Publications

Advancing bioenergy and biochemical research: This page brings together the academic publications from all aspects of the AHB research project.


Feedstock Publications

FeedstockLeaf

Increased drought tolerance of hybrid poplar by inoculation with endophyte consortia

Khan, Z., Rho, H., Luna, V., Firrincieli, A., Hung, S.H., Masciarelli, O., Kim, S.-H., and Doty, S.L. 2016. Increased drought tolerance of hybrid poplar by inoculation with endophyte consortia. Current Plant Biology.

With increasing effects of global climate change, there is a strong interest in developing biofuels from trees such as poplar (Populus sp.) that have high C sequestration rates and relatively low chemical inputs. Using plant-microbe symbiosis to maximize plant growth and increase host stress tolerance may play an important role in improving the economic viability and environmental sustainability of poplar as a feedstock.
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Containment of transgenic trees by suppression of LEAFY

Klocko, A.L., Brunner, A.M., Huang, J., Meilan, R., LU, H., Ma, C., Morel, A., Zhao, D., Ault, K., Dow, M., Howe, G., Shevcheko, O., and Strauss, S.H. (2016) Containment of transgenic trees by suppression of LEAFY. Nature Biotechnology 34: 918-922

Field studies and commercial use of genetically engineered trees is limited because of concerns over transgene flow into wild or feral tree population. This study shows that RNA interference (RNAi) can be used to suppress the LEAFY gene that makes poplar and other plants incapable of producing pollen or seeds. The LEAFY gene would still be present, but RNAi would slow down the gene’s activity.
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Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity

BUSBY, P.E., PEAY, K.G., and NEWCOMBE, G. (2016). Common foliar fungi of Populus trichocarpa modify Melampsora rust disease severity. New Phytologist 209: 1681–1692.

We tested the hypothesis that common foliar fungi of the model tree Populus trichocarpa influence the severity of disease caused by the tree’s major rust pathogen, Melampsora × columbiana. Our field-based, experimental and modeling results support the hypothesis that disease modification is an ecological function shared among common foliar fungi of P. trichocarpa.
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Morphological and molecular characterization of two Aphelenchoides endophytic in poplar leaves

CARTA, L. K., S. LI, A. M. SKANTAR, and NEWCOMBE, G. (2016). Morphological and molecular characterization of two Aphelenchoides endophytic in poplar leaves. Journal of Nematology 48:(1): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859615/

Here, we characterize these two fungal-feeding nematodes microscopically and with two DNA markers for identification and phylogenetic analysis. Their potential ecological impact is also discussed.
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Variable Nitrogen Fixation in Wild Populus. PLoS One

Doty, S.L., Sher, A.W., Fleck, N.D., Khorasani, M., Bumgarner, R.B., Khan, Z., Ko, A.W.K., Kim, S.-H., and DeLuca, T.H. (2016). Variable Nitrogen Fixation in Wild Populus. PLoS One http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155979

The overall objective of this study was to assess N2-fixation in native riparian black cottonwood (Populus trichocarpa) taken from its natural setting. We report N2-fixation within some wild poplar samples and demonstrate the presence of diazotrophic bacteria in these plants, helping to explain the biology of poplar as a pioneer plant species.
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Analysis of the genetic variation in growth, ecophysiology, and chemical and metabolomics composition of wood Populus trichocarpa provenances

Guerra, F.P., Richards, J.H., Fiehn, O., Famula, R., Stanton, B.J., Shuren, R., Sykes, R., Davis, M.F., Neale, D.B. (2016). Analysis of the genetic variation in growth, ecophysiology, and chemical and metabolomics composition of wood Populus trichocarpa provenances. Tree Genetics & Genomes 12:6.

Populus trichocarpa is a biological model and a candidate species for bioethanol production. Although intraspecific variation is recognized, knowledge about genetic variation underlying the properties of its lignocellulosic biomass is still incomplete. Genetic variation is fundamental for continuing genetic improvement. In this study, we carried out a comprehensive phenotypic characterization of this species, analyzing a suite of quantitative traits associated with growth performance and wood quality.
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“Lessons from two decades of field trials with genetically modified tress in the USA: Biology and regulatory compliance.”

