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Title: Designer synthetic media for studying microbial-catalyzed biofuel production

Abstract

Background: The fermentation inhibition of yeast or bacteria by lignocellulose-derived degradation products, during hexose/pentose co-fermentation, is a major bottleneck for cost-effective lignocellulosic biorefineries. To engineer microbial strains for improved performance, it is critical to understand the mechanisms of inhibition that affect fermentative organisms in the presence of major components of a lignocellulosic hydrolysate. The development of a synthetic lignocellulosic hydrolysate (SH) media with a composition similar to the actual biomass hydrolysate will be an important advancement to facilitate these studies. In this work, we characterized the nutrients and plant-derived decomposition products present in AFEX™ pretreated corn stover hydrolysate (ACH). The SH was formulated based on the ACH composition and was further used to evaluate the inhibitory effects of various families of decomposition products during Saccharomyces cerevisiae 424A (LNH-ST) fermentation. Results: The ACH contained high levels of nitrogenous compounds, notably amides, pyrazines, and imidazoles. In contrast, a relatively low content of furans and aromatic and aliphatic acids were found in the ACH. Though most of the families of decomposition products were inhibitory to xylose fermentation, due to their abundance, the nitrogenous compounds showed the most inhibition. From these compounds, amides (products of the ammonolysis reaction) contributed the most to the reductionmore » of the fermentation performance. However, this result is associated to a concentration effect, as the corresponding carboxylic acids (products of hydrolysis) promoted greater inhibition when present at the same molar concentration as the amides. Due to its complexity, the formulated SH did not perfectly match the fermentation profile of the actual hydrolysate, especially the growth curve. However, the SH formulation was effective for studying the inhibitory effect of various compounds on yeast fermentation. Conclusions: The formulation of SHs is an important advancement for future multi-omics studies and for better understanding the mechanisms of fermentation inhibition in lignocellulosic hydrolysates. The SH formulated in this work was instrumental for defining the most important inhibitors in the ACH. Major AFEX decomposition products are less inhibitory to yeast fermentation than the products of dilute acid or steam explosion pretreatments; thus, ACH is readily fermentable by yeast without any detoxification.« less

Authors:
 [1];  [2];  [2];  [3];  [4];  [2];  [5];  [2];  [2]
+ Show Author Affiliations
  1. Biogas Inst. of Ministry of Agriculture, Chengdu (China)
  2. Michigan State Univ., East Lansing, MI (United States)
  3. Michigan State Univ., East Lansing, MI (United States); State Univ. of New Jersey, Piscataway, NJ (United States)
  4. Baylor Univ., Waco, TX (United States)
  5. Sichuan Univ., Chengdu (China)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE Great Lakes Bioenergy Research Center (GLBRC); Foundation for Science and Technology, London, (United Kingdom); Chinese Scholarship Council
OSTI Identifier:
1204436
Grant/Contract Number:  
FC02-07ER64494; SFRH/BD/62517/2009; 2009101936
Resource Type:
Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; Synthetic hydrolysate; Lignocellulose; AFEX; Yeast fermentation inhibition; Amides inhibition; Carboxylic acids inhibition; Pretreatment decomposition products; Hydrolysate composition

