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The price gap between the market and breakeven prices of cellulosic biomass for farmers represents a significant barrier to the development of a low-carbon cellulosic bioeconomy. Using a bottom-up, agent-based modeling tool that replicates the behaviors and interactions of key stakeholders, this study analyzes the emergence of a cellulosic bioeconomy at the local scale through a wedge approach that examines an integrated portfolio of multiple policy options, including subsidies for small-scale bioproducts and environmental credits. The role of collaboration among multiple stakeholders, such as biomass producers (farmers), bio-refinery industry, government, and society, is assessed for filling the price gap. Using the Sangamon River Basin as a case study site, we evaluate the effectiveness of the wedge approach by comparing simulation results from multiple scenarios, each incorporating different combinations of bioeconomy wedges, with and without stakeholder collaboration. Results underscore that active collaboration among stakeholders acts as a catalyst enlarging the effectiveness of bioeconomy wedges. Including the carbon credits and environmental value in the policy portfolio is found to bridge the price gap through collective contributions from diverse stakeholders, where the cellulosic biofuel and bioproduct industry plays a pivotal role. Although this study is conducted at the local watershed scale, the methodology and findings offer valuable insights for market development in other watersheds and the potential scaling of local markets to regional and national levels.

Plants can influence soil microbes through resource acquisition and interference competition, with consequences for ecosystem function such as nitrification. However, how plants alter soil conditions to influence nitrifiers and nitrification rates remains poorly understood, especially in the subsoil. Here, coupling the 15N isotopic pool dilution technique, high throughput sequencing and in situ soil O2 monitoring, we investigated how a deep-rooted perennial grass, miscanthus, versus an adjacent shallow-rooted turfgrass reference shapes nitrifier assembly and function along 1 m soil profiles. In topsoil, the suppression of ammonia (NH3) oxidizing archaea (AOA) and gross nitrification rates in miscanthus relative to the reference likely resulted from nitrifiers being outcompeted by plant roots and heterotrophic bacteria for ammonium (NH4+). The stronger tripartite competition under miscanthus may have been caused in part by the lower soil organic matter (SOM) content, which supported lower gross nitrogen (N) mineralization, the major soil process that produces NH4+. In contrast, below 10 cm soil depth, significantly greater gross nitrification rates were observed in miscanthus compared to the reference. This was likely driven by the significantly lower oxygen (O2) in miscanthus than reference subsoil, which selected against aerobic heterotrophic bacteria but in favor of AOA. Overall, we found that plants can regulate AOA community structure and function through different mechanisms in topsoil and subsoil, with suppression of nitrification in topsoil and enhancement of nitrification in subsoil.

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.

Repository for Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP can use K-FIT [2] input files. Example K-FIT input files are located in the K-FIT repository at https://github.com/maranasgroup/K-FIT.

Seeds of Col-0 wild type, sig6 T-DNA mutants (CS877785, ABRC), PRL-1-OE, and sig6 T-DNA mutants transfected with PRL-1 (sig6::PRL-1) were planted in 1/2 MS media. Seedlings growth including chlorophyll development defects were investigated across the genotypes. Four-days-old-post-light exposure seedlings were harvested and performed RNAseq analysis with four biological replicates.

This dataset contains simulation results from PartMC-MOSAIC and WRF-PartMC that used in the journal article: Quantifying the Impact of Surfactants on Cloud Condensation Nuclei Activity Using a Particle-Resolved Model. Two compressed folder are uploaded here, one is for the data that used in this article, the other folder is the python scripts to process the data. For more details of the uploaded files, please check the README file.

Includes three different types of stacks, in two folders: "REC_RAW_STACKS.zip" contains: (1) Raw gray-scale reconstructed microCT x-ray scans, in the form of individual stacks per sample. "ML_STACKS.zip" contains: (2) Stacks that have been labeled using a machine-learning mask-RCNN pipeline identifying epidermis, mesophyll, airspace, vascular bundle, and background. (3) Stacks that have stomata locations labeled using a small point. The three types of stacks were used to calculate a variety of anatomical and physiological traits, using ImageJ Macros provided on Github: https://github.com/leakey-lab/microCT-Macros-Fischer. Young leaves from WT and transgenic Sorghum plants. CSV "microCT_REC2_META.csv" contains metadata, including sample/sub-sample labels.

This dataset contains the raw Florida bonneted bat echolocation calls recorded in southern Florida, USA from the years 2021 and 2022. This dataset also includes our artificial roost microclimate data (2021 only) and observations of bats recorded in our artificial roosts (2021 and 2022). Lastly, we include the R script required to analyze the Florida bonneted bat echolocation calls and the R script to produce the supplemental table and supplemental figure for our microclimate data.