Strauss, S.H., Ma, C., Ault, K., and Klocko, A.L. (2015). Lessons from two decades of field trials with genetically modified tress in the USA: Biology and regulatory compliance. Biosafety of Transgenic Forest Trees.

We summarize the many field trials that we have conducted in the USA beginning in 1995 and continuing to this day. Under USDA APHIS federal regulatory notifications and permits, we have planted nearly 20,000 trees derived from approximately 100 different constructs in more than two dozen field experiments.
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Genetically engineered trees: Paralysis from good intentions

Strauss, S.H., Constanza, A., and Seguin, A. (2015). Genetically engineered trees: Paralysis from good intentions. Science 349: 794-795.

Intensive genetic modification is a longstanding practice in agriculture, and, for some species, in woody plant horticulture and forestry. Current regulatory systems for genetically engineered crops, in which recombinant DNA is used to asexually insert or modify DNA, were created decades ago with good intentions for caution and forethought. Likewise, forest certification systems were created to promote responsible forest management and sustainable practices. However, both systems are at odds with the need for rapid and innovative biotechnologies to help forests cope with growing pest epidemics and mounting abiotic stresses as a result of global travel and climate change.
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Fungal endophytes: modifiers of plant disease

BUSBY, P.E., RIDOUT, M., and NEWCOMBE, G. (2015). Fungal endophytes: modifiers of plant disease. Plant Molecular Biology 90: (doi:10.1007/s11103-015-0412-0).

We reviewed recent literature on fungal endophyte disease modification, and here report on several emergent themes: (1) Fungal endophyte effects on plant disease span the full spectrum from pathogen antagonism to pathogen facilitation, with pathogen antagonism most commonly reported. (2) Agricultural plant pathosystems are the focus of research on endophyte disease modification. (3) A taxonomically diverse group of fungal endophytes can influence plant disease severity. And (4) Fungal endophyte effects on plant disease severity are context-dependent.
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Genetics-based interactions among plants, pathogens and herbivores define arthropod community structure

Busby, P.E., Lamit, L., Keith, A.R., Newcombe, G., Gehring, C., Whitham, T.G., and Dirzo, R. 2015. Genetics-based interactions among plants, pathogens and herbivores define arthropod community structure. Ecology 96:7.

Plant resistance to pathogens or insect herbivores is common, but its potential for indirectly influencing plant-associated communities is poorly known. Here, we test whether pathogens’ indirect effects on arthropod communities and herbivory depend on plant resistance to pathogens and/or herbivores, and address the overarching interacting foundation species hypothesis that genetics-based interactions among a few highly interactive species can structure a much larger community. In a manipulative field experiment using replicated genotypes of two Populus species and their interspecific hybrids, we found that genetic variation in plant resistance to both pathogens and insect herbivores modulated the strength of pathogens’ indirect effects on arthropod communities and insect herbivory.
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Differentiating genetic and environmental drivers of plantpathogen community interactions

Bubsy, P.E., Newcombe, G., Dirzo, R., and Whitham, T.G. 2014. Differentiating genetic and environmental drivers of plantpathogen community interactions. Journal of Ecology 102: 1300-1309.

Plant genotypic variation can shape associated arthropod and microbial communities locally, as has been demonstrated in controlled common garden experiments. However, the relative roles of plant genetics and the environment in defining communities at larger spatial scales are not well known. The environmental heterogeneity hypothesis maintains that plant genetic effects on associated communities diminish across the landscape as environmental variation predominates. Alternatively, the local adaptation hypothesis argues that plant genetic effects change across landscapes as a result of species interactions being locally adapted. Thus, very different mechanisms could produce similar patterns.
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Cry3Aa transgene expression reduces insect damage and improves growth in field-grown hybrid poplar

Klocko A., Meilan R., James R.R., Viswanath V., Ma C., Payne P., Miller L., Skinner J.S., Oppert B., Cardineau G.A., and Strauss S.H. (2014). Cry3Aa transgene expression reduces insect damage and improves growth in field-grown hybrid poplar. Can. J. For. Res. 44: 28–35.

