soil carbon–climate feedback projections.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Putting the soil health principles to the test in Iowa

One of the most popular soil conservation campaigns is based on the USDA Natural Resource Conservation Service's Soil Health Principles (NRCS-SHPs). The NRCS-SHP program identifies four principles—maximize presence of living roots, minimize disturbance, maximize soil cover, and maximize biodiversity—with the underlying assumption that the more principles one follows, the greater improvements in soil health. Despite the popularity of the NRCS-SHPs, this underlying assumption has not been rigorously tested. To do so, we used nine long-term experiments all located in central Iowa, but with varying degree of NRCS-SHP adoption, to determine if greater adoption increases three slow-changing (maximum water holding capacity, bulk density [BD], and soil organic carbon) and three dynamic (microbial biomass carbon [MBC], potentially mineralizable carbon [PMC], and permanganate oxidizable carbon [POXC]) soil health indicators. We regressed these indicators with a soil health principle score that can scale soil management based on adoption of the NRCS-SHPs. Of the slow-changing soil properties, increased adoption of NRCS-SHPs only decreased soil BD (R2 = 0.22, p = 0.024). On the other hand, increased adoption of NRCS-SHPs strongly predicted increases in both MBC and PMC and across two sampling dates (R2 > 0.23, p < 0.015); POXC, however, did not increase with greater adoption. The consistent increases in MBC and PMC with greater adoption of NRCS-SHPs supports their usefulness as sensitive indicators of positive soil health change. Our study provides scientific evidence to support the NRCS-SHPs concept, improving its usefulness as an extension campaign, and stands as a step toward evidence-based soil conservation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Terrestrial carbon dynamics in an era of increasing wildfire

In an increasingly flammable world, wildfire is altering the terrestrial carbon balance. However, the degree to which novel wildfire regimes disrupt biological function remains unclear. Here, we synthesize the current understanding of above and below ground processes that govern carbon loss and recovery across diverse ecosystems. In this study, we find that intensifying wildfire regimes are increasingly exceeding biological thresholds of resilience, causing ecosystems to convert to a lower carbon-carrying capacity. Growing evidence suggests that plants compensate for fire damage by allocating carbon below ground to access nutrients released by fire, while wildfire selects for microbial communities with rapid growth rates and the ability to metabolize pyrolyzed carbon. Determining controls on carbon dynamics following wildfire requires integration of experimental and modeling frameworks across scales and ecosystems. Fire severity is expected to increase as a result of warming. This will potentially amplify climate change due to its impact on the carbon cycle. This Review discusses ecosystem carbon loss and recovery following wildfire, and highlights where further work is needed to inform model predictions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Complete integration of carbene-transfer chemistry into biosynthesis

Biosynthesis is an environmentally benign and renewable approach that can be used to produce a broad range of natural and, in some cases, new-to-nature products. However, biology lacks many of the reactions that are available to synthetic chemists, resulting in a narrower scope of accessible products when using biosynthesis rather than synthetic chemistry. A prime example of such chemistry is carbene-transfer reactions. Although it was recently shown that carbene-transfer reactions can be performed in a cell and used for biosynthesis, carbene donors and unnatural cofactors needed to be added exogenously and transported into cells to effect the desired reactions, precluding cost-effective scale-up of the biosynthesis process with these reactions. Here, in this paper, we report the access to a diazo ester carbene precursor by cellular metabolism and a microbial platform for introducing unnatural carbene-transfer reactions into biosynthesis. The α-diazoester azaserine was produced by expressing a biosynthetic gene cluster in Streptomyces albus. The intracellularly produced azaserine was used as a carbene donor to cyclopropanate another intracellularly produced molecule—styrene. The reaction was catalysed by engineered P450 mutants containing a native cofactor with excellent diastereoselectivity and a moderate yield. Our study establishes a scalable, microbial platform for conducting intracellular abiological carbene-transfer reactions to functionalize a range of natural and new-to-nature products and expands the scope of organic products that can be produced by cellular metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) (Final Scientific/Technical Report, Subcontract Award No. 6953691)

