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Publications

When it comes to interdisciplinary collaboration, the titles of GLBRC publications speak for themselves. Each new year of operation has seen more publications from multiple labs that span the four Research Areas, accelerating the Center's production of the basic research that generates technology to convert cellulosic biomass to advanced biofuels.

Publications

Design of biofuel supply chains with variable regional depot and biorefinery locations

Rex T.L. Ng; Christos T. Maravelias

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2017

We propose a multi-period mixed-integer linear programming (MILP) model for the design and operational planning of cellulosic biofuel supply chains. Specifically, the proposed MILP model accounts for biomass selection and allocation, technology selection and capacity planning at regional depots and biorefineries. Importantly, it considers the location of regional depots and biorefineries as continuous optimization decisions. We introduce approximation and reformulation methods for the calculation of the shipments and transportation distance in order to obtain a linear model. We illustrate the applicability of the proposed methods using two medium-scale examples with realistic data.

Designing agricultural landscapes for biodiversity-based ecosystem services

Douglas A. Landis

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2017

Sustainable and resilient agricultural systems are needed to feed and fuel a growing human population. However, the current model of agricultural intensification which produces high yields has also resulted in a loss of biodiversity, ecological function, and critical ecosystem services in agricultural landscapes. A key consequence of agricultural intensification is landscape simplification, where once heterogeneous landscapes contain increasingly fewer crop and non-crop habitats. Landscape simplification exacerbates biodiversity losses which leads to reductions in ecosystem services on which agriculture depends. In recent decades, considerable research has focused on mitigating these negative impacts, primarily via management of habitats to promote biodiversity and enhance services at the local scale. While it is well known that local and landscape factors interact, modifying overall landscape structure is seldom considered due to logistical constraints. I propose that the loss of ecosystem services due to landscape simplification can only be addressed by a concerted effort to fundamentally redesign agricultural landscapes. Designing agricultural landscapes will require that scientists work with stakeholders to determine the mix of desired ecosystem services, evaluate current landscape structure in light of those goals, and implement targeted modifications to achieve them. I evaluate the current status of landscape design, ranging from fundamental ecological principles to resulting guidelines and socioeconomic tools. While research gaps remain, the time is right for ecologists to engage with other disciplines, stakeholders, and policymakers in education and advocacy to foster agricultural landscape design for sustainable and resilient biodiversity services.

Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling

Johnnie A. Walker; Sivakumar Pattathil; Lai F. Bergeman; Emily T. Beebe; Kai Deng; Maryam Mirzai; Trent R. Northen; Michael G. Hahn; Brian G. Fox

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2017

Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine soluble sugar products of their reactions.

Development of rapid bioconversion with integrated recycle technology for ethanol production from extractive ammonia pretreated corn stover

Mingjie Jin; Yanping Liu; Leonardo da Costa Sousa; Bruce E. Dale; Venkatesh Balan

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2017

High enzyme loading and low productivity are two major issues impeding low cost ethanol production from lignocellulosic biomass. This work applied rapid bioconversion with integrated recycle technology (RaBIT) and extractive ammonia (EA) pretreatment for conversion of corn stover (CS) to ethanol at high solids loading. Enzymes were recycled via recycling unhydrolyzed solids. Enzymatic hydrolysis with recycled enzymes and fermentation with recycled yeast cells were studied. Both enzymatic hydrolysis time and fermentation time were shortened to 24 h. Ethanol productivity was enhanced by two times and enzyme loading was reduced by 30%. Glucan and xylan conversions reached as high as 98% with an enzyme loading of as low as 8.4 mg protein per g glucan. The overall ethanol yield was 227 g ethanol/kg EA-CS (191 g ethanol/kg untreated CS). Biotechnol. Bioeng. 2017;9999: 1–8. © 2017 Wiley Periodicals, Inc.

