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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Genetic Architecture of Nitrogen Use Efficiency in Switchgrass ( Panicum virgatum L.)

Switchgrass (Panicum virgatum L.) has immense potential as a bioenergy crop with the aim of producing biofuel as an end goal. Nitrogen (N)-related sustainability traits, such as nitrogen use efficiency (NUE) and nitrogen remobilization efficiency (NRE), are important factors affecting switchgrass quality and productivity. Hence, it is imperative to develop nitrogen use-efficient switchgrass accessions by exploring the genetic basis of NUE in switchgrass. For that, we used 331 diverse field-grown switchgrass accessions planted under low and moderate N fertility treatments. We performed a genome wide association study (GWAS) in a holistic manner where we not only considered NUE as a single trait but also used its related phenotypic traits, such as total dry biomass at low N and moderate N, and nitrogen use index, such as NRE. We have evaluated the phenotypic characterization of the NUE and the related traits, highlighted their relationship using correlation analysis, and identified the top ten nitrogen use-efficient switchgrass accessions. Our GWAS analysis identified 19 unique single nucleotide polymorphisms (SNPs) and 32 candidate genes. Two promising GWAS candidate genes, caffeoyl-CoA O-methyltransferase (CCoAOMT) and <alfin-like 6(AL6), were further supported by linkage disequilibrium (LD) analysis. Finally, we discussed the potential role of nitrogen in modulating the expression of these two genes. Our findings have opened avenues for the development of improved nitrogen use-efficient switchgrass lines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Data for Impacts of Legacy and Contemporary Nitrogen Inputs on N2O and CO2 Emissions in Miscanthus and Maize Cultivated Soils

Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteu s ( M × g ) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M × g and maize were grown. A 150-day soil incubation experiment was conducted using soils from a long-term M × g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in M × g soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient-rich soils, also increased with higher legacy fertilization rates in M × g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.

Carbon↗
DOE OSTI2022

N and P constrain C in ecosystems under climate change: Role of nutrient redistribution, accumulation, and stoichiometry

Abstract We use the Multiple Element Limitation (MEL) model to examine responses of 12 ecosystems to elevated carbon dioxide (CO 2 ), warming, and 20% decreases or increases in precipitation. Ecosystems respond synergistically to elevated CO 2 , warming, and decreased precipitation combined because higher water‐use efficiency with elevated CO 2 and higher fertility with warming compensate for responses to drought. Response to elevated CO 2 , warming, and increased precipitation combined is additive. We analyze changes in ecosystem carbon (C) based on four nitrogen (N) and four phosphorus (P) attribution factors: (1) changes in total ecosystem N and P, (2) changes in N and P distribution between vegetation and soil, (3) changes in vegetation C:N and C:P ratios, and (4) changes in soil C:N and C:P ratios. In the combined CO 2 and climate change simulations, all ecosystems gain C. The contributions of these four attribution factors to changes in ecosystem C storage varies among ecosystems because of differences in the initial distributions of N and P between vegetation and soil and the openness of the ecosystem N and P cycles. The net transfer of N and P from soil to vegetation dominates the C response of forests. For tundra and grasslands, the C gain is also associated with increased soil C:N and C:P. In ecosystems with symbiotic N fixation, C gains resulted from N accumulation. Because of differences in N versus P cycle openness and the distribution of organic matter between vegetation and soil, changes in the N and P attribution factors do not always parallel one another. Differences among ecosystems in C‐nutrient interactions and the amount of woody biomass interact to shape ecosystem C sequestration under simulated global change. We suggest that future studies quantify the openness of the N and P cycles and changes in the distribution of C, N, and P among ecosystem components, which currently limit understanding of nutrient effects on C sequestration and responses to elevated CO 2 and climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Electrochemical sulfate production from sulfide-containing wastewaters and integration with electrochemical nitrogen recovery