The overarching objective the Baliga lab is to develop a mechanistic understanding of the field relevant metabolic processes underlying community partitioning of respiration pathways and physiological state shifts. In order to dissect how environmental perturbations influence microbial regulatory networks, we have constructed data-driven models that capture the dynamic interplay between abiotic and biotic factors during laboratory simulations. Specifically, we have developed multiple computational models (i.e., cMonkey2, EGRIN 2.0, and multiple genome-scale metabolic models) connecting environmental influence to genome-encoded regulatory programs. In addition, we have generated new tools such as Live Anaerobic Cell Sorting (LAnCS) and Fluidized Bed Reactors (FBRs) to investigate the dynamics of community partitioning of metabolic processes supporting sulfate or nitrate respiration, which are two critical activities observed from the field site at Oak Ridge National Labs (ORNL). This framework of connecting field phenomena with laboratory simulations and computational modeling has created the Environmental Simulations and Modelling (EnvSim) campaign within ENIGMA. The campaign, which spans multiple laboratories across ENIGMA and is led by the Baliga group, has established synthetic communities (SynComs) to discover, characterize, and dissect key microbial processes relevant to field observations, such as emissions of the greenhouse gas nitrous oxide (N 2 O). For example, the EnvSim campaign so far has deduced four potential mechanisms that may account for the N 2 O emissions at the FRC and are currently being investigated by labs across ENIGMA. Denitrification may be driven by complete denitrifiers, however, their NosZ enzymes, which catalyze the final step in denitrification by converting N 2 O to N 2 , may be sensitive at a lower pH. Additionally, the denitrification process could be partitioned among organisms and some may have pH-sensitive NosZ genes. Another factor contributing to variable N 2 O emissions relates to the metal co-factors involved in the denitrification pathway. For instance, excess Cu, Al, Mn, U, Ni, Co, Cu, and/or Cd may have inhibitory effects on multiple enzymatic steps during denitrification, while the enzymatic production of nitrite, the precursor of N 2 O, can be limited by the essential metal Mo. Lastly, abiotic production of N 2 O may occur as a result of chemodenitrification, in which metals like Fe, Mn, and some organic compounds can drive redox reactions that convert nitrogen cycle intermediates to N 2 O under the right conditions. Current investigations and analyses have generated multiple transcriptomic profiles aiding the refinement of new metabolic and gene regulatory network model for our denitrifying SynCom. In sum, the previous funding cycle has generated 33 peer-reviewed publications spanning predictive network biology to co-operativity of mutualistic interspecies interactions of evolved communities. Our integration of multiple omics datasets and the development of new network modelling tools has revealed important insights that can explain field observed phenomenon and generated new hypotheses to be investigated in the field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A Panspermia Origin for Venus Cloud Life

Decades of study have hinted at the astrobiological potential of Venus's cloud layers. This potential is often cast as stemming from the idea that the Venusian surface was clement in the past. As the climate changed, life then remained in, or perhaps evolved and migrated to, the last habitable niche: the altitudes above ∼50 km with Earth-like temperatures and pressures today. Here we explore an alternative scenario where life was delivered to Venus' clouds from Earth or Mars (“panspermia”). This process requires a life-containing bolide to enter the atmosphere, without experiencing complete sterilization, and then be dispersed at high altitude in fragments small enough to dwell in the clouds. We adapt a widely used model of bolide-atmosphere interaction to investigate the fate of bolides delivered to Venus from Earth and Mars. Starting at the top of the atmosphere, bolides ablate and fragment. Aerodynamic drag spreads these fragments horizontally, forming a “pancake” with an increased effective cross-section, causing rapid deceleration. An airburst occurs when the bolide deposits its highest amount of kinetic energy in the atmosphere. Observations of terrestrial meteorites provide a scaling law for the distribution of post-airburst fragment sizes. Inspired by the “Venus Life Equation,” we present a framework for calculating the rate at which panspermia delivers microbial life to the clouds of Venus. Our best estimate is an average of ∼100 cells dispersed in the clouds per Earth-year. Whether this life can survive and thrive in its new home remains an open question.