An economic model was developed that incorporates spatially varying joint yield and price distributions for the multiple crop choices a farmer faces when choosing between conventional and bioenergy crops. The model is developed in Matlab, and has options for no, annual and upfront payment results.

This dateset contains data files necessary to replicate figures from "Idealized Particle-Resolved Large-Eddy Simulations to Evaluate the Impact of Emissions Spatial Heterogeneity on CCN Activity" submitted to Atmospheric Chemistry and Physics. Within the compressed folder data.zip are two subdirectories, "processed_data" and "spatial-het". The "processed_data" directory contains netCDF files which contain a subset of simulation output used in figure generation. The "spatial-het" subdirectory contains a .csv file with spatial heterogeneity values computed via an exact algorithm of the spatial heterogeneity metric described by Mohebalhojeh et al. 2025. The subdirectory "sh-patterns" contains .csv files for each emissions scenario. Each entry corresponds to a single grid cell over a domain of dimension 100x100 (lateral resolution of the computational domain employed in this paper). Within scripts.zip are python notebooks for generating figures. Additional python modules are included which contain helper functions for notebooks. Furthermore, a Fortran version of the spatial heterogeneity metric is included alongside shells scripts for creating a python environment in which the code can be compiled and convert into a Python module. Note that the create_env.sh and compile_nsh.sh scripts must be run prior to executing cells in notebooks to make use of the spatial heterogeneity subroutines. <b>*Note*:</b> New in this V3: During review, a bug regarding vertical diffusion of particles was discovered in WRF-PartMC which necessitated re-running simulations. We present new simulations with diffusion fixed. Furthermore, we have run additional simulations in response to reviewer comments--simulations with emissions turned off at t = 4 h to investigate reversible partitioning and simulations with the RH raised near saturation throughout the domain to model the effects of co-condensation. The README PDF has been updated to reflect changes to the dataset collection. Also, we have added a shell script in scripts_v3.zip which was used to process simulation output and create the data subsets contained in data_v3.zip. Lastly, notebooks were re-run with updated datasets to create manuscript figures and additional plotting routines were added for new figures pertaining to the requested simulations.

This repository contains source data for key plots presented in the manuscript "Plasmon-driven exciton formation in a non-equilibrium Fermi liquid." Experimental data that was analyzed in Igor Pro 8 are presented as the .pxp files used to generate individual sub-plots. Electronic spectral function calculations are provided as .txt files, in which consecutive rows refer to the meshgrid x coordinate, y coordinate, spectral function (and, where relevant, axis-projected local angular momentum). We additionally include the Wannier model and DFT-obtained bulk band structure on which the Wannier model was based. Files are named as the number of the figure in the manuscript to which they correspond, with additional details included where necessary. <b>Details of file names:</b> 2a_DOS_Lxz_Ek_KGM_40layer_xnum_800kpt_tot.txt: Density of states, xz-axis projected local orbital angular momentum, for 800 points along the K-Gamma-M path, for a 40-layer model. 2c_composite_y.pxp: ARPES (angle-resolved photoemission spectroscopy) spectra along the ky axis, including both a scan near the Fermi level and a scan at high kinetic energies. 2d_LCP_RCP_diff_Sect_20K.pxp: difference between ARPES constant energy cuts at T=20 K at E0 + 0.23 eV taken with left- and right-circularly polarized photons. The polarization-integrated intensity at the constant energy cut is also included. 2e_DOS_L45_E11pt79_m0pt25to0pt25_xnum_800kpt_tot.txt: Density of states, xz-projected local orbital angular momentum, and corresponding k-points in two dimensions from ab-initio electronic structure calculations for a constant-energy cut. 3a_[x]_[y]ps: ARPES cut under excitation at a fluence of x uJ/cm2, measured y ps after photoexcitation. Measurements were performed at 9 K. 3b_[x]: Energy distribution curves under excitation at a fluence x uJ/cm2 at selected delay times after photoexcitation. 4a_ImSigma_vs_temperature.pxp: Imaginary self energy (extracted from ARPES linewidths) at different energies above E0 for selected lattice temperatures. 4b_EELS_lowE.pxp: Electron energy loss spectrum over a low energy range 5b_diff_55m15.pxp: Difference between momentum-integrated Tr-ARPES traces at 55 uJ/cm2 and 15 uJ/cm2 photoexcitation. Time-dependent intensity at each energy level has been normalized to a maximum of 1 for each individual fluence prior to subtraction. 5d_invtau_at_EX_vs_fluence.pxp: decay rate at a specified energy EX for different excitation fluences, from single exponential fits. <b>NOTE: Analyses based on the Wannier model presented here should cite both the associated Article and this dataset. For all other files in the repository, citing the dataset alone is sufficient.</b>

