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.

GLBRC Sustainability Data Catalog

This Data Catalog is a collection of data from GLBRC's Sustainability research carried out in Michigan and Wisconsin. The Data Catalog summarizes each data table in order to allow the GLBRC community to better understand the data that have been collected and encourage collaboration.

GLBRC Sustainability Data Catalog
Transcriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulation
B.A. McKinley et al. "Transcriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulation" Frontiers in Plant Science 12 (2022) [DOI: 10.3389/fpls.2022.1062264]
Bioenergy sorghum hybrids are being developed with enhanced drought tolerance and high levels of stem sugars. Raffinose family oligosaccharides (RFOs) contribute to plant environmental stress tolerance, sugar storage, transport, and signaling. To better understand the role of RFOs in sorghum, genes involved in myo-inositol and RFO metabolism were identified and relative transcript abundance analyzed during development.
Sugar levels in Della flag leaves from floral initiation to post-grain maturity.
Cold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiod
I.R. Willick and D.B. Lowry "Cold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiod" Physiologia Plantarum 174 (2022) [DOI: 10.1111/ppl.13812]
We hypothesized that the more northern upland switchgrass (Panicum virgatum L.) ecotype develops a higher degree of freezing tolerance by initiating cold acclimation at higher temperatures as compared with the coastal and southern lowland ecotypes. First, we determined the optimal method for assessing freezing tolerance and the length of exposure to 8/4°C required to induce the maximum level of freezing tolerance in the most northern upland and most southern lowland genotypes. We characterized the maximum freezing tolerance of eight uplands, three coastal and five lowland genotypes grown for 21 days at 8/4°C and a 10 or 16 h photoperiod.
Map displaying the origins of the eight upland (open circle), three coastal (hashed circle), and five lowland (closed circle) switchgrass genotypes
A broad specificity β-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including γ-valerolactone
B.W. Hall et al. "A broad specificity β-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including γ-valerolactone" Journal of Biological Chemistry 1 (2023) [DOI: 10.1016/j.jbc.2022.102782]
One compound, γ-valerolactone (GVL), is used as a solvent to dissolve plant cell walls into sugars and aromatic molecules for subsequent microbial conversion to fuels and chemicals. Despite the promise of GVL as a renewable solvent for biomass deconstruction, residual GVL can be toxic to microbial fermentation. Here, we identified a Ca2+-dependent enzyme from Rhodopseudomonas palustris (Rpa3624) and showed that it can hydrolyze aliphatic and aromatic lactones and esters, including GVL.
Time-dependent conversion of GVL (white bars) to 4-HV (black bars) using a whole cell extract from Rhodopseudomonas palustris.
TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome
E.A. McDaniel et al. "TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome" ISME Communications 2 (2022) [DOI: 10.1038/s43705-022-00189-2]
A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms.
Biosynthetic potential compared to expression of amino acid and vitamin synthesis pathways for top 15 expressed MAGs.
Integrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespiration
X. Fu et al. "Integrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespiration" Nature plants 9 (2023) [DOI: 10.1038/s41477-022-01294-9]
Photorespiration recycles inhibitory intermediates arising from oxygenation reactions catalysed by Rubisco back into the C3 cycle, but it is unclear what proportions of its nitrogen-containing intermediates (glycine and serine) are exported into other metabolisms in vivo and how these pool sizes affect net CO2 gas exchange during photorespiratory transients. Here, to address this uncertainty, we measured rates of amino acid export from photorespiration using isotopically non-stationary metabolic flux analysis.
Active and inactive pools of glycine at varying O2 levels.
Global warming intensity of biofuel derived from switchgrass grown on marginal land in Michigan
S. Kim et al. "Global warming intensity of biofuel derived from switchgrass grown on marginal land in Michigan" GCB-Bioenergy 15 (2023) [DOI:10.1111/gcbb.13024]
Energy crops for biofuel production, especially switchgrass (Panicum virgatum), are of interest from a climate change perspective. Here, we use outputs from a crop growth model and life cycle assessment (LCA) to examine the global warming intensity and greenhouse gas (GHG) mitigation potential of biofuel systems based on a spatially explicit analysis of switchgrass grown on marginal land (abandoned former cropland) in Michigan, USA.
GHG mitigation for 288,000 ha of marginal land in Michigan for biofuel production
Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage
M. Mechan et al. "Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage" Phytobiomes (2023) [DOI:10.1094/PBIOMES-08-22-0046-FI]
Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. We explored the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We assessed the microbiome associated with the wax from sorghum plants over two growth stages, and the root mucilage additionally from nitrogen-fertilized and non-fertilized plants.
Overlap in bacterial diversity found in the sorghum epicuticular wax and aerial root mucilage based on culture-independent and culture-dependent approaches.
Capturing molecular interactions in graph neural networks: a case study in multi-component phase equilibrium
S. Qin et al. "Capturing molecular interactions in graph neural networks: a case study in multi-component phase equilibrium" Digital Discovery 2 (2023) [DOI:10.1039/D2DD00045H]
In this work, we propose a GNN architecture that captures molecular interactions in an explicit manner by combining atomic-level (local) graph convolution and molecular-level (global) message passing through a molecular interaction network. We tested the architecture (which we call SolvGNN) on a comprehensive phase equilibrium case study that aims to predict activity coefficients for a wide range of binary and ternary mixtures; we built this large dataset using the COnductor-like Screening MOdel for Real Solvation (COSMO-RS).
GNN architectures studied.
The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)
L. Zhang et al. "The genetic basis for panicle trait variation in switchgrass (Panicum virgatum)" Theoretical and Applied Genetics 135 (2022) [DOI:10.1007/s00122-022-04096-x]
We investigate the genetic basis of panicle architecture in switchgrass in two mapping populations across a latitudinal gradient, and find many stable, repeatable genetic effects and limited genetic interactions with the environment.
Representative panicles of switchgrass from the four grandparents.
Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum)
K. Tiedge et al. "Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum)" New Phytologist 236 (2022) [DOI:10.1111/nph.18443]
To investigate specialized metabolic drought responses in switchgrass, we integrated tissue-specific transcriptome and metabolite analyses of the genotypes Alamo and Cave-in-Rock that feature different drought tolerance. The more drought-susceptible Cave-in-Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo.
Photographs and volcano plots of switchgrass (Panicum virgatum)
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.
Phylogenetic tree