Guinan, Emma [Arizona State Univ., Tempe, AZ (Unit↗

DOE OSTI2025

The Emergence and Promise of Functional Chemogeography of Organic Matter

Organisms in ecosystems continuously release a myriad of organic matter molecules that undergo microbial and abiotic transformation, processes that critically influence carbon storage and climate feedbacks. Yet, a systematic understanding of what determines the transformation and persistence of organic matter across spatiotemporal scales remains elusive. We propose an emerging framework, termed “functional chemogeography,” to understand transformation and persistence of organic matter based on the chemical traits of molecules. This framework extends beyond a sole focus on intrinsic traits, which remain relatively constant across spatiotemporal scales, to emphasize extrinsic traits such as biochemical transformations and environmental responses, which vary spatiotemporally and are shaped by both intrinsic traits and the environment. When upscaled to the assemblage level using functional diversity indices, these extrinsic traits reveal a significant, and in some cases superior, capacity than intrinsic traits to explain biogeochemical processes, as demonstrated through a case study of dissolved organic matter in China's lakes. In conclusion, by integrating trait-based perspectives into predictive models, this framework helps bridge chemical complexity with ecosystem biogeochemistry, thereby advancing our ability to predict the fate of global organic carbon under environmental change.

chemical traits↗

DOE OSTI2026

Model scripts associated with “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale”

NOTE: The manuscript associated with this data package is currently in review. The data/scripts may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final scripts and additional metadata. This data package is associated with the publication “Revisiting controls on hyporheic respiration with knowledge-guided machine learning at continental scale” submitted to Environmental Science & Technology (Zheng et al. 2026). The project combines mechanistic process modeling with knowledge-guided machine learning (KGML) to evaluate how organic matter chemistry, microbial biomass, and physical substrate accessibility regulate realized respiration rates across river corridors. All data used in this paper have been previously published and can be accessed at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719 (Goldman et al., 2020). This data package contains 3 R-markdown (Rmd) preprocessing scripts for the previously published data and subsequent modelling workflows. The full workflow with input and output data can be found in the associated GitHub repository at https://github.com/jianqiuz/KGML-WHONDRS.

Biogeochemistry↗

DOE OSTI2020

Collaborative Research: Natural Organic Matter and Microbial Controls on Mobilization/Immobilization of I and Pu in Soils and Waters Affected by Radionuclide Releases in USA and Japan