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

Understanding how establishment practices influence the mechanisms underlying Miscanthus × giganteus (miscanthus) productivity and canopy development is critical for optimizing management. Data was collected during the juvenile (2011–2013) and mature (2024) phases of a long-term field experiment established in Urbana, Illinois, to evaluate the effects of propagation method (plug propagation [PP] and rhizome propagation [RP]), planting density (1.0, 0.75, and 0.25 plants m⁻²), and nitrogen application (0 and 67 kg N ha⁻¹) on end-of-season biomass yield, tiller mass, tiller density, and tiller height. Linear regression models identified the dominant predictors of yield across stand ages and management regimes. Planting density, nitrogen (N) application, and propagation method significantly influenced early yield and canopy development. During the juvenile phase, biomass yield was driven by tiller density due to canopy expansion; in the mature phase, yield became driven by tiller mass. The PP plots produced higher tiller density than the RP plots, resulting in faster canopy closure and higher juvenile-phase yields. Rhizome-propagated (RP) plots produced lower tiller density, but individual tillers were 3.3–6.4 g tiller−1 heavier than PP tillers. After the canopy reached equilibrium, the PP and RP yields were similar because greater RP tiller mass compensated for its lower tiller density. Higher planting density resulted in greater yield and tiller density during the second year (2012), but this effect was absent from the third year (2013) onward. In the juvenile phase, N fertilization enhanced yield by 1.6–3.4 Mg ha−1. Initiating fertilization in 2013 on unfertilized plots produced biomass similar to that in fertilized plots, suggesting yield recovery in the mature phase. These findings revealed that establishment strategies, including propagation method and planting density, influence juvenile miscanthus canopy development and productivity, transitioning from tiller-density- to mass-dominated yields, but not mature phase productivity.

Sweet sorghum has emerged as a promising source of bioenergy mainly due to its high biomass and high soluble sugar yield in stems. Studies have shown that loss-of-function Dry locus alleles have been selected during sweet sorghum domestication, and decapitation can further boost sugar accumulation in sweet sorghum, indicating that the potential for improving sugar yields is yet to be fully realized. To maximize sugar accumulation, it is essential to gain a better understanding of the mechanism underlying the massive accumulation of soluble sugars in sweet sorghum stems in addition to the Dry locus. We performed a transcriptomic analysis upon decapitation of near-isogenic lines for mutant (d, juicy stems, and green leaf midrib) and functional (D, dry stems and white leaf midrib) alleles at the Dry locus. Our analysis revealed that decapitation suppressed photosynthesis in leaves, but accelerated starch metabolic processes in stems. SbbHLH093 negatively correlates with sugar levels supported by genotypes (DD vs. dd), treatments (control vs. decapitation), and developmental stages post anthesis (3d vs.10d). D locus gene SbNAC074A and other programmed cell death-related genes were down regulated by decapitation, while sugar transporter-encoding gene SbSWEET1A was induced. Both SbSWEET1A and Invertase 5 were detected in phloem companion cells by RNA in situ assay. Loss of the SbbHLH093 homolog, AtbHLH093, in Arabidopsis led to a sugar accumulation increase. This study provides new insights into sugar accumulation enhancement in bioenergy crops, which can be potentially achieved by reducing reproductive sink strength and enhancing phloem unloading.

Microbial production of succinic acid (SA) at an industrially relevant scale has been hindered by high downstream processing costs arising from neutral pH fermentation for over three decades. Here, we metabolically engineer the acid-tolerant yeast Issatchenkia orientalis for SA production, attaining the highest titers in sugar-based media at low pH (pH 3) in fed-batch fermentations, i.e. 109.5 g/L in minimal medium and 104.6 g/L in sugarcane juice medium. We further perform batch fermentation using sugarcane juice medium in a pilot-scale fermenter (300×) and achieve 63.1 g/L of SA, which can be directly crystallized with a yield of 64.0%. Finally, we simulate an end-to-end low-pH SA production pipeline, and techno-economic analysis and life cycle assessment indicate our process is financially viable and can reduce greenhouse gas emissions by 34–90% relative to fossil-based production processes. We expect I. orientalis can serve as a general industrial platform for production of organic acids.

