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The US-DOE Bioenergy Science Center (BESC): Findings and Perspectives

The BioEnergy Science Center (BESC) has focused on understanding lignocellulosic biomass formation and deconstruction en route to the production of biofuels.  This deeper understanding of plant cell wall structure and the biological mechanism for efficient depolymerization and fermentation was necessary to provide the underpinnings to “overcome biomass recalcitrance” – the central theme of BESC.

This special issue of Biotechnology for Biofuels is being prepared after a decade of BESC research. Among its over two dozen articles, it features both review articles as well as current topical presentations illustrative of current BESC research.  Broader papers include an overview of the ten-years of BESC research and its mission and top accomplishments (Gilna et al.), as well as articles on the insights gained regarding the role and formation of xylan (Urbanowicz et al.).

The targeted research articles cover the range of BESC research.   For example, elucidation of the functions of plant biosynthesis genes, and extension from the laboratory to successful field testing of improved plant lines (Kumar et al., Johnson et al.; Macaya-Sanz et al.), are included in this special issue. The impacts of altered plant cell wall composition on structure and conversion are featured in several articles (Harman-Ware et al.; Ding et al.; Kumar et al.).  Examples of studies of hydrolytic enzymes (e.g., cellulase) are shown for thermophiles (Brunecky et al.) and oxidative enzymes (Kruer-Zerhusen et al.) are also included. The drive for improved conversion utilizing consolidated bioprocessing examines the impacts of toxicity (Wilbanks et al.) and high biomass loadings (Verbeke et al.). There are also examples of metabolic engineering (Zheng et al.; Eminoglu et al.) as well as ‘omic’ studies (Sander et al.).

Most of these contributions draw on participants from multiple BESC partner institutions, which showcases the collaborative impacts of a multi-institutional center, critical for accelerating research in bioenergy.  Over the course of its decade long tenure, BESC researchers contributed 945 papers in peer reviewed journals and inspired countless beginning- and early-career scientists to enter the bioenergy field.

Edited by Edward Bayer, Brian Davison and Michael Himmel

  1. Content type: Review

    Production of biofuels and bioenergy precursors by phototrophic microorganisms, such as microalgae and cyanobacteria, is a promising alternative to conventional fuels obtained from non-renewable resources. Sev...

    Authors: Juan D. Tibocha-Bonilla, Cristal Zuñiga, Rubén D. Godoy-Silva and Karsten Zengler

    Citation: Biotechnology for Biofuels 2018 11:241

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  2. Content type: Research

    Lignin is a natural polymer that is interwoven with cellulose and hemicellulose within plant cell walls. Due to this molecular arrangement, lignin is a major contributor to the recalcitrance of plant materials...

    Authors: Mojdeh Faraji, Luis L. Fonseca, Luis Escamilla-Treviño, Jaime Barros-Rios, Nancy Engle, Zamin K. Yang, Timothy J. Tschaplinski, Richard A. Dixon and Eberhard O. Voit

    Citation: Biotechnology for Biofuels 2018 11:34

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  3. Content type: Research

    Thermophilic microorganisms and their enzymes offer several advantages for industrial application over their mesophilic counterparts. For example, a hyperthermophilic anaerobe, Caldicellulosiruptor bescii, was re...

    Authors: Roman Brunecky, Daehwan Chung, Nicholas S. Sarai, Neal Hengge, Jordan F. Russell, Jenna Young, Ashutosh Mittal, Patthra Pason, Todd Vander Wall, William Michener, Todd Shollenberger, Janet Westpheling, Michael E. Himmel and Yannick J. Bomble

    Citation: Biotechnology for Biofuels 2018 11:22

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  4. Content type: Research

    The development of fast-growing hardwood trees as a source of lignocellulosic biomass for biofuel and biomaterial production requires a thorough understanding of the plant cell wall structure and function that...

    Authors: Ajaya K. Biswal, Melani A. Atmodjo, Sivakumar Pattathil, Robert A. Amos, Xiaohan Yang, Kim Winkeler, Cassandra Collins, Sushree S. Mohanty, David Ryno, Li Tan, Ivana Gelineo-Albersheim, Kimberly Hunt, Robert W. Sykes, Geoffrey B. Turner, Angela Ziebell, Mark F. Davis…

    Citation: Biotechnology for Biofuels 2018 11:9

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  5. Content type: Research

    Domain of Unknown Function 231-containing proteins (DUF231) are plant specific and their function is largely unknown. Studies in the model plants Arabidopsis and rice suggested that some DUF231 proteins act in...