In this project, the relationship between natural organic matter (NOM) and two radioactive elements that are relevant to nuclear waste disposal were studied: Plutonium (Pu) and Iodine. The human and environmental risks associated with Pu stem mainly from the very long half-lives of several of its isotopes ( 238 Pu, 88 yr; 239 Pu, 24,100 yr; 240 Pu, 6560 yr) and its radiotoxicity. Understanding Pu biogeochemical behavior in both near-field (>10-11M) and far-field scales (<10-11M) is imperative to the development of approaches for reprocessing Pu, remediation of Pu contamination and accurate assessment of risks posed by disposal practices for Pu-bearing wastes. The environmental mobility of Pu can be affected by redox potential, pH, adsorption, precipitation, complexation, colloid formation, and microbial activity, of which the first characteristic has the most profound influence. Numerous studies have shown high affinity of Pu towards NOM, as well as to mineral phases. NOM is ubiquitous in the environment, e.g., both fulvic and humic acids are able to reduce Pu(V,VI) to Pu(IV) and the redox potential of NOM is positively related to the abundance of phenolic/acidic OH groups. NOM can either facilitate or limit actinide migration, depending on specific biogeochemical conditions including pH, mineral and organic matter characteristics, etc. The other radionuclide of interest is radioiodine ( 129 I). 129I is a major by-product of nuclear fission and of serious concern to the Department of Energy (DOE) as it is among the top risk drivers at existing and potential radiowaste-contaminated sites. The risk of 129 I stems largely from its high bioconcentration factor (90% of the body’s iodine is accumulated in the thyroid), a high inventory at source terms, a very long-half life (16M years), and rapid mobility in the subsurface environment. As a consequence, 129 I has the lowest drinking water standard (1 pCi/L) among all radionuclides in the Federal Register. With a novel and sensitive gas chromatography-mass spectrometry (GC-MS) method developed in our lab, it is possible to quickly and simultaneously determine the distribution of 129 I and stable 127 I forms in environments, as low as 2 pCi/L for 129 I. This method was subsequently validated using accelerator mass spectroscopy, AMS. IO 3 - and organo-I were determined as major species in the groundwater of SRS and the Hanford Site, contrary to thermodynamic predictions that I- should be the dominant species at these sites. Mobility of 129 I was also demonstrated to depend greatly on the I species and its concentration, sediment pH, and redox state, with times to achieve equilibrium taking up to 12 weeks. Along the groundwater pathway in the F-Area of SRS, 129 I- supplied from the seepage basins was transformed to 129 IO 3 - and organo- 129 I with increasing iodine sediment sorption, causing the lower total 127 I and 129 I concentrations along the gradient transect of the waste plume. By contrast, groundwater 129 I concentrations in the wetlands (as high as 1617.3 pCi/L) were greatly elevated with respect to the source term (159.3 pCi/L). While the NOM promoted the uptake of 129 I to the wetland sediment, it also promoted the formation of soluble organic fraction. A small fraction of NOM that is bound to iodine can behave as a mobile organo-I source. Iodide was enzymatically incorporated into NOM, whereas both iodide and iodate were abiotically bound to NOM, under certain conditions. Iodate removal from the mobile aqueous phase can also occur through incorporation into carbonate (e.g., at the Hanford Site, USA). Thus immobilization and re-mobilization of iodine species were influenced by pH, Eh and the presence of NOM and metal oxides, which adds to the complexity of site remediation action. A ground-breaking result was to elucidate the products (i.e. organo-iodine moieties formed via enzymatic and non-enzymatic processes) at the molecular level by nuclear magnetic resonance (NMR) and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS). We found that iodine-NOM interactions may be influenced by NOM hydrophobic aliphatic moieties. From the perspective of ESI-FTICRMS, organo-iodine formulas were ascribed to the groups of unsaturated hydrocarbons, lignins and proteins. Iodate is likely abiotically reduced to reactive iodine species by lignin- and tannin-like compounds or carboxylic-rich alicyclic molecules (CRAM). We also investigated microbial mechanisms in iodine incorporation into NOM. We established that soil bacteria isolated from F-Area of SRS did not accumulate significant amounts of I- (0.2-2%). Intracellular uptake of I- decreases with increasing pH when pH ranged from 4 to 6. In contrast, 44 out of 84 strains isolated from the F-Area of SRS can transform I- to IO 3 - and organo-iodine. In some cases, oxidation was facilitated in the presence of H 2 O 2 . Microbes can also excrete organic acids that enhance I- oxidation by lowering the ambient pH and reacting with H 2 O 2 to form peroxy carboxylic acids. At lower pH values (≤5), H 2 O 2 hydrolysis was the driving force for iodide-oxidation; whereas, at pH ≥ 6, spontaneous decomposition of peroxy carboxylic acids, originating from H 2 O 2 and organic acids were the primary cause of iodide oxidation. Lastly, it was determined that microbial processes involved in Mn (II) are capable of directly oxidizing I- via enzymatic catalysis (i.e., multicopper oxidases), or indirectly through the formation of reactive oxygen species (ROS) and/or biogenic manganese oxides. ROS-mediated oxidation of I- was found to predominate at pH >5, whereas the enzymatic and Mn oxide pathways were more active at pH < 5. Together, this project has resulted in 9 publications in high-impact journals, and the training of 1 Ph.D and 4 undergraduate students.

54 ENVIRONMENTAL SCIENCES↗