GLBRC Data Sets

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.

Nitrous oxide (N2O) is a serious concern due to its role in global warming and ozone destruction. Agricultural practices account for ∼80% of all anthropogenic N2O produced in the US, due in large part to the stimulation of microbial denitrification.

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z.

Thermodynamically constrained reactions and pathways are hypothesized to impose greater protein demands on cells, requiring higher enzyme amounts to sustain a given flux compared to those with stronger thermodynamics.

Switchgrass (Panicum virgatum L.) is a native North American grass currently considered a high-potential bioenergy feedstock crop. However, previous reports questioned its effectiveness in generating soil organic carbon (SOC) gains, with resultant uncertainty regarding the monoculture switchgrass's impact on the environmental sustainability of bioenergy agriculture.

Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection.

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain.

Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates ~ 80% of its harvested biomass in ~ 4 m long stems comprised of > 40 internodes that develop sequentially during an extended vegetative growth phase.

In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes.

The SARO_RS14285 gene, encoding a transcription factor, was deleted in Novosphingobium aromaticivorans DSM12444. The transcriptomes of the parent and ΔSARO_RS14285 strains were determined when grown in medium containing glucose with or without protocatechuic, vanillic, syringic, or 4-coumaric acid. We present the raw RNA sequencing data obtained from these cultures.

Genome-wide binding sites of 44 putative transcription factors (TFs) from Novosphingobium aromaticivorans DSM12444 were analyzed using DNA affinity purification sequencing. We report that 32 of these TFs have at least one area of enrichment. These data will help better understand aromatic metabolism and other features of N. aromaticivorans biology.

Many remarkable phenotypes have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times, many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits.

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits.

Soil diazotrophs convert atmospheric nitrogen into plant-available ammonium through free-living nitrogen fixation (FLNF). This sustainable nitrogen source can reduce our dependence on synthetic fertilizer inputs in conventional agricultural systems.

Climate change will increase soil drying, altering microbial communities via increasing water stress and decreasing resource availability. The responses of these microbial communities to changing environments could be governed by physiological tradeoffs between high yield, resource acquisition, and stress tolerance (YAS framework).

The land that is potentially available to produce dedicated cellulosic bioenergy crops, often referred to as ‘marginal’ land, depends heavily on the underlying assumptions used to classify and identify it.

A randomly barcoded transposon insertion sequencing (RB-TnSeq) library of Novosphingobium aromaticivorans DSM12444 was grown in media containing either glucose or the beta-5-linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) as the sole carbon source. The cultures were grown to saturation and then sequenced, yielding the barcode abundance data sets presented here.

Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery.

The conversion of lignin can produce biomass-derived aromatic compounds such as 2-pyrone-4,6-dicarboxylic acid (PDC), which is a potential sustainable precursor of bioplastics. PDC is a pseudoaromatic dicarboxylic acid that can aggregate in aqueous solution.

Changes in soil organic carbon (SOC) and nitrogen (SON) are strongly affected by land management but few long-term comparative studies have surveyed changes throughout the whole soil profile. We quantified 25-year SOC and SON changes to 1 m in 10 replicate ecosystems at an Upper Midwest, USA site.