Dataset Search

The plant-sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2-pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl-CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP-citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl-CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12-ACL1-ACC1 using fed-batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl-CoA-derived polyketides from low-cost carbon sources.

This dataset contains genotypic and phenotypic data, R scripts, and the results of analysis pertaining to a multi-location field trial of Miscanthus sinensis. Genome-wide association and genomic prediction were performed for biomass yield and 14 yield-component traits across six field trial locations in Asia and North America, using 46,177 single-nucleotide polymorphism (SNP) markers mined from restriction site-associated DNA sequencing (RAD-seq) and 568 M. sinensis accessions. Genomic regions and candidate genes were identified that can be used for breeding improved varieties of M. sinensis, which in turn will be used to generate new M. xgiganteus clones for biomass.

Data and code supporting the paper titled "Estimating the Electric Vehicle Charging Demand of Multi-Unit Dwelling Residents in the United States" by Xi Cheng and Eleftheria Kontou at the University of Illinois Urbana-Champaign. The data and the code enable analytics and assessment of multi-unit dwelling residents travel patterns and their electric vehicle charging demand.

Elevated tropospheric ozone concentration (O3) significantly reduces photosynthesis and productivity in several C4 crops including maize, switchgrass and sugarcane. However, it is unknown how O3 affects plant growth, development and productivity in sorghum (Sorghum bicolor L.), an emerging C4 bioenergy crop. Here, we investigated the effects of elevated O3 on photosynthesis, biomass and nutrient composition of a number of sorghum genotypes over two seasons in the field using free-air concentration enrichment (FACE), and in growth chambers. We also tested if elevated O3 altered the relationship between stomatal conductance and environmental conditions using two common stomatal conductance models. Sorghum genotypes showed significant variability in plant functional traits, including photosynthetic capacity, leaf N content and specific leaf area, but responded similarly to O3. At the FACE experiment, elevated O3 did not alter net CO2 assimilation (A), stomatal conductance (gs), stomatal sensitivity to the environment, chlorophyll fluorescence and plant biomass, but led to reductions in the maximum carboxylation capacity of phosphoenolpyruvate and increased stomatal limitation to A in both years. These findings suggest that bioenergy sorghum is tolerant to O3 and could be used to enhance biomass productivity in O3 polluted regions.

The dataset contains processed model fields used to generate data, figures and tables in the Journal of Geophysical Research article "Investigating the linear dependence of direct and indirect radiative forcing on emission of carbonaceous aerosols in a global climate model." The processed data are monthly averaged cloud properties (CCN, CDNC and LWP) and forcing variables (DRF and IRF) at original CAM5 spatial resolution (1.9° by 2.5°). Raw model output fields from CAM5 simulations are available through NERSC upon request. Please find more detailed information in the ReadMe file.

The dominant strategy for tailoring the chain-length distribution of free fatty acids (FFA) synthesized by heterologous hosts is expression of a selective acyl-acyl carrier protein (ACP) thioesterase. However, few of these enzymes can generate a precise (greater than 90% of a desired chain-length) product distribution when expressed in a microbial or plant host. The presence of alternative chain-lengths can complicate purification in situations where blends of fatty acids are not desired. We report the assessment of several strategies for improving the dodecanoyl-ACP thioesterase from the California bay laurel to exhibit more selective production of medium-chain free fatty acids to near exclusivity. We demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) was an effective library screening technique for identification of thioesterase variants with favorable shifts in chain-length specificity. This strategy proved to be a more effective screening technique than several rational approaches discussed herein. With this data, we isolated four thioesterase variants which exhibited a more selective FFA distribution over wildtype when expressed in the fatty acid accumulating E. coli strain, RL08. We then combined mutations from the MALDI isolates to generate BTE-MMD19, a thioesterase variant capable of producing free fatty acids consisting of 90% of C12 products. Of the four mutations which conferred a specificity shift, we noted that three affected the shape of the binding pocket, while one occurred on the positively charged acyl carrier protein landing pad. Finally, we fused the maltose binding protein (MBP) from E. coli to the N – terminus of BTE-MMD19 to improve enzyme solubility and achieve a titer of 1.9 g per L of twelve-carbon fatty acids in a shake flask.

This dataset contains all the necessary information to recreate the study presented in the paper entitled "Learning coagulation processes with combinatorially-invariant neural networks". This consists of (1) the aggregated output files used for machine learning, (2) the machine learning codes used to learn the presented models, (3) the PartMC model source code that was used to generate the simulation data and (4) the Python scripts used construct the scenario library for training and testing simulations. This data was used to investigate a method (combinatorally-invariant neural network) for learning the aerosol process of coagulation. This data may be useful for application of other methods.

