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Madison, WI, United States

Clowers K.J.,University of Wisconsin - Madison | Will J.L.,University of Wisconsin - Madison | Will J.L.,University of Georgia | Gasch A.P.,University of Wisconsin - Madison | Gasch A.P.,1552 University Ave
Molecular Ecology | Year: 2015

Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of S. cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak × vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases, the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche. © 2015 John Wiley & Sons Ltd.

Sanford G.R.,University of Wisconsin - Madison | Sanford G.R.,1552 University Ave | Kucharik C.J.,University of Wisconsin - Madison | Kucharik C.J.,1552 University Ave | Kucharik C.J.,1710 University Ave
Soil Biology and Biochemistry | Year: 2013

Many techniques such as the acid hydrolysis - incubation (AHI) method have been developed with the aim of elucidating the inherent complexity of soil organic carbon (SOC). While the utility of the AHI method has been demonstrated, there is no standardized protocol developed for conducting the long-term incubation component of the method. In the current study we evaluated the effects of chamber venting and mechanical headspace mixing on soil CO2 flux rates and the resultant size and mean residence time of three operationally defined pools of SOC obtained via the AHI method. Continuous chamber venting resulted in an estimate of the readily mineralized carbon pool that was 2.3 times larger and turned over 2.9 times slower than the same pool estimated using periodically vented chambers. These differences were primarily attributed to the suppression of CO2 flux in periodically vented chambers as a result of high internal CO2 concentrations, and a concomitantly reduced diffusivity gradient. Prior to venting the periodically-vented chambers, CO2 flux rates averaged 2.3μg C (g soil)-1d-1, while CO2 flux rates following venting averaged 222.6μg C (g soil)-1d-1. We did not detect internal stratification of CO2 suggesting that mechanical headspace mixing is unnecessary in incubation chambers ranging from 1 to 2L. A standardized protocol is called for that isolates SOC fractions that are useful in hypothesis testing, while simultaneously seeking to minimize laboratory artifacts.© 2013 Elsevier Ltd.

Luterbacher J.S.,University of Wisconsin - Madison | Luterbacher J.S.,1552 University Ave | Martin Alonso D.,University of Wisconsin - Madison | Dumesic J.A.,University of Wisconsin - Madison | Dumesic J.A.,1552 University Ave
Green Chemistry | Year: 2014

This review presents an overview of the initial targeted chemical processing stages for conversion of lignocellulosic biomass to platform molecules that serve as intermediates for the production of carbon-based fuels and chemicals. We identify four classes of platform molecules that can be obtained in an initial chemical processing step: (i) sugars, (ii) dehydration products, (iii) polyols and (iv) lignin monomers. Special emphasis is placed on reporting and comparing parameters that affect process economics and/or sustainability, including product yields, amount of catalyst used, processing conditions, and product concentrations. We discuss the economic trade-offs associated with choices related to these parameters, depending on the product that is targeted. We also address the effects of real biomass on the ability to recover, recycle, and potentially regenerate catalysts and solvents used in the biomass conversion processes. © 2014 The Royal Society of Chemistry.

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