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Roni MS, Lin Y, Hartley DS, Thompson DN, Hoover AN, Emerson RM. Importance of incorporating spatial and temporal variability of biomass yield and quality in bioenergy supply chain. Sci Rep 2023; 13:6813. [PMID: 37100831 PMCID: PMC10133216 DOI: 10.1038/s41598-023-28671-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 01/23/2023] [Indexed: 04/28/2023] Open
Abstract
Biofuels made from biomass and waste residues will largely contribute to United States' 2050 decarbonization goal in the aviation sector. While cellulosic biofuels have the potential fuel performance equivalent to petroleum-based jet fuel, the biofuel industry needs to overcome the supply chain barrier caused by temporal and spatial variability of biomass yield and quality. This study highlights the importance of incorporating spatial and temporal variability during biomass supply chain planning via optimization modeling that incorporates 10 years of drought index data, a primary factor contributing to yield and quality variability. The results imply that the cost of delivering biomass to biorefinery may be significantly underestimated if the multi-year temporal and spatial variation in biomass yield and quality is not captured. For long term sustainable biorefinery operations, the industry should optimize supply chain strategy by studying the variability of yield and quality of biomass in their supply sheds.
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Affiliation(s)
- Mohammad S Roni
- System Science & Engineering Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Yingqian Lin
- System Science & Engineering Department, Idaho National Laboratory, Idaho Falls, ID, USA.
| | - Damon S Hartley
- System Science & Engineering Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - David N Thompson
- Biomass Characterization Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Amber N Hoover
- Biomass Characterization Department, Idaho National Laboratory, Idaho Falls, ID, USA
| | - Rachel M Emerson
- Biomass Characterization Department, Idaho National Laboratory, Idaho Falls, ID, USA
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Badhan A, Low KE, Jones DR, Xing X, Milani MRM, Polo RO, Klassen L, Venketachalam S, Hahn MG, Abbott DW, McAllister TA. Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses. Comput Struct Biotechnol J 2022; 20:148-164. [PMID: 34976318 PMCID: PMC8702857 DOI: 10.1016/j.csbj.2021.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
There is a knowledge gap regarding the factors that impede the ruminal digestion of plant cell walls or if rumen microbiota possess the functional activities to overcome these constraints. Innovative experimental methods were adopted to provide a high-resolution understanding of plant cell wall chemistries, identify higher-order structures that resist microbial digestion, and determine how they interact with the functional activities of the rumen microbiota. We characterized the total tract indigestible residue (TTIR) from cattle fed a low-quality straw diet using two comparative glycomic approaches: ELISA-based glycome profiling and total cell wall glycosidic linkage analysis. We successfully detected numerous and diverse cell wall glycan epitopes in barley straw (BS) and TTIR and determined their relative abundance pre- and post-total tract digestion. Of these, xyloglucans and heteroxylans were of higher abundance in TTIR. To determine if the rumen microbiota can further saccharify the residual plant polysaccharides within TTIR, rumen microbiota from cattle fed a diet containing BS were incubated with BS and TTIR ex vivo in batch cultures. Transcripts coding for carbohydrate-active enzymes (CAZymes) were identified and characterized for their contribution to cell wall digestion based on glycomic analyses, comparative gene expression profiles, and associated CAZyme families. High-resolution phylogenetic fingerprinting of these sequences encoded CAZymes with activities predicted to cleave the primary linkages within heteroxylan and arabinan. This experimental platform provides unprecedented precision in the understanding of forage structure and digestibility, which can be extended to other feed-host systems and inform next-generation solutions to improve the performance of ruminants fed low-quality forages.
