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Shrestha S, Goswami S, Banerjee D, Garcia V, Zhou E, Olmsted CN, Majumder ELW, Kumar D, Awasthi D, Mukhopadhyay A, Singer SW, Gladden JM, Simmons BA, Choudhary H. Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries. CHEMSUSCHEM 2024:e202301460. [PMID: 38669480 DOI: 10.1002/cssc.202301460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/14/2024] [Indexed: 04/28/2024]
Abstract
The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Environmental Health and Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Shubhasish Goswami
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Valentina Garcia
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Elizabeth Zhou
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
| | - Charles N Olmsted
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Biomanufacturing and Biomaterials, Sandia National Laboratories, Livermore, CA 94550, United States
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA 94608, United States
- Department of Bioresource and Environmental Security, Sandia National Laboratories, Livermore, CA 94550, United States
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2
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Leggieri PA, Blair EM, Lankiewicz TS, O'Malley MA. Continuous culture of anaerobic fungi enables growth and metabolic flux tuning without use of genetic tools. BIORESOURCE TECHNOLOGY 2024; 391:129854. [PMID: 37863334 DOI: 10.1016/j.biortech.2023.129854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/14/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023]
Abstract
Anaerobic gut fungi (AGF) have potential to valorize lignocellulosic biomass owing to their diverse repertoire of carbohydrate-active enzymes (CAZymes). However, AGF metabolism is poorly understood, and no stable genetic tools are available to manipulate growth and metabolic flux to enhance production of specific targets, e.g., cells, CAZymes, or metabolites. Herein, a cost-effective, Arduino-based, continuous-flow anaerobic bioreactor with online optical density control is presented to probe metabolism and predictably tune fluxes in Caecomyces churrovis. Varying the C. churrovis turbidostat setpoint titer reliably controlled growth rate (from 0.04 to 0.20 h-1), metabolic flux, and production rates of acetate, formate, lactate, and ethanol. Bioreactor setpoints to maximize production of each product were identified, and all continuous production rates significantly exceed batch rates. Formate spike-ins increased lactate flux and decreased acetate, ethanol, and formate fluxes. The bioreactor and turbidostat culture schemes demonstrated here offer tools to tailor AGF fermentations to application-specific hydrolysate product profiles.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Elaina M Blair
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Thomas S Lankiewicz
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA; Biological Engineering Program, University of California, Santa Barbara, CA 93106, USA.
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3
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Heom KA, Wangsanuwat C, Butkovich LV, Tam SC, Rowe AR, O'Malley MA, Dey SS. Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures. mSystems 2023; 8:e0028123. [PMID: 37855606 PMCID: PMC10734481 DOI: 10.1128/msystems.00281-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE Microbes present one of the most diverse sources of biochemistry in nature, and mRNA sequencing provides a comprehensive view of this biological activity by quantitatively measuring microbial transcriptomes. However, efficient mRNA capture for sequencing presents significant challenges in prokaryotes as mRNAs are not poly-adenylated and typically make up less than 5% of total RNA compared with rRNAs that exceed 80%. Recently developed methods for sequencing bacterial mRNA typically rely on depleting rRNA by tiling large probe sets against rRNAs; however, such approaches are expensive, time-consuming, and challenging to scale to varied bacterial species and complex microbial communities. Therefore, we developed EMBR-seq+, a method that requires fewer than 10 short oligonucleotides per rRNA to achieve up to 99% rRNA depletion in diverse bacterial species. Finally, EMBR-seq+ resulted in a deeper view of the transcriptome, enabling systematic quantification of how microbial interactions result in altering the transcriptional state of bacteria within co-cultures.
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Affiliation(s)
- Kellie A. Heom
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Chatarin Wangsanuwat
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Lazarina V. Butkovich
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Scott C. Tam
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
| | - Annette R. Rowe
- Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
| | - Siddharth S. Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, USA
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4
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Lankiewicz TS, Choudhary H, Gao Y, Amer B, Lillington SP, Leggieri PA, Brown JL, Swift CL, Lipzen A, Na H, Amirebrahimi M, Theodorou MK, Baidoo EEK, Barry K, Grigoriev IV, Timokhin VI, Gladden J, Singh S, Mortimer JC, Ralph J, Simmons BA, Singer SW, O'Malley MA. Lignin deconstruction by anaerobic fungi. Nat Microbiol 2023; 8:596-610. [PMID: 36894634 PMCID: PMC10066034 DOI: 10.1038/s41564-023-01336-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 01/31/2023] [Indexed: 03/11/2023]
Abstract
Lignocellulose forms plant cell walls, and its three constituent polymers, cellulose, hemicellulose and lignin, represent the largest renewable organic carbon pool in the terrestrial biosphere. Insights into biological lignocellulose deconstruction inform understandings of global carbon sequestration dynamics and provide inspiration for biotechnologies seeking to address the current climate crisis by producing renewable chemicals from plant biomass. Organisms in diverse environments disassemble lignocellulose, and carbohydrate degradation processes are well defined, but biological lignin deconstruction is described only in aerobic systems. It is currently unclear whether anaerobic lignin deconstruction is impossible because of biochemical constraints or, alternatively, has not yet been measured. We applied whole cell-wall nuclear magnetic resonance, gel-permeation chromatography and transcriptome sequencing to interrogate the apparent paradox that anaerobic fungi (Neocallimastigomycetes), well-documented lignocellulose degradation specialists, are unable to modify lignin. We find that Neocallimastigomycetes anaerobically break chemical bonds in grass and hardwood lignins, and we further associate upregulated gene products with the observed lignocellulose deconstruction. These findings alter perceptions of lignin deconstruction by anaerobes and provide opportunities to advance decarbonization biotechnologies that depend on depolymerizing lignocellulose.