The stability and value of transgenic pest resistance for promoting tree growth are poorly understood. These data are essential for determining if such trees could be beneficial to commercial growers in the face of substantial regulatory and marketing costs. We investigated growth and insect resistance in hybrid poplar expressing the cry3Aa transgene in two field trials.
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Diseases of Poplars and Willows. Chapter 8 in The Poplar and Willows Book

Ostry, M., Ramstedt, M., Newcombe, G., and Steenackers, M. 2013. Diseases of Poplars and Willows. Chapter 8 in The Poplar and Willows Book. Edited by Jud Isebrands and Jim Richardson. Published by the International Poplar Commission of UN FAO.

Across their native and planted ranges, Populusand Salix species and hybrids are host to a wide array of microorganisms. Fortunately, only a relatively small number of these organisms are pathogens that cause economically damaging diseases (Ostry and McNabb, 1985). No single pathogen is equally important throughout the entire range of Populusand Salix, and many organisms are highly specific to only some species and hybrids (Newcombe, 1996; Newcombe et al., 2001a). Since poplars and willows are similar ecologically and closely related through evolution (Argus, 2010; Eckenwalder, 2010), there are many parallels among their collective pathogens. Many of the genera of pathogens that affect one also affect the other (Newcombe et al., 2010).
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Genetic basis of pathogen community structure for foundation tree species in a common garden and in the wild

Bubsy, P.E., Newcombe, G., Dirzo, R., and Whitham, T.G. 2013. Genetic basis of pathogen community structure for foundation tree species in a common garden and in the wild. Journal of Ecology 101: 867-877.

Genetic variation within and among foundation plant species is known to affect arthropod, plant and soil microbial communities. We hypothesized that the same would be expected for pathogen communities, which have typically been studied only as individual pathogen species. In a common garden in Utah, USA, we first tested how genetic differences within and among Populus angustifolia, P. fremontii and their interspecific hybrid P. × hinckleyana affect a fungal leaf pathogen community. Next, we tested how Populus genetic differences at the level of species and hybrids affect fungal leaf pathogen communities in the wild, specifically in a natural Populus hybridization zone (13 river km) and throughout the larger Weber River watershed (150 river km).
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Leaf endophytes and host genotype in Populus affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi.

Busby P., Zimmerman N., Weston D., Jawdy S., Houbraken J., Newcombe G.  (2013), Leaf endophytes and host genotype in Populus affect severity of damage from the necrotrophic leaf pathogen, Drepanopeziza populi. Ecosphere. 4(10).

Fungal leaf endophytes—nonpathogenic microfungi that live within plant leaves—are ubiquitous in land plants. Leaf endophytes and host plant genotypes may interact to determine plant disease severity.
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Green Revolution Plantations: Could Short Trees be a Big Thing?

Klocko A., Stanton B., Van Oosten C., and Strauss SH. (2013) Green Revolution Plantations: Could Short Trees be a Big Thing? Information Systems for Biotechnology Report.
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The contribution of foliar endophytes to quantitative resistance to Melampsora rust

Raghavendra A.,  and Newcombe G.  (2013). The contribution of foliar endophytes to quantitative resistance to Melampsora rust.  New Phytologist. 197(3):909-918.

Foliar endophytes of Populus do not induce the hypersensitive response associated with major genes for resistance to Melampsora leaf rust. But they could contribute to the quantitative resistance that represents a second line of defense. Quantitative resistance is thought to be determined by suites of minor genes in both host and pathogen that are influenced by the abiotic environment. Here, we determined the relative importance to quantitative resistance of foliar endophytes, one element of the biotic environment.
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Genetic Methods for Mitigating Invasiveness of Woody Ornamental Plants: Research Needs and Opportunities

Vining K., Contreras R., Ranik M., Strauss SH. (2012). Genetic Methods for Mitigating Invasiveness of Woody Ornamental Plants: Research Needs and Opportunities. HortScience. 47(9):1210-1216.

