GLBRC Data Sets
Highlighted below are a variety of published studies that include data sets that might be of interest to the scientific community and have been deposited in online data repositories. Only data sets published in GLBRC-approved repositories following the FAIR Guiding Principles are highlighted. More information can be found on our guidelines page.
Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms
C. S. Wadler et al. "Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms" Biotechnology for Biofuels and Bioproducts 15 (2022) [DOI:10.1186/s13068-022-02168-0]
In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts.
Metagenomes from 25 low-abundance microbes in a partial nitritation anammox microbiome
N. K. Beach et al. "Metagenomes from 25 low-abundance microbes in a partial nitritation anammox microbiome" Applied and Industrial Microbiology 11 (2022) [DOI:10.1128/mra.00212-22]
Microbial communities using anammox bacteria to remove nitrogen are increasingly important in wastewater treatment. We report on 25 metagenome-assembled genomes of low-abundance microbes from a partial nitritation anammox bioreactor system that have not been described previously. These data add to the body of information about this important wastewater treatment system.
Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars
T. C. Ulbrich et al. “Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars” Phytobiomes 5 (2021) [DOI: 10.1094/PBIOMES-12-19-0069-FI]
We used a common garden experiment to investigate variation in 12 mature switchgrass cultivar soil microbiomes and, furthermore, to examine how root traits and soil conditions influence microbiome structure. We found that average root diameter varied up to 33% among cultivars and that the cultivars also associated with distinct soil microbiomes.
An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function
J. L. Steenwyk et al. "An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function" Science Advances 8 (2022) [DOI: 10.1126/sciadv.abn0105]
Examination of the phenotypic impact of network perturbation using deletion mutant data from the baker’s yeast Saccharomyces cerevisiae, which were obtained from previously published studies, suggests that fitness in diverse environments is affected by orthologous gene neighborhood and connectivity.
Soil origin and plant genotype modulate switchgrass aboveground productivity and root microbiome assembly
P. Beschoren de Costa et al. "Soil origin and plant genotype modulate switchgrass aboveground productivity and root microbiome assembly" mBio 13 (2022) [DOI:10.1128/mbio.00079-22]
This study aims to fill important knowledge gaps and to serve as a foundation for switchgrass biomass promotion through microbe selection with an ultimate goal of facilitating sustainable bioenergy crop production.
Transcriptional competition shapes proteotoxic ER stress resolution
D. Kwan Ko and F. Brandizzi "Transcriptional competition shapes proteotoxic ER stress resolution" Nature Plants 8 (2022) [DOI: 10.1038/s41477-022-01150-w]
Here, we identified the abscisic acid-related regulator G-class bZIP TF2 (GBF2) and the cis-regulatory element G-box as regulatory components of the plant UPR led by the mTFs, bZIP28 and bZIP60.
Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans
A. M. Linz et al. "iNovo479: Metabolic Modeling Provides a Roadmap to Optimize Bioproduct Yield from Deconstructed Lignin Aromatics by Novosphingobium aromaticivorans" Metabolites 12 (2022) [DOI: 10.3390/metabo12040366]
In this work, we built a genome-scale metabolic model of N. aromaticivorans, iNovo479, to guide the engineering of strains for aromatic conversion into products. iNovo479 predicted product yields from single or multiple aromatics, and the impact of combinations of aromatic and non-aromatic substrates on product yields.
Land-based climate solutions for the United States
G.P. Robertson et al. "Land-based climate solutions for the United States" Global Change Biology 28 (2022) [DOI: 10.1111/gcb.16267]
We detail a simplified scenario for the United States that illustrates the benefits of combining approaches. We assign a portion of non-forested former cropland to bioenergy sufficient to meet projected mid-century transportation needs, with the remainder assigned to nature-based solutions such as reforestation.
Identification and characterization of a set of monocot BAHD monolignol transferases
R.A. Smith et al. "Identification and characterization of a set of monocot BAHD monolignol transferases" Plant Physiology (2022) [DOI: 10.1093/plphys/kiac035]
We identified putative FMT and PMT enzymes in sorghum (Sorghum bicolor) and switchgrass (Panicum virgatum) and have compared their activities to those of known monolignol transferases. The putative FMT enzymes produced both monolignol ferulate and monolignol p-coumarate conjugates, whereas the putative PMT enzymes produced monolignol p-coumarate conjugates.
Rapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM)
E.A. Trujillo et al. "Rapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM)" Analytical Chemistry 94 (2022) [DOI: 10.1021/acs.analchem.1c03243]
To achieve rapid and high-throughput targeted methods, here we show that nLC separations can be eliminated and replaced with direct infusion shotgun proteome analysis (DISPA) using high-field asymmetric waveform ion mobility spectrometry (FAIMS) with PRM.
Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway
F.V. Gambacorta et al. "Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway" Synthetic and Systems Biotechnology 7 (2022) [DOI: 10.1016/j.synbio.2022.02.007]
Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains. We equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway.