Electrochemical methods can help manage sulfide in wastewater, which poses environmental and health concerns due to its toxicity, malodor, and corrosiveness. In addition, sulfur could be recovered as fertilizer and commodity chemicals from sulfide-containing wastewaters. Wastewater characteristics vary widely among wastewaters; however, it remains unclear how these characteristics affect electrochemical sulfate production. Here, in this study, we evaluated how four characteristics of influent wastewaters (electrolyte pH, composition, sulfide concentration, and buffer strength) affect sulfide removal (sulfide removal rate, sulfide removal efficiency) and sulfate production metrics (sulfate production rate, sulfate production selectivity). We identified that electrolyte pH (3 × difference, i.e., 25.1 to 84.9 μM h –1 in average removal rate within the studied pH range) and sulfide concentration (16 × difference, i.e., 82.1 to 1347.2 μM h –1 in average removal rate) were the most influential factors for electrochemical sulfide removal. Sulfate production was most sensitive to buffer strength (6 × difference, i.e., 4.4 to 27.4 μM h –1 in average production rate) and insensitive to electrolyte composition. Together, these results provide recommendations for the design of wastewater treatment trains and the feasibility of applying electrochemical methods to varying sulfide-containing wastewaters. In addition, we investigated a simultaneous multi-nutrient (sulfur and nitrogen) process that leverages electrochemical stripping to further enhance the versatility and compatibility of electrochemical nutrient recovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Microbial processing of plant remains is co-limited by multiple nutrients in global grasslands

Microbial processing of aggregate-unprotected organic matter inputs is key for soil fertility, long-term ecosystem carbon and nutrient sequestration and sustainable agriculture. In this work, we investigated the effects of adding multiple nutrients (nitrogen, phosphorus and potassium plus nine essential macro- and micro-nutrients) on decomposition and biochemical transformation of standard plant materials buried in 21 grasslands from four continents. Addition of multiple nutrients weakly but consistently increased decomposition and biochemical transformation of plant remains during the peak-season, concurrent with changes in microbial exoenzymatic activity. Higher mean annual precipitation and lower mean annual temperature were the main climatic drivers of higher decomposition rates, while biochemical transformation of plant remains was negatively related to temperature of the wettest quarter. Nutrients enhanced decomposition most at cool, high rainfall sites, indicating that in a warmer and drier future fertilized grassland soils will have an even more limited potential for microbial processing of plant remains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

N-dependent dynamics of root growth and nitrate and ammonium uptake are altered by the bacterium Herbaspirillum seropedicae in the cereal model Brachypodium distachyon

Nitrogen (N) fixation in cereals by root-associated bacteria is a promising solution for reducing use of chemical N fertilizers in agriculture. However, plant and bacterial responses are unpredictable across environments. We hypothesized that cereal responses to N-fixing bacteria are dynamic, depending on N supply and time. To quantify the dynamics, a gnotobiotic, fabricated ecosystem (EcoFAB) was adapted to analyse N mass balance, to image shoot and root growth, and to measure gene expression of Brachypodium distachyon inoculated with the N-fixing bacterium Herbaspirillum seropedicae. Phenotyping throughput of EcoFAB-N was 25–30 plants h -1 with open software and imaging systems. Herbaspirillum seropedicae inoculation of B. distachyon shifted root and shoot growth, nitrate versus ammonium uptake, and gene expression with time; directions and magnitude depended on N availability. Primary roots were longer and root hairs shorter regardless of N, with stronger changes at low N. At higher N, H. seropedicae provided 11% of the total plant N that came from sources other than the seed or the nutrient solution. The time-resolved phenotypic and molecular data point to distinct modes of action: at 5 mM NH 4 NO 3 the benefit appears through N fixation, while at 0.5 mM NH 4 NO 3 the mechanism appears to be plant physiological, with H. seropedicae promoting uptake of N from the root medium.Future work could fine-tune plant and root-associated microorganisms to growth and nutrient dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Photosynthetic decline in aging perennial grass is not fully explained by leaf nitrogen