Because cultivation of exotic woody ornamental plants has led to establishment of a number of invasive species, there is considerable interest in breeding methods to reduce the propensity for spread. We review progress in conventional breeding and transgenic biotechnology approaches to producing sterile forms of ornamental woody plants.


Conversion Publications
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Fermentation of lignocellulosic sugars to acetic acid by Moorella thermoacetica

Ehsanipour, M., Suko, A. V., & Bura, R. (2016). Fermentation of lignocellulosic sugars to acetic acid by Moorella thermoacetica. Journal of Industrial Microbiology & Biotechnology, 1-10.

A systematic study of bioconversion of lignocellulosic sugars to acetic acid by Moorella thermoacetica (strain ATCC 39073) was conducted. Four different water-soluble fractions (hydrolysates) obtained after steam pretreatment of lignocellulosic biomass were selected and fermented to acetic acid in batch fermentations.
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Post-treatment mechanical refining as a method to improve overall sugar recovery of steam pretreated hybrid poplar

Dou, C., Ewanick, S., Bura, R., & Gustafson, R. (2016). Post-treatment mechanical refining as a method to improve overall sugar recovery of steam pretreated hybrid poplar. Bioresource technology, 207, 157-165.

This study investigates the effect of mechanical refining to improve the sugar yield from biomass processed under a wide range of steam pretreatment conditions.
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Hydrocarbon bio-jet fuel from bioconversion of poplar biomass: techno-economic assessment.

Crawford, J.T., Shan, C..W., Budsberg, E., Morgan, M., Bura, R., Gustafson, R. (2016) Hydrocarbon bio-jet fuel from bioconversion of poplar biomass: techno-economic assessment. Biotechnology for Biofuels 9:141.

Infrastructure compatible hydrocarbon biofuel proposed to qualify as renewable transportation fuel under the U.S. Energy Independence and Security Act of 2007 and Renewable Fuel Standard (RFS2) is evaluated. The process uses a hybrid poplar feedstock, which undergoes dilute acid pretreatment and enzymatic hydrolysis.
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Hydrocarbon bio-jet fuel from bioconversion of poplar biomass: life cycle assessment

Budsberg, E., Crawford, J.T., Morgan, H., Chin, W.S., Bura, R., Gustafson, R. (2016) Hydrocarbon bio-jet fuel from bioconversion of poplar biomass: life cycle assessment. Biotechnology for Biofuels 9:170

Bio-jet fuels compatible with current aviation infrastructure are needed as an alternative to petroleum-based jet fuel to lower greenhouse gas emissions and reduce dependence on fossil fuels. Cradle to grave life cycle analysis is used to investigate the global warming potential and fossil fuel use of converting poplar biomass to drop-in bio-jet fuel via a novel bioconversion platform.
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Ethanologens vs. acetogens: Environmental impacts of two ethanol fermentation pathways

Budsberg, E., Crawford, J., Gustafson, R., Bura, R., and Puettmann, M. 2015. Ethanologens vs. acetogens: Environmental impacts of two ethanol fermentation pathways. Biomass and Bioenergy 83: 25-31.

Bioconversion production of ethanol from cellulosic feedstock is generally proposed to use direct fermentation of sugars to ethanol. Another potential route for ethanol production is fermentation of sugars to acetic acid followed by hydrogenation to convert the acetic acid into ethanol.
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Real-time understanding of lignocellulosic bioethanol fermentation by Raman spectroscopy. Biotechnology for Biofuels

Ewanick, S.M., W. Thompson, B. Marquardt, and R. Bura. 2013. Real-time understanding of lignocellulosic bioethanol fermentation by Raman spectroscopy. Biotechnology for Biofuels.

In this paper we show that glucose and ethanol in a lignocellulosic fermentation can be accurately monitored by a 785 nm Raman spectroscopy instrument and novel immersion probe, even in the presence of an elevated background thought to be caused by lignin-derived compounds. Chemometric techniques were used to reduce the background before generating calibration models for glucose and ethanol concentration. The models show very good correlation between the real-time Raman spectra and the offline HPLC validation.


