Experimental testing of a spatiotemporal metabolic model for carbon monoxide fermentation with Clostridium autoethanogenum

Abstract Gas fermentation is an attractive route to produce alternative fuels and chemicals from non-food feedstocks, such as waste gas streams from steel mills and synthesis gas produced from agricultural residues through gasification. An improved strain of Clostridium autoethanogenum, an acetogenic bacteria, was developed by LanzaTech and shows high potential in production of ethanol and 2,3-butanediol from industry waste gas (mainly CO/CO2) via gas fermentation. In this study, a spatiotemporal metabolic model was formulated and evaluated using steady-state CO fermentation data collected from a laboratory-scale bubble column reactor. The spatiotemporal model was comprised of a genome-scale reconstruction of Clostridium autoethanogenum metabolism and multiphase convection-dispersion equations that govern transport of CO, secreted byproducts and biomass. The model provided good agreement with measured ethanol, acetate and biomass concentrations obtained at a single gas flow rate. Then to obtain satisfactory steady-state predictions at three gas flow rates, the upper bound of the proton exchange flux in the genome-scale reconstruction was correlated with the gas flow rate as an indirect means to account for the effects of acetate secretion on extracellular pH. We believe the modeling method established by this work has strong potential to facilitate commercial-scale design of gas fermentation processes for production of biofuel and biochemicals.

[1]  Thomas Millat,et al.  Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium , 2015, BMC Genomics.

[2]  Paul Richardson,et al.  The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). , 2008, Environmental microbiology.

[3]  Paul I. Barton,et al.  DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis , 2014, BMC Bioinformatics.

[4]  Michael Köpke,et al.  Gas Fermentation for Commercial Biofuels Production , 2013 .

[5]  B. Heijstra,et al.  Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks , 2016, Front. Microbiol..

[6]  J. J. Hofmeester.  Gas hold-up measurements in bioreactors , 1988 .

[7]  Timothy J. Hanly,et al.  Dynamic flux balance modeling of microbial co‐cultures for efficient batch fermentation of glucose and xylose mixtures , 2011, Biotechnology and bioengineering.

[8]  Food vs biofuel. , 2007, Journal of the American Dietetic Association.

[9]  Abdul Rahman Mohamed,et al.  Kinetic Studies on Fermentative Production of Biofuel from Synthesis Gas Using Clostridium ljungdahlii , 2014, TheScientificWorldJournal.

[10]  Wayne Mitchell,et al.  Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia , 2014, Biotechnology for Biofuels.

[11]  L. T. Angenent,et al.  Ethanol production in syngas-fermenting Clostridium ljungdahlii is controlled by thermodynamics rather than by enzyme expression , 2016 .

[12]  A. Mohamed,et al.  Sustainable ethanol fermentation from synthesis gas by Clostridium ljungdahlii in a continuous stirred tank bioreactor , 2012 .

[13]  Mari S. Chinn,et al.  Influence of process parameters on growth of Clostridium ljungdahlii and Clostridium autoethanogenum on synthesis gas , 2009 .

[14]  Zhenhong Yuan,et al.  Medium optimization for ethanol production with Clostridium autoethanogenum with carbon monoxide as sole carbon source. , 2010, Bioresource technology.

[15]  Jason A. Papin,et al.  Metabolic pathways in the post-genome era. , 2003, Trends in biochemical sciences.

[16]  P. Dürre,et al.  Clostridium ljungdahlii represents a microbial production platform based on syngas , 2010, Proceedings of the National Academy of Sciences.

[17]  Jin Chen,et al.  Spatiotemporal modeling of microbial metabolism , 2016, BMC Systems Biology.

[18]  P. Munasinghe,et al.  Biomass-derived syngas fermentation into biofuels: Opportunities and challenges. , 2010, Bioresource technology.

[19]  D. Lovley,et al.  Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii , 2013, Microbial Cell Factories.

[20]  Paul I. Barton,et al.  Metabolic modeling of synthesis gas fermentation in bubble column reactors , 2015, Biotechnology for Biofuels.

[21]  Michael Köpke,et al.  2,3-Butanediol Production by Acetogenic Bacteria, an Alternative Route to Chemical Synthesis, Using Industrial Waste Gas , 2011, Applied and Environmental Microbiology.

[22]  Henry Naveau,et al.  Clostridium autoethanogenum, sp. nov., an anaerobic bacterium that produces ethanol from carbon monoxide , 1994, Archives of Microbiology.

[23]  A. Mohamed,et al.  Ethanol and acetate production from synthesis gas via fermentation processes using anaerobic bacterium , 2005 .

[24]  L. T. Angenent,et al.  Carbon recovery by fermentation of CO-rich off gases - Turning steel mills into biorefineries. , 2016, Bioresource technology.

[25]  E. Papoutsakis,et al.  Genome‐scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub‐systems , 2008, Biotechnology and bioengineering.

[26]  M. A. Henson,et al.  Genome‐scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed‐batch culture , 2007, Biotechnology and bioengineering.

[27]  C. Kennes,et al.  Carbon monoxide fermentation to ethanol by Clostridium autoethanogenum in a bioreactor with no accumulation of acetic acid. , 2015, Bioresource technology.

[28]  J. L. Cotter,et al.  Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells , 2009, Bioprocess and biosystems engineering.

[29]  B. Palsson,et al.  Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 , 1994, Applied and environmental microbiology.

[30]  Kiyomi Akita,et al.  Gas Holdup and Volumetric Mass Transfer Coefficient in Bubble Columns. Effects of Liquid Properties , 1973 .

[31]  Ryan S. Senger,et al.  Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico , 2012, BMC Systems Biology.

[32]  R. Worden,et al.  Reactor Design Issues for Synthesis‐Gas Fermentations , 1999, Biotechnology progress.

[33]  Geoffrey Ingram Taylor,et al.  The dispersion of matter in turbulent flow through a pipe , 1954, Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences.

[34]  Lake-Ee Quek,et al.  Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen , 2016 .

[35]  R. Mahadevan,et al.  Characterization of proton production and consumption associated with microbial metabolism , 2010, BMC biotechnology.

[36]  Sagar M. Utturkar,et al.  Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies , 2015, Scientific Data.

[37]  María Carmen Veiga,et al.  Biological conversion of carbon monoxide: rich syngas or waste gases to bioethanol , 2011 .

[38]  T. Heindel,et al.  Carbon Monoxide Mass Transfer for Syngas Fermentation in a Stirred Tank Reactor with Dual Impeller Configurations , 2008, Biotechnology progress.

[39]  Karsten Zengler,et al.  Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model. , 2015, Integrative biology : quantitative biosciences from nano to macro.

[40]  P. Dürre,et al.  C1-carbon sources for chemical and fuel production by microbial gas fermentation. , 2015, Current opinion in biotechnology.

[41]  F. Doyle,et al.  Dynamic flux balance analysis of diauxic growth in Escherichia coli. , 2002, Biophysical journal.

[42]  Michael A Henson,et al.  In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation. , 2016, Metabolic engineering.