Abstract Aging in perennial plants is traditionally observed in terms of changes in end-of-season biomass; however, the driving phenological and physiological changes are poorly understood. We found that 3-year-old (mature) stands of the perennial grass Miscanthus×giganteus had 19–30% lower Anet than 1-year-old M.×giganteus (juvenile) stands; 10–34% lower maximum carboxylation rates of Rubisco and 34% lower light-saturated Anet (Asat). These changes could be related to nitrogen (N) limitations, as mature plants were larger and had 14–34% lower leaf N on an area basis (Na) than juveniles. However, N fertilization restored Na to juvenile levels but compensated only 50% of the observed decline in leaf photosynthesis with age. Comparison of leaf photosynthesis per unit of leaf N (PNUE) showed that mature stands had at least 26% lower PNUE than juvenile stands across all N fertilization rates, suggesting that other factors, besides N, may be limiting photosynthesis in mature stands. We hypothesize that sink limitations in mature stands could be causing feedback inhibition of photosynthesis which is associated with the age-related decline in photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Reinventing wastewater treatment plants: energy neutral treatment and enhanced fertilizer production through a novel resource recovery center

Wastewater treatment plants (WWTPs) are typically energy intensive, mainly due to the secondary treatment processes such as activated sludge (AS) for treatment of organics as well as nutrients like nitrogen. Nitrogen removal presents a big problem for WWTPs. The main form of nitrogen in wastewater is ammonium, and an AS process uses oxygen to convert ammonium into nitrite and nitrate which is then converted to nitrogen through denitrification process. During anaerobic digestion (AD), organic nitrogen gets degraded, resulting in an effluent stream (centrate) with a high nitrogen content, mostly in the form of ammonium. This contributes 15-30% of total nitrogen to the wastewater influent which further increases energy consumption for aeration. The project aims to transform this conventional municipal WWTPs into energy-neutral, resource-recovering facilities by integrating three core technologies: • Cloth Media Filtration (CMF) to replace conventional primary sedimentation (CPS) and increase the diversion of organics from the energy intensive secondary treatment to AD. This results in reduced energy demand for aeration in the secondary process while simultaneously increasing the biogas production in the anaerobic digesters. • Anerobic Digester to increase biogas and ammonia production. • Membrane Evaporation (ME) to recover ammonia from AD centrate and produce marketable fertilizer. The benefits of proposed WWTP process modifications were evaluated using techno economic analysis (TEA) and life cycle assessment (LCA). For CMF portion of the research a statistical analysis was employed to develop data-driven tools that could be used to enhance and optimize its performance in terms of energy savings and effluent quality. The main objective of this project is to reduce the energy demand for secondary treatment at municipal WWTPs by at least 50%, increase anaerobic digester (AD) biogas and ammonia production by 100% and 120%, respectively, and recover 90% of ammonia from the AD. Integrated CMF, AD, and ME was shown to work synergistically toward achieving these decarbonization targets through energy-positive treatment and fertilizer recovery techniques.

42 ENGINEERING↗
DOE OSTI2021

Metal Ion Fluxes Controlling Amphibian Fertilization

Mammalian oocytes undergo major changes in zinc content and localization to be fertilized, the most striking being the rapid exocytosis of over 10 billion zinc ions in what are known as zinc sparks. Here, we report that fertilization of amphibian Xenopus laevis eggs also initiates a zinc spark that progresses across the cell surface in coordination with dynamic calcium waves. This zinc exocytosis is accompanied by a newly recognized loss of intracellular manganese. Synchrotron-based X-ray fluorescence and analytical electron microscopy reveal that zinc and manganese are sequestered in a system of cortical granules that are abundant at the animal pole. Through electron-nuclear double-resonance studies, we rule out Mn2+ complexation with phosphate or nitrogenous ligands in intact eggs, but the data are consistent with a carboxylate coordination environment. Our observations suggest that zinc and manganese fluxes are a conserved feature of fertilization in vertebrates and that they function as part of a physiological block to polyspermy.