Distribution of switchgrass (Panicum virgatum L.) aboveground biomass in response to nitrogen addition and across harvest dates

Jessica R. Miesel; Laura C. Jach-Smith; Mark J. Renz; Randall D. Jackson

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2017

Decisions about the harvest timing for switchgrass (Panicum virgatum L.) crops has important implications for economic and environmental objectives because there may be a significant trade-off between harvestable yield, bioenergy crop quality, and environmental cost or benefit. We investigated the effects of harvest timing and nitrogen (N) addition on switchgrass crops established in Wisconsin, USA to investigate the causes of biomass loss over time and to identify plant components that contribute to N loss or retention at each harvest date. We found that harvestable yield decreased over successive harvest dates, as a result of the physical loss of leaves and inflorescence biomass. Although N addition increased total aboveground biomass, it also increased the proportion of biomass occurring as leaves and infloresence. Leaf and infloresence biomass decreased over time and during harvest operations; however, this biomass became incorporated into the litter pool and increased on-site N retention. We conclude that although adding N to switchgrass is unlikely to increase harvestable yield when harvests are conducted after plant senescence, retention of high-N plant components will help maintain long-term site productivity and ecosystem function of bioenergy cropping systems, especially for sites targeted for low-input management.

Ecoinformatics (big data) for agricultural entomology: pitfalls, progress, and promise

Jay A. Rosenheim; Claudio Gratton

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2017

Ecoinformatics, as defined in this review, is the use of pre-existing, observational datasets to address questions in ecology. We provide the first review of ecoinformatics methods in agricultural entomology. Ecoinformatics methods have been used to address the full range of questions studied by agricultural entomologists, enabled by the special opportunities associated with datasets that are larger, that are more diverse, and that embrace larger spatial and temporal scales than most experimental studies. We argue that ecoinformatics research methods and traditional, experimental research methods have strengths and weaknesses that are largely complementary. We address the important interpretational challenges associated with observational datasets, highlight common pitfalls, and propose some best practices for researchers using these methods. Ecoinformatics methods hold great promise as a vehicle for capitalizing on the explosion of data emanating from farmers, researchers, and the public, as novel sampling and sensing techniques are developed and digital data sharing becomes more widespread. Expected final online publication date for the Annual Review of Entomology Volume 62 is January 7, 2017. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

Ecological patterns of seed microbiome diversity, transmission, and assembly

Ashley Shade; Marie-Agnès Jacques; Matthieu Barret

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2017

Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently act as the initial inoculum for the plant microbiota. The purpose of this mini-review is to provide an overview of current knowledge on the diversity, structure and role of the seed microbiota. The relative importance of the mode of transmission (vertical vs horizontal) of the microbial entities composing the seed microbiota as well as the potential connections existing between seed and other plant habitats such as the anthosphere and the spermosphere is discussed. Finally the governing processes (niche vs neutral) involved in the assembly and the dynamics of the seed microbiota are examined.

Effect of ethanol blending on particulate formation from premixed combustion in spark-ignition engines

Stephen Sakai; David A. Rothamer

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2017

Particulate formation due to combustion of a wide range of ethanol-gasoline blends were investigated in an internal combustion engine. The engine used for this study is a single-cylinder research engine, the architecture of which is representative of a modern spark ignited direct injected (SIDI) engine. Instead of direct injection, the engine was fueled using a premixed prevaporized (PMPV) mode, which supplied the fuel to the engine in a well-mixed, gas-phase air-fuel mixture in order to isolate physical effects of the fuel. This created a completely homogenous air-fuel mixture with no pockets of significantly differing equivalence ratio, liquid fuel droplets, or wetted surfaces, ensuring that particulate formation was due to homogenous, gas-phase combustion. The engine was operated at a fixed load and phasing so that the effects of varying equivalence ratio and ethanol content could be examined. The results in this work show that the addition of ethanol results in a consistent decrease in engine-out particulate proportional to ethanol content. Moreover, the critical equivalence ratio, the equivalence ratio at which significant sooting begins, increases in a linear fashion with ethanol addition. It was also shown that the shape of the particulate size distribution (PSD) is affected by ethanol content, with increased ethanol leading to more nucleation-mode dominated distributions.