Citation Formats

Tang, Xiaoyu, da Costa Sousa, Leonardo, Jin, Mingjie, Chundawat, Shishir, Chambliss, Charles, Lau, Ming W, Xiao, Zeyi, Dale, Bruce E, and Balan, Venkatesh. Designer synthetic media for studying microbial-catalyzed biofuel production. United States: N. p., 2015. Web. doi:10.1186/s13068-014-0179-6.
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Tang, Xiaoyu, da Costa Sousa, Leonardo, Jin, Mingjie, Chundawat, Shishir, Chambliss, Charles, Lau, Ming W, Xiao, Zeyi, Dale, Bruce E, & Balan, Venkatesh. Designer synthetic media for studying microbial-catalyzed biofuel production. United States. https://doi.org/10.1186/s13068-014-0179-6
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Tang, Xiaoyu, da Costa Sousa, Leonardo, Jin, Mingjie, Chundawat, Shishir, Chambliss, Charles, Lau, Ming W, Xiao, Zeyi, Dale, Bruce E, and Balan, Venkatesh. Thu . "Designer synthetic media for studying microbial-catalyzed biofuel production". United States. https://doi.org/10.1186/s13068-014-0179-6. https://www.osti.gov/servlets/purl/1204436.
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@article{osti_1204436,
title = {Designer synthetic media for studying microbial-catalyzed biofuel production},
author = {Tang, Xiaoyu and da Costa Sousa, Leonardo and Jin, Mingjie and Chundawat, Shishir and Chambliss, Charles and Lau, Ming W and Xiao, Zeyi and Dale, Bruce E and Balan, Venkatesh},
abstractNote = {Background: The fermentation inhibition of yeast or bacteria by lignocellulose-derived degradation products, during hexose/pentose co-fermentation, is a major bottleneck for cost-effective lignocellulosic biorefineries. To engineer microbial strains for improved performance, it is critical to understand the mechanisms of inhibition that affect fermentative organisms in the presence of major components of a lignocellulosic hydrolysate. The development of a synthetic lignocellulosic hydrolysate (SH) media with a composition similar to the actual biomass hydrolysate will be an important advancement to facilitate these studies. In this work, we characterized the nutrients and plant-derived decomposition products present in AFEX™ pretreated corn stover hydrolysate (ACH). The SH was formulated based on the ACH composition and was further used to evaluate the inhibitory effects of various families of decomposition products during Saccharomyces cerevisiae 424A (LNH-ST) fermentation. Results: The ACH contained high levels of nitrogenous compounds, notably amides, pyrazines, and imidazoles. In contrast, a relatively low content of furans and aromatic and aliphatic acids were found in the ACH. Though most of the families of decomposition products were inhibitory to xylose fermentation, due to their abundance, the nitrogenous compounds showed the most inhibition. From these compounds, amides (products of the ammonolysis reaction) contributed the most to the reduction of the fermentation performance. However, this result is associated to a concentration effect, as the corresponding carboxylic acids (products of hydrolysis) promoted greater inhibition when present at the same molar concentration as the amides. Due to its complexity, the formulated SH did not perfectly match the fermentation profile of the actual hydrolysate, especially the growth curve. However, the SH formulation was effective for studying the inhibitory effect of various compounds on yeast fermentation. Conclusions: The formulation of SHs is an important advancement for future multi-omics studies and for better understanding the mechanisms of fermentation inhibition in lignocellulosic hydrolysates. The SH formulated in this work was instrumental for defining the most important inhibitors in the ACH. Major AFEX decomposition products are less inhibitory to yeast fermentation than the products of dilute acid or steam explosion pretreatments; thus, ACH is readily fermentable by yeast without any detoxification.},
doi = {10.1186/s13068-014-0179-6},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 8,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2015},
month = {Thu Jan 01 00:00:00 EST 2015}
}
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Journal Article:
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https://doi.org/10.1186/s13068-014-0179-6
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    • DOI: 10.1186/s13068-017-0995-6

    Development of a cooperative two-factor adaptive-evolution method to enhance lipid production and prevent lipid peroxidation in Schizochytrium sp.
    journal, March 2018

    Ethanol production potential from AFEX™ and steam-exploded sugarcane residues for sugarcane biorefineries
    journal, May 2018

    • Mokomele, Thapelo; da Costa Sousa, Leonardo; Balan, Venkatesh
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-018-1130-z

    A synthetic medium to simulate sugarcane molasses
    journal, August 2018

    • Lino, Felipe Senne de Oliveira; Basso, Thiago Olitta; Sommer, Morten Otto Alexander
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-018-1221-x

    Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation
    journal, October 2018

    Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains
    journal, March 2019

    Effective continuous acetone–butanol–ethanol production with full utilization of cassava by immobilized symbiotic TSH06
    journal, September 2019

    Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica
    journal, January 2017

    • Vásquez-Mayorga, Marcela; Fuchs, Eric J.; Hernández, Eduardo J.
    • PeerJ, Vol. 5
    • DOI: 10.7717/peerj.2931

    High-efficient n-butanol production by co-culturing Clostridium acetobutylicum and Saccharomyces cerevisiae integrated with butyrate fermentative supernatant addition
    journal, March 2017

    • Luo, Hongzhen; Zeng, Qingwei; Han, Shuo
    • World Journal of Microbiology and Biotechnology, Vol. 33, Issue 4
    • DOI: 10.1007/s11274-017-2246-1

    Notes for genera: Ascomycota
    journal, September 2017

    • Wijayawardene, Nalin N.; Hyde, Kevin D.; Rajeshkumar, Kunhiraman C.
    • Fungal Diversity, Vol. 86, Issue 1
    • DOI: 10.1007/s13225-017-0386-0

    Characterization of a novel bioflocculant from a marine bacterium and its application in dye wastewater treatment
    journal, November 2017

    Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei
    journal, June 2016

    • Bischof, Robert H.; Ramoni, Jonas; Seiboth, Bernhard
    • Microbial Cell Factories, Vol. 15, Issue 1
    • DOI: 10.1186/s12934-016-0507-6

    Effective isopropanol–butanol (IB) fermentation with high butanol content using a newly isolated Clostridium sp. A1424
    journal, October 2016

    The transcription factor TpRfx1 is an essential regulator of amylase and cellulase gene expression in Talaromyces pinophilus
    journal, October 2018

    Expression of benzoyl-CoA metabolism genes in the lignocellulolytic host Caldicellulosiruptor bescii
    journal, May 2019

    Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica
    posted_content, January 2017

    Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model
    journal, November 2019

    Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa
    journal, February 2020

    Influence of electron beam irradiation on water-saturated biodiesel
    journal, August 2018

    • Grabowski, Paweł; Jarosiński, Przemysław; Szajerski, Piotr
    • Journal of Radioanalytical and Nuclear Chemistry, Vol. 318, Issue 2
    • DOI: 10.1007/s10967-018-6153-1

    Insight into thermophiles and their wide-spectrum applications
    journal, February 2016

    Cellulase production using natural medium and its application on enzymatic hydrolysis of thermo chemically pretreated biomass
    journal, June 2016

    Pilot-scale production of xylo-oligosaccharides and fermentable sugars from Miscanthus using steam explosion pretreatment
    journal, January 2020

    Design, analysis and application of synthetic microbial consortia
    journal, June 2016

    In vitro reconstitution guide for targeted synthetic metabolism of chemicals, nutraceuticals and drug precursors
    journal, March 2016

    Towards improved butanol production through targeted genetic modification of Clostridium pasteurianum
    journal, March 2017

    Periphyton effects on bacterial assemblages and harmful cyanobacterial blooms in a eutrophic freshwater lake: a mesocosm study
    journal, August 2017

    A novel 3-hydroxypropionic acid-inducible promoter regulated by the LysR-type transcriptional activator protein MmsR of Pseudomonas denitrificans
    journal, March 2019

    Seed protein content and its relationships with agronomic traits in pigeonpea is controlled by both main and epistatic effects QTLs
    journal, January 2020

    Metabolic engineering of a synergistic pathway for n-butanol production in Saccharomyces cerevisiae
    journal, May 2016

    • Shi, Shuobo; Si, Tong; Liu, Zihe
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep25675

    Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors
    journal, June 2016

    • Kougias, Panagiotis G.; Treu, Laura; Campanaro, Stefano
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep28810

    Modification of Monolignol Biosynthetic Pathway in Jute: Different Gene, Different Consequence
    journal, January 2017

    • Shafrin, Farhana; Ferdous, Ahlan Sabah; Sarkar, Suprovath Kumar
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/srep39984

    Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas
    journal, January 2017

    • Sun, Yanwei; Wang, Chunming; Wang, Ning
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/srep40844

    The draft genome ofRuellia speciosa(Beautiful Wild Petunia: Acanthaceae)
    journal, January 2017

    Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation
    journal, June 2017

    • Jansen, Mickel L. A.; Bracher, Jasmine M.; Papapetridis, Ioannis
    • FEMS Yeast Research, Vol. 17, Issue 5
    • DOI: 10.1093/femsyr/fox044

    Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa
    journal, December 2019

    • Waters, Joshua C.; Jhaveri, Deval; Biffinger, Justin C.
    • PLOS ONE
    • DOI: 10.1101/736470

    Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation
    journal, August 2019

    • Daly, Paul; Peng, Mao; Mitchell, Hugh D.
    • Environmental Microbiology, Vol. 22, Issue 3
    • DOI: 10.1111/1462-2920.14907

    The effect of the algal microbiome on industrial production of microalgae
    journal, July 2018

    • Lian, Jie; Wijffels, Rene H.; Smidt, Hauke
    • Microbial Biotechnology, Vol. 11, Issue 5
    • DOI: 10.1111/1751-7915.13296

    Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel)
    journal, July 2018

    • Gontikaki, E.; Potts, L. D.; Anderson, J. A.
    • Journal of Applied Microbiology, Vol. 125, Issue 4
    • DOI: 10.1111/jam.14030

    Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model
    journal, November 2019

    Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit
    journal, November 2016

    Characterization of a novel bioflocculant from a marine bacterium and its application in dye wastewater treatment
    journal, November 2017

    Cellulases and beyond: the first 70 years of the enzyme producer Trichoderma reesei
    journal, June 2016