Miscanthus is a close relative of saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between miscanthus and saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of saccharum and miscanthus genotypes. We found that day length was an important factor influencing when miscanthus and saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 miscanthus genotypes, including 28 M. sinensis, 2 M. floridulus, and 3 M. ×giganteus collected from 20.9° S to 44.9° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted M. sinensis flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for M. sinensis and M. floridulus from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-day treatments and the 15 h day treatment. Under short days, short culms for high-latitude accessions was achieved by different physiological mechanisms for M. sinensis genetic groups from the mainland in comparison to those from Japan; for mainland accessions, the mechanism was reduced internode length, whereas for Japanese accessions the phyllochron under short days was greater than under long days. Thus, for M. sinensis, short days typically hastened floral induction, consistent with the expectations for a facultative short-day plant. However, for high latitude accessions of M. sinensis, days less than 12.5 h also signaled that plants should prepare for winter by producing many short culms with limited elongation and development; moreover, this response was also epistatic to flowering. Thus, to flower M. sinensis that originates from high latitudes synchronously with sugarcane, the former needs day lengths >12.5 h (perhaps as high as 15 h), whereas that the latter needs day lengths <12.5 h.

This upload contains all datasets used in Experiment 2 of the EMMA paper (appeared in WABI 2023): Shen, Chengze, Baqiao Liu, Kelly P. Williams, and Tandy Warnow. "EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment". The zip file has the following structure (presented as an example): salma_paper_datasets/ |_README.md |_10aa/ |_crw/ |_homfam/ |_aat/ | |_... |_... |_het/ |_5000M2-het/ | |_... |_5000M3-het/ ... |_rec_res/ Generally, the structure can be viewed as: [category]/[dataset]/[replicate]/[alignment files] # Categories: 1. 10aa: There are 10 small biological protein datasets within the `10aa` directory, each with just one replicate. 2. crw: There are 5 selected CRW datasets, namely 5S.3, 5S.E, 5S.T, 16S.3, and 16S.T, each with one replicate. These are the cleaned version from Shen et. al. 2022 (MAGUS+eHMM). 3. homfam: There are the 10 largest Homfam datasets, each with one replicate. 4. het: There are three newly simulated nucleotide datasets from this study, 5000M2-het, 5000M3-het, and 5000M4-het, each with 10 replicates. 5. rec\_res: It contains the Rec and Res datasets. Detailed dataset generation can be found in the supplementary materials of the paper. # Alignment files There are at most 6 `.fasta` files in each sub-directory: 1. `all.unaln.fasta`: All unaligned sequences. 2. `all.aln.fasta`: Reference alignments of all sequences. If not all sequences have reference alignments, only the sequences that have will be included. 3. `all-queries.unaln.fasta`: All unaligned query sequences. Query sequences are sequences that do not have lengths within 25% of the median length (i.e., not full-length sequences). 4. `all-queries.aln.fasta`: Reference alignments of query sequences. If not all queries have reference alignments, only the sequences that have will be included. 5. `backbone.unaln.fasta`: All unaligned backbone sequences. Backbone sequences are sequences that have lengths within 25% of the median length (i.e., full-length sequences). 6. `backbone.aln.fasta`: Reference alignments of backbone sequences. If not all backbone sequences have reference alignments, only the sequences that have will be included. >If all sequences are full-length sequences, then `all-queries.unaln.fasta` will be missing. >If fewer than two query sequences have reference alignments, then `all-queries.aln.fasta` will be missing. >If fewer than two backbone sequences have reference alignments, then `backbone.aln.fasta` will be missing. # Additional file(s) 1. `350378genomes.txt`: the file contains all 350,378 bacterial and archaeal genome names that were used by Prodigal (Hyatt et. al. 2010) to search for protein sequences.

Data includes carbon mineralization rates, potential denitrification rates, net nitrous oxide fluxes, and soil chemical properties from a laboratory incubation of soil samples collected from 20 locations across an Illinois maize field.

