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.

Seasonal activities of the phyllosphere microbiome of perennial crops

A. Howe et al. "Seasonal activities of the phyllosphere microbiome of perennial crops" Nature Communications 14:1039 (2023) [DOI:10.1038/s41467-023-36515-y]

Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass.

Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory

A.E. Bryson et al. "Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory" Nature Communications 14:343 (2023) [DOI:10.1038/s41467-023-35845-1]

The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus.

Predicted Lamiaceae minimal ancestral BGC and species-specific expansion of each

Lignin deconstruction by anaerobic fungi

T.S. Lankiewicz et al. "Lignin deconstruction by anaerobic fungi" Nature Microbiology 8:596-610 (2023) [DOI:10.1038/s41564-023-01336-8]

Lignocellulose forms plant cell walls, and its three constituent polymers, cellulose, hemicellulose and lignin, represent the largest renewable organic carbon pool in the terrestrial biosphere.

Differential regulation of KEGG-categorized N. californiae genes in response to lignocellulose availability reveals fungal transcriptome dynamics associated with carbohydrate metabolismChoudhary

Plant terpenoid permeability through biological membranes explored via molecular simulations

S. Raza et al. "Plant terpenoid permeability through biological membranes explored via molecular simulations" The Journal of Physical Chemistry B 127:1144-1157 (2023) [DOI:10.1021/acs.jpcb.2c07209]

Plants synthesize small molecule diterpenes composed of 20 carbons from precursor isopentenyl diphosphate and dimethylallyl disphosphate, manufacturing diverse compounds used for defense, signaling, and other functions. Industrially, diterpenes are used as natural aromas and flavoring, as pharmaceuticals, and as natural insecticides or repellents.

Schematic of three representative diterpenes moving across the cell membrane

Downregulation of barley ferulate 5-hydroxylase dramatically alters straw lignin structure without impact on mechanical properties

R. Shafiei et al. "Downregulation of barley ferulate 5-hydroxylase dramatically alters straw lignin structure without impact on mechanical properties" Frontiers in Plant Science 13:1125003 [DOI:10.3389/fpls.2022.1125003]

Barley is a major cereal crop for temperate climates, and a diploid genetic model for polyploid wheat. Cereal straw biomass is an attractive source of feedstock for green technologies but lignin, a key determinant of feedstock recalcitrance, complicates bio-conversion processes. However, manipulating lignin content to improve the conversion process could negatively affect agronomic traits.

Phenotypic characterization of the HvF5H1-RNAi lines and controls from the T2 generation; (A) plant stature and (B) spikes at harvest time (C) mechanical strength of the second and fourth internodes sampled from main tillers of the ripe senesced straw

Pest suppression potential varies across 10 bioenergy cropping systems

N.L. Haan and D.A. Landis "Pest suppression potential varies across 10 bioenergy cropping systems" Global Change Biology - Bioenergy 15:765-775 (2023) [DOI: 10.1111/gcbb.13053]

Top-down suppression of herbivores is a fundamental ecological process and a critical service in agricultural landscapes. Adoption of bioenergy cropping systems is likely to become an increasingly important driver causing loss or gain of this service in coming decades.

Examples of marks left by (a) chewing arthropods, (b) arthropod proboscis or ovipositor, (c) bird beak, and (d) rodent teeth.

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).

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