    Authors: Yongil Yang, Chang Geun Yoo, Kimberly A. Winkeler, Cassandra M. Collins, Maud A. W. Hinchee, Sara S. Jawdy, Lee E. Gunter, Nancy L. Engle, Yunqiao Pu, Xiaohan Yang, Timothy J. Tschaplinski, Arthur J. Ragauskas, Gerald A. Tuskan and Jin-Gui Chen

    Citation: Biotechnology for Biofuels 2017 10:311

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  6. Content type: Research

    The mission of the BioEnergy Science Center (BESC) was to enable efficient lignocellulosic-based biofuel production. One BESC goal was to decrease poplar and switchgrass biomass recalcitrance to biofuel conver...

    Authors: Richard S. Nelson, C. Neal Stewart Jr., Jiqing Gou, Susan Holladay, Lina Gallego-Giraldo, Amy Flanagan, David G. J. Mann, Hiroshi Hisano, Wegi A. Wuddineh, Charleson R. Poovaiah, Avinash Srivastava, Ajaya K. Biswal, Hui Shen, Luis L. Escamilla-Treviño, Jiading Yang, C. Frank Hardin…

    Citation: Biotechnology for Biofuels 2017 10:309

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  7. Content type: Research

    Populus natural variants have been shown to realize a broad range of sugar yields during saccharification, however, the structural features responsible for higher sugar release from na...

    Authors: Vanessa A. Thomas, Ninad Kothari, Samarthya Bhagia, Hannah Akinosho, Mi Li, Yunqiao Pu, Chang Geun Yoo, Sivakumar Pattathil, Michael G. Hahn, Arthur J. Raguaskas, Charles E. Wyman and Rajeev Kumar

    Citation: Biotechnology for Biofuels 2017 10:292

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  8. Content type: Review

    Xylans are the most abundant noncellulosic polysaccharides in lignified secondary cell walls of woody dicots and in both primary and secondary cell walls of grasses. These polysaccharides, which comprise 20–35...

    Authors: Peter J. Smith, Hsin-Tzu Wang, William S. York, Maria J. Peña and Breeanna R. Urbanowicz

    Citation: Biotechnology for Biofuels 2017 10:286

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  9. Content type: Commentary

    The DOE BioEnergy Science Center has operated as a virtual center with multiple partners for a decade targeting overcoming biomass recalcitrance. BESC has redefined biomass recalcitrance from an observable phe...

    Authors: Paul Gilna, Lee R. Lynd, Debra Mohnen, Mark F. Davis and Brian H. Davison

    Citation: Biotechnology for Biofuels 2017 10:285

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  10. Content type: Research

    The development of genome editing technologies offers new prospects in improving bioenergy crops like switchgrass (Panicum virgatum). Switchgrass is an outcrossing species with an allotetraploid genome (2n = 4x =...

    Authors: Jong-Jin Park, Chang Geun Yoo, Amy Flanagan, Yunqiao Pu, Smriti Debnath, Yaxin Ge, Arthur J. Ragauskas and Zeng-Yu Wang

    Citation: Biotechnology for Biofuels 2017 10:284

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  11. Content type: Research

    With the discovery of interspecies hydrogen transfer in the late 1960s (Bryant et al. in Arch Microbiol 59:20–31, 1967), it was shown that reducing the partial pressure of hydrogen could cause mixed acid fermenti...

    Authors: Ayşenur Eminoğlu, Sean Jean-Loup Murphy, Marybeth Maloney, Anthony Lanahan, Richard J. Giannone, Robert L. Hettich, Shital A. Tripathi, Ali Osman Beldüz, Lee R. Lynd and Daniel G. Olson

    Citation: Biotechnology for Biofuels 2017 10:282

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  12. Content type: Research

    Clostridium thermocellum is a promising microorganism for conversion of cellulosic biomass to biofuel, without added enzymes; however, the low ethanol titer produced by strains develop...

    Authors: Liang Tian, Skyler J. Perot, David Stevenson, Tyler Jacobson, Anthony A. Lanahan, Daniel Amador-Noguez, Daniel G. Olson and Lee R. Lynd

    Citation: Biotechnology for Biofuels 2017 10:276

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  13. Content type: Research

    Glycoside hydrolase (GH) family 48 is an understudied and increasingly important exoglucanase family found in the majority of bacterial cellulase systems. Moreover, many thermophilic enzyme systems contain GH4...

    Authors: Roman Brunecky, Markus Alahuhta, Deanne W. Sammond, Qi Xu, Mo Chen, David B. Wilson, John W. Brady, Michael E. Himmel, Yannick J. Bomble and Vladimir V. Lunin

    Citation: Biotechnology for Biofuels 2017 10:274

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  14. Content type: Methodology

    Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are prominent candidate biocatalysts that, together, can enable the direct biotic conversion of lignocellulosic bioma...

    Authors: Kyle Sander, Keiji G. Asano, Deepak Bhandari, Gary J. Van Berkel, Steven D. Brown, Brian Davison and Timothy J. Tschaplinski

    Citation: Biotechnology for Biofuels 2017 10:270

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  15. Content type: Research

    Plant cell walls contribute the majority of plant biomass that can be used to produce transportation fuels. However, the complexity and variability in composition and structure of cell walls, particularly the ...