Grass lignocelluloses feature complex compositions and structures. In addition to the presence of conventional lignin units from monolignols, acylated monolignols and flavonoid tricin also incorporate into lignin polymer; moreover, hydroxycinnamates, particularly ferulate, cross-link arabinoxylan chains with each other and/or with lignin polymers. These structural complexities make grass lignocellulosics difficult to optimize for effective agro-industrial applications. In the present study, we assess the applications of two engineered monolignol 4-O-methyltransferases (MOMTs) in modifying rice lignocellulosic properties. Two MOMTs confer regiospecific para-methylation of monolignols but with different catalytic preferences. The expression of MOMTs in rice resulted in differential but drastic suppression of lignin deposition, showing more than 50% decrease in guaiacyl lignin and up to an 90% reduction in syringyl lignin in transgenic lines. Moreover, the levels of arabinoxylan-bound ferulate were reduced by up to 50%, and the levels of tricin in lignin fraction were also substantially reduced. Concomitantly, up to 11 μmol/g of the methanol-extractable 4-O-methylated ferulic acid and 5–7 μmol/g 4-O-methylated sinapic acid were accumulated in MOMT transgenic lines. Both MOMTs in vitro displayed discernible substrate promiscuity towards a range of phenolics in addition to the dominant substrate monolignols, which partially explains their broad effects on grass phenolic biosynthesis. The cell wall structural and compositional changes resulted in up to 30% increase in saccharification yield of the de-starched rice straw biomass after diluted acid-pretreatment. These results demonstrate an effective strategy to tailor complex grass cell walls to generate improved cellulosic feedstocks for the fermentable sugar-based production of biofuel and bio-chemicals.

Lipids accumulated in the vegetative tissues of cellulosic feedstocks can be a potential raw material for biodiesel and bioethanol production. In this work, bagasse of genetically engineered sorghum was subjected to liquid hot-water pretreatment at 170, 180, and 190 °C for different reaction time. Under the optimal pretreatment condition (170 °C, 20 min), the residue was enriched in glucan (57.39 ± 2.63 % w/w) and xylan (13.38 ± 0.49 % w/w). The total lipid content of the pretreated residue was 6.81% w/w, similar to that observed in untreated bagasse (6.30% w/w). Pretreatment improved the enzymatic digestibility of bagasse, allowing a recovery of 79% w/w and 86% w/w of glucose and xylose, respectively. The pretreatment and enzymatic saccharification resulted in a 2-fold increase in total lipid in enzymatic residue compared to the original bagasse. Thus, pretreatment and enzymatic hydrolysis enabled high sugar recovery while concentrating triglycerides and free fatty acids in the residue.

Creating controlled lipid unsaturation locations in oleochemicals can be a key to many bioengineered products. However, evaluating the effects of modifications to the acyl-ACP desaturase on lipid unsaturation is not currently amenable to high-throughput assays, limiting the scale of redesign efforts to <200 variants. Here, we report a rapid mass spectrometry (MS) assay for profiling the positions of double bonds on membrane lipids produced by Escherichia coli colonies after treatment with ozone gas. By MS measurement of the ozonolysis products of Δ6 and Δ8 isomers of membrane lipids from colonies expressing recombinant Thunbergia alata desaturase, we screened a randomly mutagenized library of the desaturase gene at 5 s per sample. Two variants with altered regiospecificity were isolated, indicated by an increase in 16:1 Δ8 proportion. We also demonstrated the ability of these desaturase variants to influence the membrane composition and fatty acid distribution of E. coli strains deficient in the native acyl-ACP desaturase gene, fabA. Finally, we used the fabA deficient chassis to concomitantly express a non-native acyl-ACP desaturase and a medium-chain thioesterase from Umbellularia californica, demonstrating production of only saturated free fatty acids.

Microbial oils are a sustainable biomass-derived substitute for liquid fuels and vegetable oils. Oilcane, an engineered sugarcane with superior feedstock characteristics for biodiesel production, is a promising candidate for bioconversion. This study describes the processing of oilcane stems into juice and hydrothermally pretreated lignocellulosic hydrolysate and their valorization to ethanol and microbial oil using Saccharomyces cerevisiae and engineered Rhodosporidium toruloides strains, respectively. A bioethanol titer of 106 g/L was obtained from S. cerevisiae grown on oilcane juice in a 3 L fermenter, and a lipid titer of 8.8 g/L was obtained from R. toruloides grown on oilcane hydrolysate in a 75 L fermenter. Oil was extracted from the R. toruloides cells using supercritical CO2, and the observed fatty acid profile was consistent with previous studies on this strain. These results demonstrate the feasibility of pilot-scale lipid production from oilcane hydrolysate as part of an integrated bioconversion strategy.