Sustainability Publications

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Impact of biases in gridded weather datasets on biomass estimates of short rotation woody cropping systems

Bandaru, V., Pei, Y., B.M. Jenkins. 2016. Impact of biases in gridded weather datasets on biomass estimates of short rotation woody cropping systems. Agricultural and Forest Meteorology: 233.

Short rotation woody crop (SRWC) systems continue to be investigated as energy crops for a range of energy products including liquid biofuels and electricity. To understand their market potential and economic viability, regional biomass yield and production estimates are used as primary inputs. Biomass is generally estimated using growth models which often utilize gridded weather datasets when implemented for regional simulations. With such models, the accuracy of weather data will affect the uncertainty of estimated biomass and subsequent bioenergy analyses. This study evaluates the biases in weather variables of commonly used high resolution gridded datasets including PRISM, Daymet, NARR, and NLDAS in comparison with observed weather at five flux tower stations. Further, impacts of inaccuracies in gridded data sources on biomass estimates of SRWC hybrid poplar was investigated at site and regional levels using a version of the 3-PG growth model modified to model production with multiple harvests through coppicing or periodic cutting of the trees with regrowth from the tree stump.
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The impact of combined torrefaction and pelletization process on forestry biomass supply chain in California

Yuanzhe, L., P.W. Tittmann, B.M. Jenkins. 2015. The impact of combined torrefaction and pelletization process on forestry biomass supply chain in California. Bioresource Technology.

The cost of supplying wood biomass from forestry operations in remote areas has been an obstacle to expansion of forest-based bioenergy in much of the western United States. Economies of scale in the production of liquid fuels from lignocellulosic biomass feedstocks favor large centralized biorefineries. Increasing transportation efficiency through torrefaction and pelletization at distributed satellite facilities may serve as a means to expand the utilization of forestry residuals in biofuel production. To investigate this potential, a mixed-integer linear program was developed to optimize the feedstock supply chain design with and without distributed pretreatment.
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Ethanologens vs. acetogens: Environmental impacts of two ethanol fermentation pathways

Budsberg, E., J. Crawford, R. Gustafson, R. Bura, and M. Puettmann. 2015. Ethanologens vs. acetogens: Environmental impacts of two ethanol fermentation pathways. Biomass and Bioenergy. 83: 23-31
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Economic sustainability modeling provides decision support for assessing hybrid poplar-based biofuel development in California

Bandaru, V., Parker, N.C., Hart, Q.,Jenner, M., Yeo, B.L., Crawford, J.T., Li, Y., Tittmann, P., Rogers, L., Kaffka, S., Jenkins, B.M. (2015). Economic sustainability modeling provides decision support for assessing hybrid poplar-based biofuel development in California. California Agriculture.

Biofuels are expected to play a major role in meeting California’s long-term energy needs, but many factors influence the commercial viability of the various feedstock and production technology options. We developed a spatially explicit analytic framework that integrates models of plant growth, crop adoption, feedstock location, transportation logistics, economic impact, biorefinery costs and biorefinery energy use and emissions.
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Modeling Poplar Growth as a Short Rotation Woody Crop for Biofuels in the Pacific Northwest

Hart, Q.J., Tittmann, P.W., Bandaru, V., & Jenkins, B.M. (2015). Modeling Poplar Growth as a Short Rotation Woody Crop for Biofuels in the Pacific Northwest. Biomass and Bioenergy.

Predicting the economic viability and environmental sustainability of a biofuels industry based on intensively cultivated short rotation woody crops (SRWC) requires spatial predictions of growth and yield under various environmental conditions and across large regions. The Physiological Principles in Predicting Growth (3PG) model was modified to evaluate the growth and yield of coppiced poplar (Populus spp). This included an additional biomass partitioning method and developing a sub-model which takes into account the impact of coppicing on post harvest regeneration, extending the applicability of the 3PG model to coppice management regimes.
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Effects of Air Pollution Control Costs on U.S. Biofuel System Development

Murphy C. and Parker N. (2014). Effects of Air Pollution Control Costs on U.S. Biofuel System Development. Environmental Science and Technology. 48(4) 2157-2164.