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Key Words
- AB, arabinan
- ADF, acid detergent fibre
- AG, arabinogalactan
- AGP, arabinogalactan protein
- AIR, alcohol insoluble residue
- AO, ammonium oxalate
- AX, arabinoxylan
- BS, barley straw
- CAZyme, carbohydrate active enzyme
- CAZymes
- CE, carbohydrate esterase
- CH, chlorite
- DE, differentially expressed
- Dietary polysaccharides
- Differential gene expression
- ELISA, enzyme-linked immunosorbent assay
- FID, flame ionization detection GC, gas chromatography
- GH, glycosyl hydrolase
- Glycome profiling
- Glycoside hydrolase
- HG, homogalacturonan
- HPAEC-PAD, high performance anion exchange chromatography coupled with pulsed amperometric detection
- HX, heteroxylan
- Linkage analysis
- MS, mass spectrometry
- NDF, neutral detergent fibre
- Nutrient utilization
- PC, post-chlorite
- PL, polysaccharide lyase
- RG, rhamnogalacturonan
- Rumen microbiome
- SC, sodium carbonate
- TTIR, total tract indigestible residue
- Transcriptome
- XG, xyloglucan
- mAbs, monoclonal antibodies
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Affiliation(s)
- Ajay Badhan
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Kristin E Low
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Darryl R Jones
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Xiaohui Xing
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Mohammad Raza Marami Milani
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Rodrigo Ortega Polo
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Leeann Klassen
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Sivasankari Venketachalam
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
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ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content. Proc Natl Acad Sci U S A 2020; 117:3281-3290. [PMID: 31974310 PMCID: PMC7022211 DOI: 10.1073/pnas.1914422117] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
There is considerable interest in engineering plant cell wall components, particularly lignin, to improve forage quality and biomass properties for processing to fuels and bioproducts. However, modifying lignin content and/or composition in transgenic plants through down-regulation of lignin biosynthetic enzymes can induce expression of defense response genes in the absence of biotic or abiotic stress. Arabidopsis thaliana lines with altered lignin through down-regulation of hydroxycinnamoyl CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) or loss of function of cinnamoyl CoA reductase 1 (CCR1) express a suite of pathogenesis-related (PR) protein genes. The plants also exhibit extensive cell wall remodeling associated with induction of multiple cell wall-degrading enzymes, a process which renders the corresponding biomass a substrate for growth of the cellulolytic thermophile Caldicellulosiruptor bescii lacking a functional pectinase gene cluster. The cell wall remodeling also results in the release of size- and charge-heterogeneous pectic oligosaccharide elicitors of PR gene expression. Genetic analysis shows that both in planta PR gene expression and release of elicitors are the result of ectopic expression in xylem of the gene ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1), which is normally expressed during anther and silique dehiscence. These data highlight the importance of pectin in cell wall integrity and the value of lignin modification as a tool to interrogate the informational content of plant cell walls.
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Pattathil S, Ingwers MW, Aubrey DP, Li Z, Dahlen J. A quantitative method for analyzing glycome profiles of plant cell walls. Carbohydr Res 2017; 448:128-135. [DOI: 10.1016/j.carres.2017.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/16/2017] [Accepted: 06/16/2017] [Indexed: 10/19/2022]
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Johnson CM, Subramanian A, Pattathil S, Correll MJ, Kiss JZ. Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight. AMERICAN JOURNAL OF BOTANY 2017; 104:1219-1231. [PMID: 28827451 PMCID: PMC5821596 DOI: 10.3732/ajb.1700079] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/16/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Plants will play an important role in the future of space exploration as part of bioregenerative life support. Thus, it is important to understand the effects of microgravity and spaceflight on gene expression in plant development. METHODS We analyzed the transcriptome of Arabidopsis thaliana using the Biological Research in Canisters (BRIC) hardware during Space Shuttle mission STS-131. The bioinformatics methods used included RMA (robust multi-array average), MAS5 (Microarray Suite 5.0), and PLIER (probe logarithmic intensity error estimation). Glycome profiling was used to analyze cell wall composition in the samples. In addition, our results were compared to those of two other groups using the same hardware on the same mission (BRIC-16). KEY RESULTS In our BRIC-16 experiments, we noted expression changes in genes involved in hypoxia and heat shock responses, DNA repair, and cell wall structure between spaceflight samples compared to the ground controls. In addition, glycome profiling supported our expression analyses in that there was a difference in cell wall components between ground control and spaceflight-grown plants. Comparing our studies to those of the other BRIC-16 experiments demonstrated that, even with the same hardware and similar biological materials, differences in results in gene expression were found among these spaceflight experiments. CONCLUSIONS A common theme from our BRIC-16 space experiments and those of the other two groups was the downregulation of water stress response genes in spaceflight. In addition, all three studies found differential regulation of genes associated with cell wall remodeling and stress responses between spaceflight-grown and ground control plants.
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Affiliation(s)
- Christina M. Johnson
- Miami University, Department of Biology 212 Pearson Hall, Oxford, Ohio 45056 USA
| | - Aswati Subramanian
- Miami University, Department of Biology 212 Pearson Hall, Oxford, Ohio 45056 USA
| | - Sivakumar Pattathil
- University of Georgia Complex Carbohydrate Research Center, 315 Riverbend Road, Athens, Georgia 30602 USA
- Mascoma, LLC (Lallemand Inc.) 67 Etna Road Lebanon, New Hampshire 03766 USA
| | - Melanie J. Correll
- University of Florida, Department of Agricultural and Biological Engineering 209 Frazier Rogers Hall, Gainesville, Florida 32611 USA
| | - John Z. Kiss
- University of North Carolina at Greensboro, Department of Biology, Greensboro, North Carolina 27412 USA
- Author for correspondence ()
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