Triacetic acid lactone (TAL) can be microbially produced and further chemically upgraded to several high-value chemicals. In this work, several acidic and basic ion-exchange resins and activated charcoal were evaluated for their ability to adsorb microbially produced TAL. Activated charcoal and a weak base resin, Dowex 66, showed similar TAL adsorption capacity of 0.18 ± 0.002 g/g. At 15% w/v activated charcoal, about 98% of TAL present in fermentation broth could be adsorbed. Further, ethanol washing allowed recovery of 72% of adsorbed TAL. A biorefinery producing TAL from sucrose was designed, simulated, and evaluated (through technoeconomic analysis) under uncertainty, for an estimated TAL minimum product selling price (MPSP) of $4.27/kg [$3.71−4.94/kg; 5th-95th percentiles] for the current state of technology and $2.83/kg [$2.46–3.29/kg] following potential near-term improvements to fermentation. Thus, this work provides an adsorptive process to recover microbially produced TAL that can be chemically upgraded to several industrial products.

This data set is related to the SoyFACE experiments, which are open-air agricultural climate change experiments that have been conducted since 2001. The fumigation experiments take place at the SoyFACE farm and facility in Champaign County, Illinois during the growing season of each year, typically between June and October. This V4 contains new experimental data files, hourly fumigation files, and weather/ambient files for 2022 and 2023, since the original dataset only included files for 2001-2021. The MATLAB code has also been updated for efficiency, and explanatory files have been updated accordingly. Below are new changes in V4: - The "SoyFACE Plot Information 2001 to 2021" file is renamed to “SoyFACE ring information 2001 to 2023.xlsx”. Data for 2022 and 2023 were added. File contains information about each year of the SoyFACE experiments, including the fumigation treatment type (CO2, O3, or a combination treatment), the crop species, the plots (also referred to as 'rings' and labeled with numbers between 2 and 31) used in each experiment, important experiment dates, and the target concentration levels or 'setpoints' for CO2 and O3 in each experiment. - The "SoyFACE 1-Minute Fumigation Data Files" were updated to contain sub-folders for each year of the experiments (2001-2023), each of which contains sub-folders for each ring used in that year's experiments. This data set also includes hourly data files for the fumigation experiments ("SoyFACE Hourly Fumigation Data Files" folder) created from the 1-minute files, and hourly ambient/weather data files for each year of the experiments ("Hourly Weather and Ambient Data Files" folder which has also been updated to include 2022 and 2023 data). The ambient CO2 and O3 data are collected at SoyFACE, and the weather data are collected from the SURFRAD and WARM weather stations located near the SoyFACE farm. - “Rings.xlsx” is new in this version. This file lists the rings and treatments used in each year of the SoyFACE experiments between 2001 and 2023 and is used in several of the MATLAB codes. - “CMI Weather Data Explanation.docx” is newly added. This file contains specific information about the processing of raw weather data, which is used in the hourly weather and ambient data files. - Files that were in RAR format in V3 are now updated and saved as ZIP format, including: Hourly Weather and Ambient Data Files.zip , SoyFACE 1-Minute Fumigation Data Files.zip , SoyFACE Hourly Fumigation Data Files.zip, and Matlab Files.zip. - The "Fumigation Target Percentages" file was updated to add data for 2022 and 2023. This file shows how much of the time the CO2 and O3 fumigation levels are within a 10 or 20 percent margin of the target levels when the fumigation system is turned on. - The "Matlab Files" folder contains custom code (Aspray, E.K.) that was used to clean the "SoyFACE 1-Minute Fumigation Data" files and to generate the "SoyFACE Hourly Fumigation Data" and "Fumigation Target Percentages" files. Code information can be found in the various "Explanation" files. The Matlab code changes are as follows: 1. “Data_Issues_Finder.m” code was changed to use the “Ring.xlsx” file to gather ring and treatment information based on the contents of the file rather than being hardcoded in the Matlab code itself. 2. “Data_Issues_Finder_all.m” code is new. This code is the same as the “Data_Issues_Finder.m” code except that it identifies all CO2 and O3 repeats. In contrast, the “Data_Issues_Finder.m” code only identifies CO2 and O3 repeats that occur when the fumigation system is turned on. 3. “Target_Yearly.m” code was changed to use the “Ring.xlsx” file to gather ring and treatment information based on the contents of the file rather than being hardcoded in the Matlab code itself. 4. “HourlyFumCode.m” code is new. This code uses the “Rings.xlsx” file to gather ring and treatment information based on the contents of the file instead of the user needing to define these values explicitly. This code also defines a list of all ring folders for the year selected and runs the hourly code for each ring, instead of the user having to run the hourly code for each ring individually. Finally, the code generates two dialog boxes for the user, one which allows user to specify whether they want the hourly code to be run for 1-minute fumigation files or 1-minute ambient files, and another which allows user to specify whether they would like the hourly fumigation averages to be replaced with hourly ambient averages when the fumigation system is turned off. 5. “HourlyDataFun.m” code was changed to run either “HourlyData.m” code or “HourlyDataAmb.m” code, depending on user input in the first dialog box. 6. “HourlyData.m” code was changed to replace hourly fumigation averages with hourly ambient averages when the fumigation system is turned off, depending on user input in the second dialog box. 7. “HourlyDataAmb.m” code is new. This code is similar to “HourlyData.m” code but is used to calculate hourly averages for 1-minute ambient files instead 1-minute fumigation files. 8. “batch.m” code was changed to account for new function input variables in “HourlyDataFun.m” code, along with adding header columns for “FumOutput.xlsx” and “AmbOutput.xlsx” output files generated by “HourlyData.m” and “HourlyDataAmb.m” code. - Finally, the " * Explanation" files contain information about the column names, units of measurement, steps needed to use Matlab code, and other pertinent information for each data file. Some of them have been updated to reflect the current change of data.