    Authors: Xiaolan Rao, Hui Shen, Sivakumar Pattathil, Michael G. Hahn, Ivana Gelineo-Albersheim, Debra Mohnen, Yunqiao Pu, Arthur J. Ragauskas, Xin Chen, Fang Chen and Richard A. Dixon

    Citation: Biotechnology for Biofuels 2017 10:266

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  16. Content type: Review

    Understanding plant cell wall cross-linking chemistry and polymeric architecture is key to the efficient utilization of biomass in all prospects from rational genetic modification to downstream chemical and bi...

    Authors: Yining Zeng, Michael E. Himmel and Shi-You Ding

    Citation: Biotechnology for Biofuels 2017 10:263

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  17. Content type: Research

    Genetic engineering has been effective in altering cell walls for biofuel production in the bioenergy crop, switchgrass (Panicum virgatum). However, regulatory issues arising from gene flow may prevent commercial...

    Authors: Chelsea R. Johnson, Reginald J. Millwood, Yuhong Tang, Jiqing Gou, Robert W. Sykes, Geoffrey B. Turner, Mark F. Davis, Yi Sang, Zeng-Yu Wang and C. Neal Stewart Jr.

    Citation: Biotechnology for Biofuels 2017 10:255

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  18. Content type: Research

    One of the major barriers to the development of lignocellulosic feedstocks is the recalcitrance of plant cell walls to deconstruction and saccharification. Recalcitrance can be reduced by targeting genes invol...

    Authors: David Macaya-Sanz, Jin‐Gui Chen, Udaya C. Kalluri, Wellington Muchero, Timothy J. Tschaplinski, Lee E. Gunter, Sandra J. Simon, Ajaya K. Biswal, Anthony C. Bryan, Raja Payyavula, Meng Xie, Yongil Yang, Jin Zhang, Debra Mohnen, Gerald A. Tuskan and Stephen P. DiFazio

    Citation: Biotechnology for Biofuels 2017 10:253

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  19. Content type: Research

    Consolidated bioprocessing (CBP) by anaerobes, such as Clostridium thermocellum, which combine enzyme production, hydrolysis, and fermentation are promising alternatives to historical economic challenges of using...

    Authors: Vanessa A. Thomas, Bryon S. Donohoe, Mi Li, Yunqiao Pu, Arthur J. Ragauskas, Rajeev Kumar, Thanh Yen Nguyen, Charles M. Cai and Charles E. Wyman

    Citation: Biotechnology for Biofuels 2017 10:252

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  20. Content type: Research

    Xylan is a major hemicellulosic component in the cell walls of higher plants especially in the secondary walls of vascular cells which are playing important roles in physiological processes and overall mechani...

    Authors: Angelo G. Peralta, Sivasankari Venkatachalam, Sydney C. Stone and Sivakumar Pattathil

    Citation: Biotechnology for Biofuels 2017 10:245

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  21. Content type: Research

    Auxiliary activity (AA) enzymes are produced by numerous bacterial and fungal species to assist in the degradation of biomass. These enzymes are abundant but have yet to be fully characterized. Here, we report...

    Authors: Nathan Kruer-Zerhusen, Markus Alahuhta, Vladimir V. Lunin, Michael E. Himmel, Yannick J. Bomble and David B. Wilson

    Citation: Biotechnology for Biofuels 2017 10:243

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  22. Content type: Research

    Hydrothermal pretreatment using liquid hot water (LHW) is capable of substantially reducing the cell wall recalcitrance of lignocellulosic biomass. It enhances the saccharification of polysaccharides, particul...

    Authors: Mi Li, Shilin Cao, Xianzhi Meng, Michael Studer, Charles E. Wyman, Arthur J. Ragauskas and Yunqiao Pu

    Citation: Biotechnology for Biofuels 2017 10:237

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  23. Content type: Research

    Efficient deconstruction and bioconversion of solids at high mass loadings is necessary to produce industrially relevant titers of biofuels from lignocellulosic biomass. To date, only a few studies have invest...

    Authors: Tobin J. Verbeke, Gabriela M. Garcia and James G. Elkins

    Citation: Biotechnology for Biofuels 2017 10:233

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  24. Content type: Research

    Genetically engineered biofuel crops, such as switchgrass (Panicum virgatum L.), that produce their own cell wall-digesting cellulase enzymes would reduce costs of cellulosic biofuel production. To date, non-bioe...

    Authors: Jonathan D. Willis, Joshua N. Grant, Mitra Mazarei, Lindsey M. Kline, Caroline S. Rempe, A. Grace Collins, Geoffrey B. Turner, Stephen R. Decker, Robert W. Sykes, Mark F. Davis, Nicole Labbe, Juan L. Jurat-Fuentes and C. Neal Stewart Jr.

    Citation: Biotechnology for Biofuels 2017 10:230

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