Deconstruction

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GLBRC's Deconstruction Research Area

Deconstruction

GLBRC's Deconstruction Lead takes top academic slot

Located at the intersection of the U.S.’s agricultural heartland and its northern forests, the GLBRC has access to a rich diversity of raw biomass for study. The Center's Deconstruction research focuses on identifying the best combinations of enzymes, chemicals, and physical processing methods for enhancing the digestibility of specific biomass sources.

Learn about the Center's research approach

Deconstruction Leadership

Deconstruction Lead

Dale is an expert on making ethanol from cellulose, plant stalks, grass, corn cobs and other woody plant parts and has developed a patented process called ammonia fiber expansion (AFEXTM), which makes the breakdown of cellulose more efficient, thus tackling...

Deconstruction Lead

Fox's research goals are to define the structure and the reactivity of the active site diiron center, to probe the catalytic contributions of the active site protein residues and to determine the consequences of protein-protein and protein-substrate interactions on the...

Project Overview

A biofuels reactor designed to produce ethanol at Michigan State University's Biomass Conversion Research Lab (BCRL)GLBRC Deconstruction research maintains a focus on the entire biofuels production pipeline: in addition to identifying and improving natural cellulose-degrading enzymes extracted from diverse environments, researchers apply unique biomass pretreatment technologies—such as ammonia fiber expansion (AFEX™), alkaline hydrogen peroxide (AHP), and extractive ammonia (EA)—that enable conversion technologies to maximize plant biomass utilization.. Researchers also explore strategies to add value to these processes by developing co-products from materials that would otherwise be treated as waste, such as lignin. Specific deconstruction projects include:

  • Pretreatment effects on biomass, alkaline peroxide pretreatment, fuel production from alkaline-pretreated biomass
  • Optimization of enzymes for biomass conversion, discovery of natural cellulolytic microbes, identification of novel microbial enzymes, and combinatorial discovery of enzymes and proteins

Deconstruction Publications

Lateral gene transfer dynamics in the ancient bacterial genus Streptomyces

Brandon R. McDonald; Cameron R. Currie

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2017

Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces. Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.

Lignocellulosic pretreatment in a fungus-cultivating termite

Hongjie Li; Daniel J. Yelle; Chang Li; Mengyi Yang; Jing Ke; Ruijuan Zhang; Yu Liu; Na Zhu; Shiyou Liang; Xiaochang Mo; John Ralph; Cameron R. Currie; Jianchu Mo

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2017

Depolymerizing lignin, the complex phenolic polymer fortifying plant cell walls, is an essential but challenging starting point for the lignocellulosics industries. The variety of ether– and carbon–carbon interunit linkages produced via radical coupling during lignification limit chemical and biological depolymerization efficiency. In an ancient fungus-cultivating termite system, we reveal unprecedentedly rapid lignin depolymerization and degradation by combining laboratory feeding experiments, lignocellulosic compositional measurements, electron microscopy, 2D-NMR, and thermochemolysis. In a gut transit time of under 3.5 h, in young worker termites, poplar lignin sidechains are extensively cleaved and the polymer is significantly depleted, leaving a residue almost completely devoid of various condensed units that are traditionally recognized to be the most recalcitrant. Subsequently, the fungus-comb microbiome preferentially uses xylose and cleaves polysaccharides, thus facilitating final utilization of easily digestible oligosaccharides by old worker termites. This complementary symbiotic pretreatment process in the fungus-growing termite symbiosis reveals a previously unappreciated natural system for efficient lignocellulose degradation.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

Erin A. Gontang; Frank O. Aylward; Camila Carlos; Tijana Glavina del Rio; Mansi Chovatia; Alison Fern; Chien-Chi Lo; Stephanie A. Malfatti; Susannah G. Tringe; Cameron R. Currie; Roberto Kolter

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2017

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach’s food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

Mining the isotopic complexity of nitrous oxide: a review of challenges and opportunities

Nathaniel E. Ostrom; Peggy H. Ostrom

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2017

Nitrous oxide (N2O) is an important focus of international greenhouse gas accounting agreements and mitigation of emissions will likely depend on understanding the mechanisms of its formation and reduction. Consequently, applications of stable isotope techniques to understand N2O cycling are proliferating and recent advances in technology are enabling (1) increases in the frequency of isotope analyses and (2) analyses not previously possible. The two isotopes of N and 3 isotopes of O combine to form a total of 12 possible isotopic molecules of N2O. Consequently, this remarkably simple molecule contains a wealth of isotopic information in the form of bulk (δ15N, δ18O), position dependent (site preference), mass independent (Δ17O) and multiply-substituted or clumped isotope compositions. With recent developments in high-mass resolution double sector instruments all 12 isotopic molecules will likely be resolved in the near future. Advances in spectroscopic instruments hold the promise of substantial increases in sample throughput; however, spectroscopic analyses require corrections due to interferences from other gases and frequent and accurate calibration. Mass spectrometric approaches require mass overlap corrections that are not uniform between research groups and interlaboratory comparisons remain imprecise. The continued lack of attention to calibration by both funding agencies and investigators can only perpetuate disagreement between laboratories in reported isotope values for N2O that, in turn, will compromise global assessments of N2O sources and sinks based on isotope ratios. This review discusses the challenges and opportunities offered by the isotopic complexity of N2O.

Shotgun approach to increasing enzymatic saccharification yields of ammonia fiber expansion pretreated cellulosic biomass

Shishir P.S. Chundawat; Nirmal Uppugundla; Dahai Gao; Paul G. Curran; Venkatesh Balan; Bruce E. Dale

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2017

Most cellulolytic enzyme blends, either procured from a commercial vendor or isolated from a single cellulolytic microbial secretome, do not efficiently hydrolyze ammonia-pretreated (e.g., ammonia fiber expansion or AFEX) lignocellulosic agricultural crop residues like corn stover to fermentable sugars. Typically reported commercial enzyme loading (30-100 mg protein/g glucan) necessary to achieve >90% total hydrolysis yield (to monosaccharides) for AFEX treated biomass, within a short saccharification time frame (24-48 h), is economically unviable. Unlike acid based pretreatments, AFEX retains most of the hemicelluloses in the biomass and therefore requires a more complex suite of enzymes for efficient hydrolysis of cellulose and hemicellulose at industrially relevant high solids loadings. One strategy to reduce enzyme dosage while improving cocktail effectiveness for AFEX treated biomass has been to use individually purified enzymes to determine optimal enzyme combinations to maximize hydrolysis yields. However, this approach is limited by the selection of heterologous enzymes available or the labor required for isolating low abundance enzymes directly from the microbial secretomes. Here, we show that directly blending crude cellulolytic and hemicellulolytic enzymes-rich microbial secretomes can maximize specific activity on AFEX treated biomass without having to isolate individual enzymes. Fourteen commercially available cellulolytic and hemicellulolytic enzymes were procured from leading enzyme companies (Novozymes®, Genencor®, and Biocatalysts®) and were mixed together to generate several hundred unique cocktail combinations. The mixtures were assayed for activity on AFEX treated corn stover (AFEX-CS) using a previously established high-throughput methodology. The optimal enzyme blend combinations identified from these screening assays were enriched in various low abundance hemicellulases and accessory enzymes typically absent in most commercial cellulases cocktails. Our simple approach of blending crude commercially available enzyme cocktails allowed a drastic four-fold reduction in total enzyme requirements (from 30 to 7.5 mg enzyme/g glucan loading) to achieve near-theoretical cellulose and hemicellulose saccharification yields for AFEX treated corn stover.

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