Microbial production of chemicals may suffer from inadequate cofactor provision, a challenge further exacerbated in yeasts due to compartmentalized cofactor metabolism. Here, we perform cofactor engineering through the decompartmentalization of mitochondrial metabolism to improve succinic acid (SA) production in Issatchenkia orientalis. We localize the reducing equivalents of mitochondrial NADH to the cytosol through cytosolic expression of its pyruvate dehydrogenase (PDH) complex and couple a reductive tricarboxylic acid pathway with a glyoxylate shunt, partially bypassing an NADH-dependent malate dehydrogenase to conserve NADH. Cytosolic SA production reaches a titer of 104 g/L and a yield of 0.85 g/g glucose, surpassing the yield of 0.66 g/g glucose constrained by cytosolic NADH availability. Additionally, expressing cytosolic PDH, we expand our I. orientalis platform to enhance acetyl-CoA-derived citramalic acid and triacetic acid lactone production by 1.22- and 4.35-fold, respectively. Our work establishes I. orientalis as a versatile platform to produce markedly reduced and acetyl-CoA-derived chemicals.

Data sets for material included in "A 13-year record indicates differences in the duration and depth of soil carbon accrual among potential bioenergy crops" by Kantola et al., 2025, in Global Change Biology Bioenergy. Data include soil organic carbon (SOC), carbon stable isotope ratios, annual belowground biomass, and annual post-harvest litter for four crops, maize/soybean, miscanthus, switchgrass, and prairie, between 2008 and 2021.

Microbial fermentation provides a sustainable method of producing valuable chemicals. Adding dynamic control to fermentations can significantly improve titers, but most systems rely on transcriptional controls of metabolic enzymes, leaving existing intracellular enzymes unregulated. This limits the ability of transcriptional controls to switch off metabolic pathways, especially when metabolic enzymes have long half-lives. We developed a two-layer transcriptional/post-translational control system for yeast fermentations. Specifically, the system uses blue light to transcriptionally activate the major pyruvate decarboxylase PDC1, required for cell growth and concomitant ethanol production. Switching to darkness transcriptionally inactivates PDC1 and instead activates the anti-Pdc1p nanobody, NbJRI, to act as a genetically encoded inhibitor of Pdc1p accumulated during the growth phase. This dual transcriptional/post-translational control improves the production of 2,3-BDO and citramalate by up to 100 and 92% compared to using transcriptional controls alone in dynamic two-phase fermentations. This study establishes the NbJRI nanobody as an effective genetically encoded inhibitor of Pdc1p that can enhance the production of pyruvate-derived chemicals.

