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.

Metagenome-assembled genomes from a microbiome grown in dairy manure hydrolysate

A.T. Ingle et al. "Metagenome-assembled genomes from a microbiome grown in dairy manure hydrolysate" Microbiology Resource Announcement 11 (2022) [DOI: 10.1128/mra.00292-22]

Anaerobic microbiomes can be used to recover the chemical energy in agroindustrial and municipal wastes as useful products. Here, we report a total of 109 draft metagenome-assembled genomes from a bioreactor-fed carbohydrate-rich dairy manure hydrolysate.

Phylogeny of dRep-identified representative MAGs

Metagenomes and metagenome-assembled genomes from microbiomes metabolizing thin stillage from an ethanol biorefinery

N.W. Fortney et al. "Metagenomes and metagenome-assembled genomes from microbiomes metabolizing thin stillage from an ethanol biorefinery" Microbiology Resource Announcements 11 (2022) [DOI:10.1128/mra.00290-22]

Here, we report the metagenomes from five anaerobic bioreactors, operated under different conditions, that were fed carbohydrate-rich thin stillage from a corn starch ethanol plant. The putative functions of the abundant taxa identified here will inform future studies of microbial communities involved in valorizing this and other low-value agroindustrial residues.

Phylogeny of representative MAGs and their presence in the five different bioreactors

Functional divergence in a multi-gene family is a key evolutionary innovation for anaerobic growth in Saccharomyces cerevisiae

D. Krause and C. Hittinger "Functional divergence in a multi-gene family is a key evolutionary innovation for anaerobic growth in Saccharomyces cerevisiae" Molecular Biology and Revolution 39 (2022) [DOI:10.1093/molbev/msac202]

When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression of seven serine/threonine-rich anaerobically-induced cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here, we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event.

Maximum likelihood phylogeny of the anCWMP genes and AFB1 genes from the budding yeast

Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions

E. Vanacloig-Pedros et al. "Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions" FEMS Yeast Research 21 (2021) [DOI: 10.1093/femsyr/foac036]

To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates.

Classification of inhibitors based on similarities in gene-fitness profiles

Host genotype controls ecological change in the leaf fungal microbiome

A. VanWallendael et al. "Host genotype controls ecological change in the leaf fungal microbiome" PLOS Biology (2022) [DOI:10.1371/journal.pbio.3001681]

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum).

Structural and successional change in the leaf phyllosphere community shown by 2 methods.

Transcriptomic data sets for Zymomonas mobilis 2032 during fermentation of Ammonia Fiber Expansion (AFEX)-Pretreated corn stover and switchgrass hydrolysates

Y. Zhang et al. "Transcriptomic data sets for Zymomonas mobilis 2032 during fermentation of Ammonia Fiber Expansion (AFEX)-Pretreated corn stover and switchgrass hydrolysates" Bacteriology (2022) [DOI:10.1128/mra.00564-22]

The transcriptomes of Zymomonas mobilis 2032 were captured during the fermentation of ammonia fiber expansion (AFEX)-pretreated corn stover and switchgrass hydrolysates containing different concentrations of glucose and xylose. RNA samples were collected when Z. mobilis was fermenting glucose or xylose.

Summary of genes with significant DE by RNA-Seq under different growth conditions.

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]

Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol, a next-generation biofuel, in Saccharomyces cerevisiae. Here, we explore how two of these strategies, pathway re-localization and redox cofactor-balancing, affect the performance and physiology of isobutanol producing strains.

Proteomics response of sulfur-related pathways in the engineered strains

Metagenomes and metagenome-assembled genomes from microbial communities fermenting ultrafiltered milk permeate

K. A. Walters et al. "Metagenomes and metagenome-assembled genomes from microbial communities fermenting ultrafiltered milk permeate" Applied and Industrial Microbiology (2022) [DOI: 10.1128/mra.00293-22]

Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs).

Phylogenic tree of dRep representative bacterial MAGs

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" Applied and Industrial Microbiology 6 (2022) [DOI: 10.1128/mSystems.00906-21]

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.

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.

Composition of lignocellulosic conversion residue

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.

Extensive coevolution in DNA replication genes.

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.

Community structure shown by principal coordinate analysis (PCoA) and distance to centroid distributions.

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.

Ratio of aromatic:glucose and impact on PDC production.

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.

Annual mitigation potentials through 2100.

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.

Results of feruloyl-CoA monolignol transferase (FMT) and p-coumaroyl-CoA monolignol transferase (PMT) competition enzyme assays.

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.

The application of DISPA-PRM for rapid targeted quantification of bacterial enzymes

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.

Transcriptomics overview of the engineered isobutanol strains.