Seeler, John F.↗
DOE OSTI2025

Optimization of a Secondary Air Injector for a Rich-Quench-Lean (RQL) Ammonia Combustor Using Computational Fluid Dynamics

Ammonia has emerged as a promising medium for moving hydrogen around the globe due to its energy density, existing infrastructure for production, transportation, and storage, and multiple applications from fertilizer to power generation. However, one of the most significant challenges with ammonia combustion for power generation is the formation of nitrogen oxides (NOx) during combustion. Several combustion strategies have been developed to minimize the formation of NOx. One such strategy, known as rich-quench-lean (RQL), is a method that combusts NH3 in a fuel-rich environment, followed by a quick mix section and a lean burnout section. Rapid mixing of secondary air before lean burnout is thought to be important to minimize the formation of NOx. A genetic algorithm (GA) is used to parametrically vary the secondary air injector design, including the diameter, count, and angles over a constrained design space. The designs are evaluated using a non-reacting OpenFOAM model, with the objective function being the uniformity index of the secondary air (modeled as a scalar). Optimization campaigns show that traditional correlation-based designs might not be adequate. After running 414 OpenFOAM models, the optimal design is 32, 1 mm diameter, angled air injectors, increasing the uniformity index at the outlet of the quick mix zone by 36.8%. The most promising designs will be manufactured and tested in a small RQL burner setup, which is expected to lead to validation and insight into the practical usage of NH3 combustion for power generation.

ammonia combustion↗
DOE OSTI2026

Electrochemically recovered struvite matches conventional fertilizers in soil nutrient supply

Phosphorus (P) is an essential macronutrient for agriculture, yet global reliance on finite phosphorite reserves raises concerns about long-term food and nutrient security. Struvite (MgNH 4 PO 4 ·6H 2 O), a mineral recovered from municipal wastewater, represents a sustainable and circular source of P, but uncertainty remains regarding its nutrient availability relative to conventional fertilizers. This study evaluated the fertilizer value and environmental safety of electrochemically recovered struvite (RecoP) in comparison with diammonium phosphate (DAP), triple superphosphate (TSP), and rock phosphate (RockP). Nutrient availability, potential contaminant concentrations, and soil P and nitrogen (N) dynamics were assessed using standardized chemical analyses and an 8-week incubation experiment across three soils with contrasting soil types. RecoP contained 14.7% citrate-soluble P, significantly greater than RockP and comparable to DAP and TSP. Across all soils, RecoP increased both readily available and moderately labile P pools (p < 0.01), matching the performance of conventional fast-release fertilizers. Despite containing approximately half the total of DAP, RecoP stimulated nitrification rates that were 2.2 times greater than the control and exceeded those of TSP, suggesting that fertilizer-derived N bioavailability, rather than total N loading, governed microbial N transformation responses. Concentrations of potentially toxic elements in RecoP were consistently well below US Environmental Protection Agency regulatory limits thresholds. Collectively, these results indicate that RecoP functions as a readily available source of both P and N, comparable to widely used conventional fertilizers, while meeting environmental safety standards. RecoP therefore represents a viable component of sustainable nutrient management strategies that support P recycling and agricultural productivity.