Effect of increased fuel volatility on CDC operation in a light-duty CIDI engine

Michael A. Groendyk; David A. Rothamer

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2017

Alternative diesel fuels derived from biomass can vary significantly in volatility compared to their petroleum-derived counterparts, and their appropriate utilization is contingent on their compatibility with existing engine infrastructure. To investigate this compatibility, experiments were carried out to study the effect of fuel volatility on conventional diesel combustion (CDC) performance under a wide range of in-cylinder thermodynamic conditions at start of injection (SOI). Fuels of matched reactivity (i.e., cetane number (CN)) and varying volatility were produced by blending binary mixtures of 2,6,10-trimethyldodecane (farnesane) and 2,2,4,4,6,8,8-heptamethylnonane, octane number primary reference fuels (PRF), and cetane number secondary reference fuels (SRF). Nine fuel blends were tested in total, consisting of 3 volatility characteristics at 3 reactivity levels. Five engine operating conditions were utilized, ranging from 14.7–29 kg/m3 and 980–1120 K in-cylinder density and temperature at SOI. Testing was performed in a single-cylinder GM 1.9 L diesel engine. Only small differences in ignition delay (ID), in-cylinder pressure, and heat release rate (HRR) were observed between fuels of matched CN, regardless of their volatility. An analysis of the spray breakup and mixture formation process indicated that there were only small variations in ambient air entrainment and jet temperature between fuel blends, in agreement with the observed combustion behavior.

Enhanced delignification of steam-pretreated poplar by a bacterial laccase

Rahul Singh; Jinguang Hu; Matthew R. Regner; James W. Round; John Ralph; John N. Saddler; Lindsay D. Eltis

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2017

The recalcitrance of woody biomass, particularly its lignin component, hinders its sustainable transformation to fuels and biomaterials. Although the recent discovery of several bacterial ligninases promises the development of novel biocatalysts, these enzymes have largely been characterized using model substrates: direct evidence for their action on biomass is lacking. Herein, we report the delignification of woody biomass by a small laccase (sLac) from Amycolatopsis sp. 75iv3. Incubation of steam-pretreated poplar (SPP) with sLac enhanced the release of acid-precipitable polymeric lignin (APPL) by ~6-fold, and reduced the amount of acid-soluble lignin by ~15%. NMR spectrometry revealed that the APPL was significantly syringyl-enriched relative to the original material (~16:1 vs. ~3:1), and that sLac preferentially oxidized syringyl units and altered interunit linkage distributions. sLac's substrate preference among monoaryls was also consistent with this observation. In addition, sLac treatment reduced the molar mass of the APPL by over 50%, as determined by gel-permeation chromatography coupled with multi-angle light scattering. Finally, sLac acted synergistically with a commercial cellulase cocktail to increase glucose production from SPP ~8%. Overall, this study establishes the lignolytic activity of sLac on woody biomass and highlights the biocatalytic potential of bacterial enzymes.

Enhancing the soil and water assessment tool model for simulating N2O emissions of three agricultural systems

Qichun Yang; Xuesong Zhang; Michael Abraha; Stephen Del Grosso; G. P. Robertson; Jiquan Chen

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2017

Nitrous oxide (N2O) is a potent greenhouse gas (GHG) contributing to global warming, with the agriculture sector as the major source of anthropogenic N2O emissions due to excessive fertilizer use. There is an urgent need to enhance regional-/watershed-scale models, such as Soil and Water Assessment Tool (SWAT), to credibly simulate N2O emissions to improve assessment of environmental impacts of cropping practices. Here, we integrated the DayCent model's N2O emission algorithms with the existing widely tested crop growth, hydrology, and nitrogen cycling algorithms in SWAT and evaluated this new tool for simulating N2O emissions in three agricultural systems (i.e., a continuous corn site, a switchgrass site, and a smooth brome grass site which was used as a reference site) located at the Great Lakes Bioenergy Research Center (GLBRC) scale-up fields in southwestern Michigan. These three systems represent different levels of management intensity, with corn, switchgrass, and smooth brome grass (reference site) receiving high, medium, and zero fertilizer application, respectively. Results indicate that the enhanced SWAT model with default parameterization reproduced well the relative magnitudes of N2O emissions across the three sites, indicating the usefulness of the new tool (SWAT-N2O) to estimate long-term N2O emissions of diverse cropping systems. Notably, parameter calibration can significantly improve model simulations of seasonality of N2O fluxes, and explained up to 22.5%–49.7% of the variability in field observations. Further sensitivity analysis indicates that climate change (e.g., changes in precipitation and temperature) influences N2O emissions, highlighting the importance of optimizing crop management under a changing climate in order to achieve agricultural sustainability goals.

