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.
The sorghum (Sorghum bicolor) brown midrib 30 gene encodes a chalcone isomerase required for cell wall lignification
In sorghum (Sorghum bicolor) and other C4 grasses, brown midrib (bmr) mutants have long been associated with plants impaired in their ability to synthesize lignin. The brown midrib 30 (Bmr30) gene, identified using a bulk segregant analysis and next-generation sequencing, was determined to encode a chalcone isomerase (CHI).
A new open-path eddy covariance method for nitrous oxide and other trace gases that minimizes temperature corrections
We demonstrate a new laser-based, open-path N2O sensor and a general approach applicable to other gases that minimizes temperature-related corrections for EC flux measurements. The method identifies absorption lines with spectroscopic effects in the opposite direction of density effects from temperature and, thus, density and spectroscopic effects nearly cancel one another.
Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates
We used environmental sampling and isolation to assemble a dataset of 1962 isolates collected from throughout the contiguous United States of America (USA) and Alaska, which were then used to uncover geographic patterns, along with substrate and temperature associations among yeast taxa.
Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce monoaromatic diketones
In this work, we report a newly discovered activity of previously characterized dehydrogenase enzymes with a chemically modified by-product of lignin depolymerization. We propose that the activity of N. aromaticivorans enzymes with both native lignin aromatics and those produced by chemical depolymerization will expand opportunities for producing industrial chemicals from the heterogenous components of this abundant plant polymer.
Mapping annual irrigation from Landsat imagery and environmental variables across the conterminous United States
In this study, we present an approach to map the extent of irrigated croplands across the conterminous U.S. (CONUS) for each year in the period of 1997–2017. To scale nationwide, we developed novel methods to generate training datasets covering both the western and eastern U.S.
Landsat-based Irrigation Dataset (LANID): 30 m resolution maps of irrigation distribution, frequency, and change for the US, 1997–2017
Here we present the new Landsat-based Irrigation Dataset (LANID), which is comprised of 30 m resolution annual irrigation maps covering the conterminous US (CONUS) for the period of 1997–2017. The main dataset identifies the annual extent of irrigated croplands, pastureland, and hay for each year in the study period. Derivative maps include layers on maximum irrigated extent, irrigation frequency and trends, and identification of formerly irrigated areas and intermittently irrigated lands.
Metabolic remodeling during nitrogen fixation in Zymomonas mobilis
In Z. mobilis, the factors that control glycolytic rates, ethanol production, and isoprenoid production are still not fully understood. In this study, we performed metabolomic, proteomic, and thermodynamic analysis of Z. mobilis during N2 fixation. This analysis identified key changes in metabolite levels, enzyme abundance, and glycolytic thermodynamic favorability that occurred during changes in NH4+ availability, helping to inform future efforts in metabolic engineering.
Mixed acid fermentation of carbohydrate-rich dairy manure hydrolysate
The aim of this study was to investigate if carbon derived from DM fibers can be recovered as medium-chain fatty acids (MCFAs), which are mixed culture fermentation products of economic interest. DM fibers were subjected to combinations of physical, enzymatic, chemical, and thermochemical pretreatments to evaluate the possibility of producing carbohydrate-rich hydrolysates suitable for microbial fermentation by mixed cultures.
Diverse profile of fermentation byproducts from thin stillage
Here, we explored the formation of different fermentation products by microbial communities grown on TS using different bioreactor conditions. At the baseline operational condition (6-day retention time, pH 5.5, 35°C), we observed a mixture of MCFAs as the principal fermentation products.
A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis
A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of 10 new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and MS.
Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum)
To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression.
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation.
A facile spectroscopic method for measuring lignin content in lignocellulosic biomass
A facile spectroscopic method, our CASA (Cysteine–Assisted Sulfuric Acid) method, was developed to quantify the lignin content of lignocellulosic biomass, based on an extraordinary system in which biomass samples are fully dissolved in H2SO4.
Crabtree/Warburg-like aerobic xylose fermentation by engineered Saccharomyces cerevisiae
Here, we evolved respiration-deficient S. cerevisiae strains that can grow on and ferment xylose to ethanol aerobically, a trait analogous to the Crabtree/Warburg Effect for glucose.
Nitrification is a minor source of nitrous oxide in an agricultural landscape and declines with increasing management intensity
Using Bayesian inference to couple 25 years of in situ N2O flux measurements with site-specific Michaelis–Menten kinetics of nitrification-derived N2O, we test the relative importance of nitrification-derived N2O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest.
Modeled surface-atmosphere fluxes from paired sites in the Upper Great Lakes Region using neural networks
Here we use a long-term record of carbon cycling from six paired sites plus a seventh reference site that are all spatially close to each other, with an average of ∼11 km separation. The goal is to use field observations from one of the paired sites, along with observations from the second site that can be measured easily, in order to estimate carbon cycling at the second site using artificial intelligence methods.
Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics
Here, we performed time series genome-resolved metatranscriptomics to explore gene expression patterns of coexisting Accumulibacter clades in the same bioreactor ecosystem. Our work provides an approach for elucidating ecologically relevant functions based on gene expression patterns between closely related microbial populations.
Hanseniaspora smithiae sp. nov., a novel apiculate yeast species from Patagonian forests that lacks the typical genomic domestication signatures for fermentative environments
During a survey of Nothofagus trees and their parasitic fungi in Andean Patagonia (Argentina), genetically distinct strains of Hanseniaspora were obtained from the sugar-containing stromata of parasitic Cyttaria spp.
Contributions of environmental and maternal transmission to the assembly of leaf fungal endophyte communities
We used amplicon sequencing to track switchgrass (Panicum virgatum) LFEs in a greenhouse and field experiment as communities assembled from seed endophytes and rain fungi (integration of wet and dry aerial dispersal) in germinating seeds, seedlings, and adult plants.