Bioenergy with carbon capture and storage (BECCS) sits at the nexus of the climate and energy security. We evaluated trade-offs between scenarios that support climate stabilization (negative emissions and net climate benefit) or energy security (ethanol production). Our spatially explicit model indicates that the foregone climate benefit from abandoned cropland (opportunity cost) increased carbon emissions per unit of energy produced by 14–36%, making geologic carbon capture and storage necessary to achieve negative emissions from any given energy crop. The toll of opportunity costs on the climate benefit of BECCS from set-aside land was offset through the spatial allocation of crops based on their individual biophysical constraints. Dedicated energy crops consistently outperformed mixed grasslands. We estimate that BECCS allocation to land enrolled in the Conservation Reserve Program (CRP) could capture up to 9 Tg C year–1 from the atmosphere, deliver up to 16 Tg CE year–1 in emissions savings, and meet up to 10% of the US energy statutory targets, but contributions varied substantially as the priority shifted from climate stabilization to energy provision. Our results indicate a significant potential to integrate energy security targets into sustainable pathways to climate stabilization but underpin the trade-offs of divergent policy-driven agendas.

This dataset includes five files developed using the procedures described in the article 'Developing County-level Data of Nitrogen Fertilizer and Manure Inputs for Corn Production in the United States' and Supplemental Information published in the Journal of Cleaner Production in 2021. Citation: Xia, Yushu, Hoyoung Kwon, and Michelle Wander. "Developing county-level data of nitrogen fertilizer and manure inputs for corn production in the United States." Journal of Cleaner Production 309 (2021): e126957. Brief method: The fertilizer and manure inputs for corn were generated with a top-down approach by assigning county-level total N inputs reported by USGS to different crops using state- and county-level survey data. The corn N needs were estimated using empirical extension-based equations coupled with soil and environmental covariates. The estimates of fertilizer N inputs were further refined for corn grain and silage production at the county level and gap-filling (using state-level averages) was carried out to generate final files for U.S. county-level N inputs. The dataset is provided in an alternative format in Google Earth Engine: https://code.earthengine.google.com/13a0078e7ee727bc001e045ad0e8c6fc

The compiled datasets include plot level observations of energy crops (miscanthus and switchgrass) from recent experimental field trials in the US including dry biomass yield, location, state, region, harvest year, growing season degree days (GDD), winter season heating degree days (HDD), growing season cumulative precipitation, annual nitrogen application rate, age of the pant when harvested, National Commodity Crop Productivity Index (NCCPI) values, and cultivar type (switchgrass) from various published and unpublished sources. The stata codes include estimation procedures for four different specifications, i.e., Model A includes deterministic effect without interaction terms; Model B includes deterministic effect with interaction terms (N2, age2, N × age, GDD2, precip2, N × NCCPI); Model C includes deterministic effect with interaction terms, study, and location random effect; Model D includes deterministic effect with interaction terms, harvest year augmented study, and location random effect.

Aging-related yield decline in Miscanthus × giganteus (miscanthus) remains a major constraint to sustainable biomass production. This study evaluated how nitrogen (N) management and soil fertility influence yield-component traits and productivity in aging miscanthus. Trials were conducted at two sites established in 2008 at the University of Illinois Energy Farm, Urbana, IL. (i) The Sun Grant trial received 0, 60, and 120 kg N ha−1 annually until 2015. Starting 2021, half of each plot received 60 or 120 kg N ha−1, resulting in six legacy-contemporary treatments: 0N–0N, 0N–120N, 60N–0N, 60N–60N, 120N–0N, 120N–120N. (ii) The Energy Farm trial remained unfertilized until 2014, when one half of each plot received 56 kg N ha−1, forming two treatments: 0N–0N, 0N–56N. Sun Grant trial results showed N fertilization increased tiller density (tillers m−2) and tiller weight (g tiller−1) in juvenile to early-mature miscanthus (2011–2015). After N withdrawal, both traits declined (20 % and 40 %), though legacy effects persisted in tiller weight in the aging stands (2020–2023). Contemporary N had little effect on tiller density but increased tiller weight by 34 %–77 %, resulting in 23 %–106 % higher machine-harvested biomass yield in 0–120N, 60-60N, and 120-120N plots. At the Energy Farm trial, 0N–56N plots yielded 59 %–108 % more biomass than 0N–0N. Soil total N increased (Sun Grant: 47 % by 2020; Energy Farm: 58 % by 2023), while Mehlich-3 P (42 %–44 %) and K (21 %–46 %) declined. These findings identify tiller weight as a key determinant of biomass yield in aging miscanthus and highlight the need for P and K management for long-term productivity.

Dataset with numerical routines and laboratory testing data associated with the manuscript: Bondarenko, N., Podladchikov, Y., Williams‐Stroud, S., & Makhnenko, R. (2025). Stratigraphy‐induced localization of microseismicity during CO2 injection in Illinois Basin. Journal of Geophysical Research: Solid Earth, 130, e2024JB029526. https://doi.org/10.1029/2024JB029526