Establishment of a vernalization requirement in Brachypodium distachyon requires REPRESSOR OF VERNALIZATION1

Daniel P. Woods; Thomas S. Ream; Frédéric Bouché; Joohyun Lee; Nicholas Thrower; Curtis Wilkerson; Richard M. Amasino

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2017

A requirement for vernalization, the process by which prolonged cold exposure provides competence to flower, is an important adaptation to temperate climates that ensures flowering does not occur before the onset of winter. In temperate grasses, vernalization results in the up-regulation of VERNALIZATION1 (VRN1) to establish competence to flower; however, little is known about the mechanism underlying repression of VRN1 in the fall season, which is necessary to establish a vernalization requirement. Here, we report that a plant-specific gene containing a bromo-adjacent homology and transcriptional elongation factor S-II domain, which we named REPRESSOR OF VERNALIZATION1 (RVR1), represses VRN1 before vernalization in Brachypodium distachyon That RVR1 is upstream of VRN1 is supported by the observations that VRN1 is precociously elevated in an rvr1 mutant, resulting in rapid flowering without cold exposure, and the rapid-flowering rvr1 phenotype is dependent on VRN1 The precocious VRN1 expression in rvr1 is associated with reduced levels of the repressive chromatin modification H3K27me3 at VRN1, which is similar to the reduced VRN1 H3K27me3 in vernalized plants. Furthermore, the transcriptome of vernalized wild-type plants overlaps with that of nonvernalized rvr1 plants, indicating loss of rvr1 is similar to the vernalized state at a molecular level. However, loss of rvr1 results in more differentially expressed genes than does vernalization, indicating that RVR1 may be involved in processes other than vernalization despite a lack of any obvious pleiotropy in the rvr1 mutant. This study provides an example of a role for this class of plant-specific genes.

Fed-batch hydrolysate addition and cell separation by settling in high cell density lignocellulosic ethanol fermentations on AFEX™ corn stover in the Rapid Bioconversion with Integrated recycling Technology process

Cory Sarks; Mingjie Jin; Venkatesh Balan; Bruce E. Dale

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2017

The Rapid Bioconversion with Integrated recycling Technology (RaBIT) process uses enzyme and yeast recycling to improve cellulosic ethanol production economics. The previous versions of the RaBIT process exhibited decreased xylose consumption using cell recycle for a variety of different micro-organisms. Process changes were tested in an attempt to eliminate the xylose consumption decrease. Three different RaBIT process changes were evaluated in this work including (1) shortening the fermentation time, (2) fed-batch hydrolysate addition, and (3) selective cell recycling using a settling method. Shorting the RaBIT fermentation process to 11 h and introducing fed-batch hydrolysate addition eliminated any xylose consumption decrease over ten fermentation cycles; otherwise, decreased xylose consumption was apparent by the third cell recycle event. However, partial removal of yeast cells during recycle was not economical when compared to recycling all yeast cells.

Functionality and molecular weight distribution of red oak lignin before and after pyrolysis and hydrogenation

Daniel J. McClelland; Ali Hussain Motagamwala; Yanding Li; Marjorie R. Rover; Ashley M. Wittrig; Chunping Wu; Scott Buchanan; Robert C. Brown; John Ralph; James A. Dumesic; George W. Huber

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2017

Genetic architecture of flowering-time variation in Brachypodium distachyon

Daniel P. Woods; Ryland Bednarek; Frédéric Bouché; Sean P. Gordon; John P. Vogel; David F. Garvin; Richard M. Amasino

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2017

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a non-domesticated pooid grass closely related to cereals such as wheat and barley. A recombinant inbred line (RIL) population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing (GBS) approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.

Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species Candida tenuis

Max A.B. Haase; Jacek Kominek; Quinn K. Langdon; Cletus P. Kurtzman; Chris T. Hittinger

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2017

Xylose fermentation is a rare trait that is immensely important to the cellulosic biofuel industry, and Candida tenuis is one of the few yeasts that has been reported with this trait. Here we report the isolation of two strains representing a candidate sister species of C. tenuis. Integrated analysis of genome sequence and physiology suggested the genetic basis of a number of traits, including variation between the novel species and C. tenuis in lactose metabolism due to the loss of genes encoding lactose permease and β-galactosidase in the former. Surprisingly, physiological characterization revealed that neither the type strain of C. tenuis nor this novel species fermented xylose in traditional assays. We reexamined three xylose-fermenting strains previously identified as C. tenuis and found that these strains belong to the genus Scheffersomyces and are not C. tenuis. We propose Yamadazyma laniorum f.a. sp. nov. to accommodate our new strains and designate its type strain as yHMH7T ( = CBS 14780 = NRRL Y-63967). Furthermore, we propose the transfer of Candida tenuis to the genus Yamadazyma as Yamadazyma tenuis comb. nov. This approach provides a roadmap for how integrated genome sequence and physiological analysis can yield insight into the mechanisms that generate yeast biodiversity.

Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data

Paul P. Grabowski; Joseph Evans; Chris Daum; Shweta Deshpande; Kerrie W. Barry; Megan Kennedy; Guillaume Ramstein; Shawn M. Kaeppler; Robin Buell; Yiwei Jiang; Michael D. Casler

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2017

Flowering time is a major determinant of biomass yield in switchgrass (Panicum virgatum), a perennial bioenergy crop, because later flowering allows for an extended period of vegetative growth and increased biomass production. A better understanding of the genetic regulation of flowering time in switchgrass will aid the development of switchgrass varieties with increased biomass yields, particularly at northern latitudes, where late-flowering but southern-adapted varieties have high winter mortality. We use genotypes derived from recently published exome-capture sequencing, which mitigates challenges related to the large, highly repetitive and polyploid switchgrass genome, to perform genome-wide association studies (GWAS) using flowering time data from a switchgrass association panel in an effort to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We identify associations with flowering time at multiple loci, including in a homolog of FLOWERING LOCUS T and in a locus containing TIMELESS, a homolog of a key circadian regulator in animals. Our results suggest that flowering time variation in switchgrass is due to variation at many positions across the genome. The relationship of flowering time and geographic origin indicates likely roles for genes in the photoperiod and autonomous pathways in generating switchgrass flowering time variation.

Habitat management to suppress pest populations: progress and prospects

Geoff M. Gurr; Stephen D. Wratten; Douglas A. Landis; Minsheng You

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2017

Habitat management involving manipulation of farmland vegetation can exert direct suppressive effects on pests and promote natural enemies. Advances in theory and practical techniques have allowed habitat management to become an important subdiscipline of pest management. Improved understanding of biodiversity-ecosystem function relationships means that researchers now have a firmer theoretical foundation on which to design habitat management strategies for pest suppression in agricultural systems, including landscape scale effects. Supporting natural enemies with shelter, nectar, alternative prey and hosts, and pollen (SNAP) has emerged as a major research topic and applied tactic with field tests and adoption often preceded by rigorous laboratory experimentation. As a result, the promise of habitat management is increasingly being realized in the form of practical implementation globally. Uptake is facilitated by farmer participation in research and is made more likely by the simultaneous delivery of ecosystem services other than pest suppression. Expected final online publication date for the Annual Review of Entomology Volume 62 is January 7, 2017. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.

Harvesting biofuel grasslands has mixed effects on natural enemy communities and no effects on biocontrol services

Tania N. Kim; Aaron F. Fox; Bill D. Wills; Timothy D. Meehan; Douglas A. Landis; Claudio Gratton

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2017

Hotspots of soil N2O emission enhanced through water absorption by plant residue

A. N. Kravchenko; E. R. Toosi; A. K. Guber; N. E. Ostrom; J. Yu; K. Azeem; M. L. Rivers; G. P. Robertson

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2017

N2O is a highly potent greenhouse gas and arable soils represent its major anthropogenic source. Field-scale assessments and predictions of soil N2O emission remain uncertain and imprecise due to the episodic and microscale nature of microbial N2O production, most of which occurs within very small discrete soil volumes. Such hotspots of N2O production are often associated with decomposing plant residue. Here we quantify physical and hydrological soil characteristics that lead to strikingly accelerated N2O emissions in plant residue-induced hotspots. Results reveal a mechanism for microscale N2O emissions: water absorption by plant residue that creates unique micro-environmental conditions, markedly different from those of the bulk soil. Moisture levels within plant residue exceeded those of bulk soil by 4-10-fold and led to accelerated N2O production via microbial denitrification. The presence of large ([empty] >35[thinsp][mu]m) pores was a prerequisite for maximized hotspot N2O production and for subsequent diffusion to the atmosphere. Understanding and modelling hotspot microscale physical and hydrologic characteristics is a promising route to predict N2O emissions and thus to develop effective mitigation strategies and estimate global fluxes in a changing environment.

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