Kharal, Sudarshan [Ohio Univ., Athens, OH (United ↗
DOE OSTI2023

Synthesis and Structural Study of Substituted Ternary Nitrides for Ammonia Production

Over the past few decades, inorganic nitride materials have grown in importance in part due to their potential as catalysts for the synthesis of NH 3 , a key ingredient in fertilizer and precursor to industrial chemicals. Of particular interest are the ternary (ABN) or higher-order nitrides with high metal-to-nitrogen ratios that show promise in enhancing NH 3 synthesis reaction rates and yields via heterogeneous catalysis or chemical looping. Although metal nitrides are predicted to be numerous, the stability of nitrogen triple bonds found in N 2 , especially in comparison to the metal–nitrogen bonds, has considerably hindered synthetic efforts to produce complex nitride compounds. In this study, we present an exhaustive down-selection process to identify ternary nitrides for a promising chemical looping NH 3 production mechanism. We also report on a facile and efficient two-step synthesis method that can produce well-characterized η-carbide Co 3 Mo 3 N/Fe 3 Mo 3 N or filled β-manganese Ni 2 Mo 3 N ternaries, as well as their associated quaternary, (Co,Fe) 3 Mo 3 N, (Fe,Ni) 2 Mo 3 N, and (Co,Ni) 2 Mo 3 N, solid solutions. To further explore the quaternary space, syntheses of (Co,Ni) 3 Mo 3 N (Ni ≤ 10 mol %) and Co 3 (Mo,W) 3 N (W ≤ 10 mol %) were also investigated. The structures of the nitrides were characterized via X-ray powder diffraction. The morphology and compositions were characterized with scanning electron microscopy. In conclusion, the multitude of chemically unique, but structurally related, nitrides suggests that properties such as nitrogen activity may be tunable, making the materials of great interest for NH 3 synthesis schemes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Effects of Cinnamomum camphora coppice planting on soil fertility, microbial community structure and enzyme activity in subtropical China

Cinnamomum camphora ( C. camphora ) is a broad-leaved evergreen tree cultivated in subtropical China. Currently, the use of C. camphora clonal cuttings for coppice management has become popular. However, the effects of C. camphora coppice planting on soil abiotic and biotic variances remained unclear. In this study, we collected soil from three points in the seven-year C. camphora coppice planting land: under the tree canopy (P15), between trees (P50), and abandoned land (Control) to investigate the effects of C. camphora coppice planting on soil fertility, microbial community structure and enzyme activity. The results revealed that C. camphora coppice planting significantly increased soil fertility in the point under the tree canopy (P15) and point between trees (P50), and P15 had more significant effects than P50. Meanwhile, in P15 and P50, soil bacterial, fungal alpha-diversity were improved and microbial community structures were also changed. And the changes of soil organic carbon and total nitrogen promote the transformation of soil bacterial, fungal community structures, respectively. In addition, C. camphora coppice planting significantly ( p < 0.05) increased soil urease (UE), polyphenol oxidase, and peroxidase activities, while significantly decreased soil ACP activity. This study demonstrated that the C. camphora coppice planting could improve soil fertility in subtropical China, which promoted the transformation of soil microbial community from oligotrophs ( K -strategist) to copiotrophs ( r -strategist). Thus, this work can provide a theoretical basis for soil nutrient variation and productive management of C. camphora coppice plantation in subtropical China.

Sun, Luyuan↗
DOE OSTI2024

Printed Potentiometric Ammonium Sensors for Agriculture Applications

Ammonium (NH 4 + ) concentration is critical to both nutrient availability and nitrogen (N) loss in soil ecosystems but can be highly variable across spatial and temporal scales. For this reason, effectively informing agricultural practices such as fertilizer management and understanding of mechanisms of soil N loss require sensor technologies to monitor ammonium concentrations in real time. Our work investigates the performance of fully printed ammonium ion-selective sensors used in diverse soil environments. Ammonium sensors consisting of a printed ammonium ion-selective electrode and a printed Ag/AgCl reference were fabricated and characterized in aqueous solutions and three different soil types (sand, peat, and clay) under the range of ion concentrations likely to be present in soil (0.01–100 mM). The response of ammonium sensors was further evaluated under variable gravimetric moisture content in the soil to reflect their reliability under field conditions. Ammonium sensors demonstrated a sensitivity of 53.6 ± 5.1 mV/decade when tested in aqueous solution, and a sensitivity of 55.7 ± 11 mV/dec, 57.5 ± 4.1 mV/dec, and 43.7 ± 4 mV/dec was measured in sand, clay, and peat soils, respectively.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices

Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N 2 O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N 2 O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N 2 O emissions. Among the management practices, N fertilization – a known driver of N 2 O emissions – had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N 2 O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N 2 O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N 2 O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N 2 O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N 2 O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N 2 O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.