Air pollution emissions regulation can affect the location, size, and technology choice of potential biofuel production facilities. Difficulty in obtaining air pollutant emission permits and the cost of air pollution control devices have been cited by some fuel producers as barriers to development. This paper expands on the Geospatial Bioenergy Systems Model (GBSM) to evaluate the effect of air pollution control costs on the availability, cost, and distribution of U.S. biofuel production by subjecting potential facility locations within U.S. Clean Air Act nonattainment areas, which exceed thresholds for healthy air quality, to additional costs.
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Design of a GISbased Web Application for Simulating Biofuel Feedstock Yields

Prilepova O., Hart Q., Merz J., Parker N. C., Bandaru V., Jenkins B. (2014). Design of a GISbased Web Application for Simulating Biofuel Feedstock Yields. ISPRS International Journal of Geo-Information. 3(3), 929-941.

Short rotation woody crops (SRWC), such as hybrid poplar, have the potential to serve as a valuable feedstock for cellulosic biofuels. Spatial estimates of biomass yields under different management regimes are required for assisting stakeholders in making better management decisions and to establish viable woody cropping systems for biofuel production. To support stakeholders in their management decisions, we have developed a GIS-based web interface using a modified 3PG model for spatially predicting poplar biomass yields under different management and climate conditions in the U.S. Pacific Northwest region.
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Spatially explicit projection of biofuel supply for meeting renewable fuel standard

Parker, N. 2012. Spatially explicit projection of biofuel supply for meeting renewable fuel standard. Transportation Research Record: Journal of the Transportation Research Board, No. 2287:72-79.

In this study, the author simulated the industry required to meet the 2018 mandate, with special attention to the geographic layout. The methodology built a series of scenarios by varying market and technology parameters that influence the design of the biofuel industry. The industry was then modeled with an integrated supply chain model that was spatially explicit. This model described the optimal behavior of a biofuel industry given the constraints of fuel demand, biofuel selling price, and feedstock supply. All the analyzed scenarios achieved the 2018 RFS2 mandate at wholesale fuel prices between $2.65 and $3.78/gal of gasoline-equivalent biofuels. Between $57.7 billion and $140.7 billion in capital investment was required to bring the fuels to market. The results were most sensitive to the level of technological optimism and the access to waste and residue biomass resources.


Extension Publications

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Extension Professionals’ Perspectives on Supporting Feedstock Production for Biofuels: Concerns, Challenges, and Opportunities

Townsend, Patricia A.; Haider, Nora M.; Asah, Stanley T.; Zobrist, Kevin W. (2016). Extension Professionals’ Perspectives on Supporting Feedstock Production for Biofuels: Concerns, Challenges, and Opportunities Journal of Extension. 54(6).

The development of successful bioenergy programs will depend on informed and prepared Extension professionals who are willing and equipped to provide technical support. A survey of Extension professionals in the Pacific Northwest revealed barriers to program development, including limits on time and knowledge and concerns about economic returns for biofuel crops.
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Growing Green Energy: Extension’s Role in the Development of Advanced Biofuels

Haider N., Kar S., Townsend P. A., and Zobrist K. W. (2015). Growing Green Energy: Extension’s Role in the Development of Advanced Biofuels. Journal of Extension.  53(1).

The development of advanced biofuels is expanding the possibilities for purpose-grown energy crops. Growers, producers, and other stakeholders will need a reliable source of information to assist with decision-making regarding renewable fuel supply chains. This review examines Extension’s role in the innovation of advanced biofuels by documenting and summarizing Extension work in existing biomass-derived energy programs. This review highlights strategies used by Extension programs that help make renewable energy innovations successful.
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Poplar (Populus spp.) Trees for Biofuel  Production

Townsend P.A., Kar S., and Miller R.  (2013).  Poplar (Populus spp.) Trees for Biofuel  Production.  eXtension.

Poplars show promise as a feedstock for biofuels. The trees are fast growing and able to produce large quantities of biomass in a short amount of time, easy to propagate and cultivate, and can grow in many regions.