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds
S. Ohnuki et al. "High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds" npj Systems Biology and Applications 8 (2022) [DOI: 10.1038/s41540-022-00212-1]
In this study, we developed a reliable high-throughput (HT) platform for yeast morphological profiling using drug-hypersensitive strains to minimize compound use, HT microscopy to speed up data generation and analysis, and a generalized linear model to predict targets with high reliability.
Environmental outcomes of the US Renewable Fuel Standard
Lark et al. "Environmental outcomes of the US Renewable Fuel Standard" PNAS 119 (2022) [DOI: 10.1073/pnas.2101084119]
Biofuels are included in many proposed strategies to reduce anthropogenic greenhouse gas emissions and limit the magnitude of global warming. The US Renewable Fuel Standard is the world’s largest existing biofuel program, yet despite its prominence, there has been limited empirical assessment of the program’s environmental outcomes.
Soils of the GLBRC Marginal Land Expeirment (MLE) Sites
C.S. Kasmerchak and R. Schaetzl "Soils of the GLBRC Marginal Land Experiment (MLE) Sites" KBS LTER Special Publication (2018) [DOI: 10.5281/zenodo.2578238]
The Great Lakes Bioenergy Research Center (GLBRC) Marginal Land Experiment (MLE) was established in 2013 at various sites in Wisconsin and Michigan to evaluate the potential use of low productivity or abandoned agricultural fields for low input bioenergy feedstocks.
Boosting climate change mitigation potential of perennial lignocellulosic crops grown on marginal lands
R.A. Martinez-Feria and B. Basso "Boosting climate change mitigation potential of perennial lignocellulosic crops grown on marginal lands" Environmental Research Letters 17 (2022) [DOI: 10.1088/1748-9326/ac541b]
Here, we show the potential GHG mitigation of fertilizing switchgrass (Panicum virgatum) at the NF rate that minimizes net GHG emissions across 7.1 million ha of marginal lands in the Midwest US, with long-term production advantages surpassing emitted GHG by 0.66 Mg CO2e ha−1 yr−1 on the aggregate.
Modeling temporal and hormonal regulation of plant transcriptional response to wounding
Moore et al. "Modeling temporal and hormonal regulation of plant transcriptional response to wounding" The Plant Cell (2021) [DOI:10.1093/plcell/koab287]
Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation.
Exploring the meta-regulon of the CRP/FNR family of global transcriptional regulators in a partial-nitritation anammox microbiome
N.K. Beach et al. "Exploring the meta-regulon of the CRP/FNR family of global transcriptional regulators in a partial-nitritation anammox microbiome" mSystems 6 (2021) [DOI:10.1128/mSystems.00906-21]
Optimizing cyclic aeration helps reduce energy needs and maximize microbiome performance during wastewater treatment; however, little is known about how most microbial community members respond to these alternating conditions. We defined the meta-regulon of a PNA microbiome by combining existing knowledge of how the CRP/FNR family of bacterial TFs respond to stimuli, with metatranscriptomic analyses to characterize gene expression changes during aeration cycles.
Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland
A. Lamb et al. "Bioenergy sorghum’s deep roots: A key to sustainable biomass production on annual cropland" GCB-Bioenergy 14 (2021) [DOI:10.1111/gcbb.12907]
In this study, field grown bioenergy sorghum root systems were analyzed during the growing season to characterize their depth, biomass, morphology, anatomy, and gene expression profiles. Bioenergy sorghum roots grew continuously during a 155-day growing season producing ~175 nodal roots, accumulating ~7 Mg of dry biomass per hectare, and reaching >2 m deep in the soil profile.
Investigating the chemolithoautotrophic and formate metabolism of Nitrospira moscoviensis by constraint-based metabolic modeling and 13C-tracer analysis
C.E. Lawson et al. "Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13C-Tracer Analysis" mSystems 6 (2021) [DOI:10.1128/mSystems.00173-21]
We provide the first constraint-based metabolic model of Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II and subsequently validate this model using proteomics and 13C-tracers combined with intracellular metabolomic analysis. The resulting genome-scale model will serve as a knowledge base of Nitrospira metabolism and lays the foundation for quantitative systems biology studies of these globally important nitrite-oxidizing bacteria.
Regulation of dhurrin pathway gene expression during Sorghum bicolor development
R.M. Gleadow et al. "Regulation of dhurrin pathway gene expression during Sorghum bicolor development" Planta 254 (2021) [DOI:10.1007/s00425-021-03774-2]
In this study, RNA-seq was used to investigate the expression of genes involved in the biosynthesis, bio-activation and recycling of dhurrin in Sorghum bicolor. Genes involved in dhurrin biosynthesis were highly expressed in all young developing vegetative tissues (leaves, leaf sheath, roots, stems), tiller buds and imbibing seeds and showed gene specific peaks of expression in leaves during diel cycles.