16S rRNA gene sequencing↗
DOE OSTI2023

FUN-BioCROP model with litter decomposition parameters derived from the LIDET dataset

This repository contains the code and data necessary to run the FUN-BioCROP (Fixation and Uptake of Nitrogen-Bioenergy Carbon, Rhizosphere, Organisms, and Protection) model with litter decomposition parameters derived from a modified Monte Carlo simulation that used the Long-term Intersite Decomposition Experiment Team dataset. Related publication:Juice, S.M., Ridgeway, J.R., Hartman, M.D., Parton, W.J., Berardi, D.M., Sulman, B.N., Allen, K.E., & Brzostek, E.R. Reparameterizing litter decomposition using a simplified Monte Carlo method improves litter decay simulated by a microbial model and alters bioenergy soil carbon estimates. Description of Files: FUNBioCROP_LIDET Study.Rmd R code with FUN-BioCROP model that can be run with 10 different sets of parameters for litter decomposition (Baseline, LIDET, or eight other best parameter sets identified in the modified Monte Carlo simulation. CORPSE Functions_Bioenergy_V2.R Code with CORPSE model functions, called by FUNBioCROP_LIDET Study.Rmd Model Input Data: bulk.csv, bulk_till.csv, rhizo.csv, rhizo_till.csv, litter.csv Initial C and N (kg C or N/m2) pool values for each soil compartment, final values from spin up. All five files have the same columns: (Column - Description - Units) uFastC - Unprotected fast decomposing carbon - kg carbon/m2 uSlowC - Unprotected slow decomposing carbon - kg carbon/m2 uNecroC - Unprotected necromass carbon - kg carbon/m2 pFastC - Protected fast decomposing carbon - kg carbon/m2 pSlowC - Protected slow decomposing carbon - kg carbon/m2 pNecroC - Protected necromass carbon - kg carbon/m2 livingMicrobeC - Carbon in living microbial biomass - kg carbon/m2 uFastN - Unprotected fast decomposing nitrogen - kg nitrogen/m2 uSlowN - Unprotected slow decomposing nitrogen - kg nitrogen/m2 uNecroN - Unprotected necromass nitrogen - kg nitrogen/m2 pFastN - Protected fast decomposing nitrogen - kg nitrogen/m2 pSlowN - Protected slow decomposing nitrogen - kg nitrogen/m2 pNecroN - Protected necromass nitrogen - kg nitrogen/m2 inorganicN - Inorganic nitrogen - kg nitrogen/m2 CO2 - Carbon in carbon dioxide - kg carbon/m2 livingMicrobeN - Nitrogen in living microbial biomass - kg nitrogen/m2 Model Input Data: FluxTower_AvgSoilT.csv: Average daily soil temperature (oC) at 10 cm depth at University of Illinois Urbana-Champaign (UIUC) Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data) Model Input Data: FluxTower_AvgSoilVWC.csv: Average daily soil volumetric water content (VWC) at 10 cm depth at UIUC Energy Farm flux tower from 7/2008-3/2016. (One year of averaged data) Model Input Data: input_CCS_LIDET Study.csv: This file has daily data to run FUN-BioCROP (Column - Description - Units): yr - calendar year - year doy - day of year (1 to 365) (no leap year) - day anpp - aboveground NPP (DayCent) - kg C/m2/day bnpp - belowground NPP (DayCent) - kg C/m2/day aglivc - live aboveground biomass carbon (DayCent) - kg C/m2 bglivcj - live juvenile fine root biomass carbon (DayCent) - kg C/m2 bglivcm - live mature fine root biomass carbon (DayCent) - kg C/m2 aglivn - live aboveground biomass nitrogen (DayCent) - kg N/m2 bglivnj - live juvenile fine root biomass nitrogen (DayCent) - kg N/m2 bglivnm - live mature fine root biomass nitrogen (DayCent) - kg N/m2 nyr - simulation year - year cult - indicates a cultivation event (0 or 1) crop - indicates a new crop (0 or 1) fert - indicates a fertilizer event (0 or 1) frst - indicates the first day of the growing season (0 or 1) harv - indicates a harvest event (0 or 1) last - indicates the end of the growing season (0 or 1) croptype - crop type (0=none; 1=alfalfa; 2=corn; 3=grass clover pasture; 4=soybean; 5=wheat) cropsrl - crop specific root length - mm/g root cultrhizmix - fraction of rhizosphere mixed with bulk soil during cultivation (0.0-1.0) - fraction cultlitmix - fraction of litter mixed with bulk soil during cultivation (0.0-1.0) - fraction harvremov - fraction of above ground biomass removed during harvest (0.0-1.0) - fraction fertamt - fertilization amount - g N/m2 lifehist - plant life history (0 = annual, 1 = perennial) froot_turnover_c - amount of C in fine root turnover - kg C/m2 froot_turnover_n - amount of N in fine root turnover - kg N/m2 agrd_turnover_c - amount of C in aboveground biomass turnover - kg C/m2 agrd_turnover_n - amount of N in aboveground biomass turnover - kg N/m2 leaf_litter_fastfrac - Fast decomposing fraction of leaf litter (0.0-1.0) - fraction root_litter_fastfrac - Fast decomposing fraction of root litter (0.0-1.0) - fraction root_diameter - root diameter - mm root_length - root length - mm root/m2 rhizo_frac - fraction of total soil volume that is rhizosphere (0.0 - 1.0) - fraction date - date in format YYYY-MM-DD Instructions: Save the model code ("FUN-BioCROP_LIDET Study.Rmd") and accompanything files (data streams and CORPSE function code) in the same folder. In model code "Chunk 3: Load CORPSE Data Streams" set the working directory (setwd) to the folder with the files saved in step #1. In "Chunk 5: Define LIDET parameter sets" select the litter decomposition parameter set to be used in the run, and comment out all other sets. If changing any parameter values, edit them in "Chunk 6: Load parameters." Run all chunks up to and including "Chunk 10: Prepare Data for Export." In "Chunk 11: Export Output Data" edit data frames for export and filenames, as necessary. "Chunk 12: Graph Total Soil C" makes a figure of C remaining over the model run period. Description of each model chunk (in file FUN-BioCROP_LIDET Study.Rmd): Chunk 1: Remove all functions, clear memory. Removes all functions from R environment, clears the memory. Chunk 2: Load Packages. Loads packages necessary to run the code. Chunk 3: Load CORPSE Data Streams. Sets the working directory and loads the data files necessary to run CORPSE. Chunk 4: Load CORPSE Functions. Loads the R script with CORPSE functions from the working directory, "CORPSE Functions_Bioenergy_V2.R". Chunk 5: Define LIDET parameter sets. Has ten different parameter sets for litter decomposition tested in this study: Baseline parameters, LIDET parameters, and the other 8 best performing parameter sets identified in the modified Monte Carlo. To run the model, all but one parameter set must be commented out. Chunk 6: Load Parameters. Loads all fixed parameters to run the model. Data frame with definitions of parameters is in the CORPSE function script "CORPSE Functions_Bioenergy_V2.R" Chunk 7: Prepare Data Streams. Takes data streams loaded in Chunk 3 and puts them in the format necessary to run the model. The model is coded to run at least two sites at a time, so if only one site is being run it must be run in duplicate. Individual data tables of daily values are created in this chunk from the input data file. Chunk 8: Set Initial Conditions. Creates data tables of soil C and N pools for each soil compartment (rhizo_till, rhizo, bulk_till, bulk, litter) and loads initial values into the data tables. Creates lists for each soil compartment to hold model output. Chunk 9: Load FUN Data and Set Up Matrices. Uses DayCent data to calculate FUN input data: root and leaf N demand, total N demand, plant CN, leaf N available for retranslocation, and litter production. Creates matrices for FUN model outputs. Chunk 10: Run Model. Runs the model. Chunk 11: Prepare Data for Export. Combines data from each day saved as lists into data frames for each soil compartment. Adds values from all soil compartments together to calculate total soil values, creates separate data frames for each soil C and N pool (e.g., protected slow C) for the total soil value. Adds different C and N pools together to calculate total soil C and N for all layers. Creates data frame of ratio of protected to unprotected SOC. Organizes FUN data for export. Chunk 12: Export Results. Exports CSV files of model results to the working directory. Chunk 13: Graph Total Soil C. Makes figure of C remaining over time. Related Links: Original FUN-BioCROP model: https://github.com/BrzostekEcologyLab/FUN-BioCROP LIDET dataset: https://andlter.forestry.oregonstate.edu/data/abstract.aspx?dbcode=TD023