    • Bischof, Robert H.; Ramoni, Jonas; Seiboth, Bernhard
    • Microbial Cell Factories, Vol. 15, Issue 1
    • DOI: 10.1186/s12934-016-0507-6

    Comparative assessment of fermentative capacity of different xylose-consuming yeasts
    journal, September 2017

    • Veras, Henrique César Teixeira; Parachin, Nádia Skorupa; Almeida, João Ricardo Moreira
    • Microbial Cell Factories, Vol. 16, Issue 1
    • DOI: 10.1186/s12934-017-0766-x

    Optimizing a CRISPR-Cpf1-based genome engineering system for Corynebacterium glutamicum
    journal, March 2019

    Bioflocculant production from untreated corn stover using Cellulosimicrobium cellulans L804 isolate and its application to harvesting microalgae
    journal, October 2015

    Characterization of sugarcane (Saccharum spp.) leaf senescence: implications for biofuel production
    journal, July 2016

    • Martins, Maria Thereza Bazzo; de Souza, Wagner Rodrigo; da Cunha, Bárbara Andrade Dias Brito
    • Biotechnology for Biofuels, Vol. 9, Issue 1
    • DOI: 10.1186/s13068-016-0568-0

    Diversity of fungal feruloyl esterases: updated phylogenetic classification, properties, and industrial applications
    journal, October 2016

    • Dilokpimol, Adiphol; Mäkelä, Miia R.; Aguilar-Pontes, Maria Victoria
    • Biotechnology for Biofuels, Vol. 9, Issue 1
    • DOI: 10.1186/s13068-016-0651-6

    Continuous production of biohythane from hydrothermal liquefied cornstalk biomass via two-stage high-rate anaerobic reactors
    journal, November 2016

    Metabolic engineering of Saccharomyces cerevisiae to produce a reduced viscosity oil from lignocellulose
    journal, March 2017

    • Tran, Tam N. T.; Breuer, Rebecca J.; Avanasi Narasimhan, Ragothaman
    • Biotechnology for Biofuels, Vol. 10, Issue 1
    • DOI: 10.1186/s13068-017-0751-y

    Comprehensive characterization of non-cellulosic recalcitrant cell wall carbohydrates in unhydrolyzed solids from AFEX-pretreated corn stover
    journal, March 2017

    • Gunawan, Christa; Xue, Saisi; Pattathil, Sivakumar
    • Biotechnology for Biofuels, Vol. 10, Issue 1
    • DOI: 10.1186/s13068-017-0757-5

    Insect biorefinery: a green approach for conversion of crop residues into biodiesel and protein
    journal, December 2017

    Conversion of lignocellulosic agave residues into liquid biofuels using an AFEX™-based biorefinery
    journal, January 2018

    • Flores-Gómez, Carlos A.; Escamilla Silva, Eleazar M.; Zhong, Cheng
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-017-0995-6

    Ethanol production potential from AFEX™ and steam-exploded sugarcane residues for sugarcane biorefineries
    journal, May 2018

    • Mokomele, Thapelo; da Costa Sousa, Leonardo; Balan, Venkatesh
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-018-1130-z

    Enrichment of syngas-converting mixed microbial consortia for ethanol production and thermodynamics-based design of enrichment strategies
    journal, July 2018

    • Grimalt-Alemany, Antonio; Łężyk, Mateusz; Lange, Lene
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-018-1189-6

    Microalgae for the production of lipid and carotenoids: a review with focus on stress regulation and adaptation
    journal, October 2018

    Effective continuous acetone–butanol–ethanol production with full utilization of cassava by immobilized symbiotic TSH06
    journal, September 2019

    Constraints and advances in high-solids enzymatic hydrolysis of lignocellulosic biomass: a critical review
    journal, March 2020

    • da Silva, Ayla Sant’Ana; Espinheira, Roberta Pereira; Teixeira, Ricardo Sposina Sobral
    • Biotechnology for Biofuels, Vol. 13, Issue 1
    • DOI: 10.1186/s13068-020-01697-w

    Expression of benzoyl-CoA metabolism genes in the lignocellulolytic host Caldicellulosiruptor bescii
    journal, May 2019

    Dynamic changes of nutrient composition throughout the entire life cycle of black soldier fly
    journal, August 2017

    Genome-wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.)
    journal, January 2018

    Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation
    journal, January 2017

    • Kameshwar, Ayyappa Kumar Sista; Qin, Wensheng
    • International Journal of Biological Sciences, Vol. 13, Issue 1
    • DOI: 10.7150/ijbs.17390

    Microbial communities mediating algal detritus turnover under anaerobic conditions
    posted_content, September 2016

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