Height is a critical component of plant architecture, significantly affecting crop yield. The genetic basis of this trait in soybean remains unclear. In this study, we report the characterization of the Compact mutant of soybean, which has short internodes. The candidate gene was mapped to chromosome 17, and the interval containing the causative mutation was further delineated using biparental mapping. Whole-genome sequencing of the mutant revealed an 8.7 kb deletion in the promoter of the Glyma.17g145200 gene, which encodes a member of the class III gibberellin (GA) 2-oxidases. The mutation has a dominant effect, likely via increased expression of the GA 2-oxidase transcript observed in green tissue, as a result of the deletion in the promoter of Glyma.17g145200. We further demonstrate that levels of GA precursors are altered in the Compact mutant, supporting a role in GA metabolism, and that the mutant phenotype can be rescued with exogenous GA3. We also determined that overexpression of Glyma.17g145200 in Arabidopsis results in dwarfed plants. Thus, gain of promoter activity in the Compact mutant leads to a short internode phenotype in soybean through altered metabolism of gibberellin precursors. These results provide an example of how structural variation can control an important crop trait and a role for Glyma.17g145200 in soybean architecture, with potential implications for increasing crop yield.

This project aims to study the microbial structure and potential functions of bacterial and fungal microbiomes in leaves, stems, roots, rhizospheres, and bulk soils of energy crops (oilcane) grown in greenhouses.

Rising concerns for sustainability and global climate change have driven the development of sustainable production pathways for biofuels and chemicals from lignocellulosic biomass via integrated biological and chemical processes. We constructed an engineered Saccharomyces cerevisiae capable of producing 2,3-butanediol (2,3-BDO) from glucose without accumulating ethanol and glycerol, which hinder downstream processing of 2,3-BDO, through extensive metabolic reprogramming. Specifically, we introduced heterologous 2,3-BDO biosynthetic enzymes and deleted the major isozymes of ethanol and glycerol biosynthetic enzymes. In addition, we introduced an NAD+ regenerating Pyruvate-Malate (PM) cycle and enhanced the NAD+ regenerating capability of the PM cycle to resolve the redox imbalance from the deletion of ethanol and glycerol production pathways. The resulting engineered yeast produced 109.9 g/L of 2,3-BDO with a productivity of 1.0 g/L/h and a yield of 0.36 g/g glucose in a fed-batch fermentation. We also conducted techno-economic analysis (TEA) and life cycle assessment (LCA) of the production of methyl ethyl ketone (MEK) through catalytic dehydration of 2,3-BDO. A TEA based on the experimental results indicated that the minimum product selling price (MPSP) was estimated to be $1.90/kg. Regarding cradle-to-grave LCA, 100-year global warming potential (GWP100) and fossil energy consumption (FEC) were found to be 0.37 kg CO2 eq/kg and 3.1 MJ/kg, respectively. These results demonstrated the feasibility of cost-competitive and sustainable bio-based MEK production via yeast fermentation. In addition, we explored the possibility of using the fermentation broth containing 2,3-BDO as a biostimulant inducing drought tolerance in plants. As a result, the yeast 2,3-BDO fermentation broth can induce drought tolerance in Arabidopsis thaliana without a complicated purification process.

Saccharum yield decline results from long-term monoculture practices. Changes in cropping management can improve soil health and productivity. Below-ground bacterial community diversity and composition across soybean (Glycine max (L.) Merr) cover crop, Saccharum monoculture (30+ year) and fallowed soil were determined. Near full length (~1,400 base pairs) of 16S rRNA gene sequences were extracted from the rhizospheres of sugarcane and soybean and fallowed soil were compared. Higher soil bacterial diversity was observed in the soybean cover crop than sugarcane monoculture across all measured indices (observed operationational taxonomic units, Chao1, Shannon, reciprocal Simpson and Jackknife). Acidocateria, Proteobacteria, Bacteroidetes and Planctomycetes were the most abundant bacterial phyla across the treatments. Indicator species analysis identified nine indicator phyla. Planctomycetes, Armatimonadetes and candidate phylum FBP were associated with soybean; Proteobacteria and Firmicutes were linked with sugarcane and Gemmatimonadetes, Nitrospirae, Rokubacteria and unclassified bacteria were associated with fallowed soil. Non-metric multidimensional scaling analysis showed distinct groupings of bacterial operational taxonomic units (97% identity) according to management system (soybean, sugarcane or fallow) indicating compositional differences among treatments. This is confirmed by the results of the multi-response permutation procedures (A = 0.541, p = 0.00045716). No correlation between soil parameters and bacterial community structure was observed according to Mantel test (r = 211865, p = 0.14). Use of soybean cover-crop fostered bacterial diversity and altered community structure. This indicates cover crops could have a restorative effect and potentially promote sustainability in long-term Saccharum production systems.

Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus, and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids.

A new GAL4-based feed-forward loop circuit enhances β-glucuronidase (GUS) reporter gene expression in leaves and stems of stably transformed sugarcane plants.

This dataset contains biomass yield measurements and associated vegetation index data collected from commercial Miscanthus × giganteus fields in eastern Iowa during the 2022–2023 growing seasons. The data support the analyses presented in the article: “Yield From Iowa's First Commercial Miscanthus Fields: Implications of Spatial Variability for Productivity and Sustainability Beyond Research Plots.” We collected 105 ground-truth biomass samples from four mature commercial fields (>4 years old) covering 92.81 ha. Samples were taken from 3 m² quadrats that were hand-harvested in alignment with commercial harvest timing. Stem biomass (excluding leaves) was weighed, moisture-corrected, and converted to dry-matter yield expressed in Mg DM ha⁻¹. Sampling locations were selected to capture spatial variability visible in aerial imagery and were recorded using RTK GPS. Each biomass observation was paired with vegetation indices derived from high-resolution PlanetScope satellite imagery (3 m resolution). Images were acquired throughout the growing season, and indices were calculated to evaluate their ability to predict end-of-season biomass yield. Statistical and machine learning approaches were used to identify key predictors, and a linear regression model based on end-of-July Green Normalized Difference Vegetation Index (GNDVI) was developed and evaluated. This repository includes the data used in that modeling workflow. Management practices, economic data, full imagery time series, and additional methodological details are described in the associated publication and are not included here. The dataset consists of three comma-separated value (CSV) files: 1. Combine_Groundtruth_Yield_VI_22_23.csv This file contains ground-truth biomass yield measurements and associated key vegetation index values collected during the 2022 and 2023 growing seasons. Rows: 105 observations Columns: Year — Year of observation (2022 or 2023) Field — Field location identifier Sample_number — Unique sample identifier GNDVI_End_Jul — Green Normalized Difference Vegetation Index calculated at end of July GNDVI_End_Aug — Green Normalized Difference Vegetation Index calculated at end of August NDRE_End_Aug — Normalized Difference Red Edge index calculated at end of August Biomass_Stem_Yield_MgDM/ha — Measured stem biomass yield (megagrams dry matter per hectare) 2. trainData_GNDVI.csv This file contains the subset of observations used to train the predictive relationship between July GNDVI and biomass yield. Rows: 76 observations Columns: Unnamed: 0 — Row index retained from the original data processing workflow GNDVI_End_Jul — GNDVI at end of July Stem_Yield_MgDM/ha — Observed stem biomass yield (Mg DM ha⁻¹) 3. testData_GNDVI.csv This file contains the test dataset used to evaluate model performance. Rows: 29 observations Columns: Unnamed: 0 — Row index retained from the original data processing workflow GNDVI_End_Jul — GNDVI at end of July Predicted_Yield_MgDM/ha — Model-predicted stem biomass yield (Mg DM ha⁻¹) Observed_Yield_MgDM/ha — Measured stem biomass yield (Mg DM ha⁻¹)

The dataset contains a jupyter notebook intended for anyone who wants to apply the Empirical Bayes method described in the paper titled 'Data for Improving individual committor estimates and data efficiency in reaction coordinate tests with the Empirical Bayes method' to committor data with a simple and lucid python script.

Data related to a publication, "Emulating 2D Materials with magnons" to be published, but also as a preprint on arXiv https://arxiv.org/abs/2601.03210. It contains scripts for the simulation program Mumax3, and python scripts for conversion and analysis.

Growth-coupling product formation can facilitate strain stability by aligning industrial objectives with biological fitness. Organic acids make up many building block chemicals that can be produced from sugars obtainable from renewable biomass. Issatchenkia orientalis is a yeast strain tolerant to acidic conditions and is thus a promising host for industrial production of organic acids. Here, we use constraint-based methods to assess the potential of computationally designing growth-coupled production strains for I. orientalis that produce 22 different organic acids under aerobic or microaerobic conditions. We explore native and engineered pathways using glucose or xylose as the carbon substrates as proxy constituents of hydrolyzed biomass. We identified growth-coupled production strategies for 37 of the substrate-product pairs, with 15 pairs achieving production for any growth rate. We systematically assess the strain design solutions and categorize the underlying principles involved.