Juice, Stephanie↗
DOE OSTI2024

The elite haplotype OsGATA8 -H coordinates nitrogen uptake and productive tiller formation in rice

Excessive nitrogen promotes the formation of nonproductive tillers in rice, which decreases nitrogen use efficiency (NUE). Developing high-NUE rice cultivars through balancing nitrogen uptake and the formation of productive tillers remains a long-standing challenge, yet how these two processes are coordinated in rice remains elusive. Here we identify the transcription factor OsGATA8 as a key coordinator of nitrogen uptake and tiller formation in rice. OsGATA8 negatively regulates nitrogen uptake by repressing transcription of the ammonium transporter gene OsAMT3.2. Meanwhile, it promotes tiller formation by repressing the transcription of OsTCP19, a negative modulator of tillering. We identify OsGATA8-H as a high-NUE haplotype with enhanced nitrogen uptake and a higher proportion of productive tillers. The geographical distribution of OsGATA8-H and its frequency change in historical accessions suggest its adaption to the fertile soil. Overall, this study provides molecular and evolutionary insights into the regulation of NUE and facilitates the breeding of rice cultivars with higher NUE.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback

Methane (CH 4 ) and nitrous oxide (N 2 O) are major greenhouse gases that are predominantly generated by microbial activities in anoxic environments. N 2 O inhibition of methanogenesis has been reported, but comprehensive efforts to obtain kinetic information are lacking. Using the model methanogen Methanosarcina barkeri strain Fusaro and digester sludge-derived methanogenic enrichment cultures, we conducted growth yield and kinetic measurements and showed that micromolar concentrations of N 2 O suppress the growth of methanogens and CH 4 production from major methanogenic substrate classes. Acetoclastic methanogenesis, estimated to account for two-thirds of the annual 1 billion metric tons of biogenic CH 4 , was most sensitive to N 2 O, with inhibitory constants (K I ) in the range of 18–25 μM, followed by hydrogenotrophic (K I , 60–90 μM) and methylotrophic (K I , 110–130 μM) methanogenesis. Dissolved N 2 O concentrations exceeding these K I values are not uncommon in managed (i.e. fertilized soils and wastewater treatment plants) and unmanaged ecosystems. Future greenhouse gas emissions remain uncertain, particularly from critical zone environments (e.g. thawing permafrost) with large amounts of stored nitrogenous and carbonaceous materials that are experiencing unprecedented warming. Incorporating relevant feedback effects, such as the significant N 2 O inhibition on methanogenesis, can refine climate models and improve predictive capabilities.

54 ENVIRONMENTAL SCIENCES↗