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Affiliation(s)
- Thomas S Lankiewicz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Hemant Choudhary
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Yu Gao
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bashar Amer
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Stephen P Lillington
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Patrick A Leggieri
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hyunsoo Na
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mojgan Amirebrahimi
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael K Theodorou
- Department of Agriculture and Environment, Harper Adams University, Newport, UK
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - John Gladden
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Seema Singh
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Biomaterials and Biomanufacturing, Sandia National Laboratories, Livermore, CA, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - John Ralph
- Great Lakes Bioenergy Research Center, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin Madison, Madison, WI, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
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5
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Hooker CA, Hanafy R, Hillman ET, Muñoz Briones J, Solomon KV. A Genetic Engineering Toolbox for the Lignocellulolytic Anaerobic Gut Fungus Neocallimastix frontalis. ACS Synth Biol 2023; 12:1034-1045. [PMID: 36920337 DOI: 10.1021/acssynbio.2c00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Anaerobic fungi are powerful platforms for biotechnology that remain unexploited due to a lack of genetic tools. These gut fungi encode the largest number of lignocellulolytic carbohydrate active enzymes (CAZymes) in the fungal kingdom, making them attractive for applications in renewable energy and sustainability. However, efforts to genetically modify anaerobic fungi have remained limited due to inefficient methods for DNA uptake and a lack of characterized genetic parts. We demonstrate that anaerobic fungi are naturally competent for DNA and leverage this to develop a nascent genetic toolbox informed by recently acquired genomes for transient transformation of anaerobic fungi. We validate multiple selectable markers (HygR and Neo), an anaerobic reporter protein (iRFP702), enolase and TEF1A promoters, TEF1A terminator, and a nuclear localization tag for protein compartmentalization. This work establishes novel methods to reliably transform the anaerobic fungus Neocallimastix frontalis, thereby paving the way for strain development and various synthetic biology applications.
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Affiliation(s)
- Casey A Hooker
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Radwa Hanafy
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Ethan T Hillman
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Javier Muñoz Briones
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kevin V Solomon
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
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6
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Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability. Mater Today Bio 2023; 19:100560. [PMID: 36756210 PMCID: PMC9900623 DOI: 10.1016/j.mtbio.2023.100560] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023] Open
Abstract
Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.
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7
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Enzyme Discovery in Anaerobic Fungi (Neocallimastigomycetes) Enables Lignocellulosic Biorefinery Innovation. Microbiol Mol Biol Rev 2022; 86:e0004122. [PMID: 35852448 PMCID: PMC9769567 DOI: 10.1128/mmbr.00041-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Lignocellulosic biorefineries require innovative solutions to realize their full potential, and the discovery of novel lignocellulose-active enzymes could improve biorefinery deconstruction processes. Enzymatic deconstruction of plant cell walls is challenging, as noncarbohydrate linkages in hemicellulosic sidechains and lignin protect labile carbohydrates from hydrolysis. Highly specialized microbes that degrade plant biomass are attractive sources of enzymes for improving lignocellulose deconstruction, and the anaerobic gut fungi (Neocallimastigomycetes) stand out as having great potential for harboring novel lignocellulose-active enzymes. We discuss the known aspects of Neocallimastigomycetes lignocellulose deconstruction, including their extensive carbohydrate-active enzyme content, proficiency at deconstructing complex lignocellulose, unique physiology, synergistic enzyme complexes, and sizeable uncharacterized gene content. Progress describing Neocallimastigomycetes and their enzymes has been rapid in recent years, and it will only continue to expand. In particular, direct manipulation of anaerobic fungal genomes, effective heterologous expression of anaerobic fungal enzymes, and the ability to directly relate chemical changes in lignocellulose to fungal gene regulation will accelerate the discovery and subsequent deployment of Neocallimastigomycetes lignocellulose-active enzymes.
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8
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Activity-based protein profiling reveals dynamic substrate-specific cellulase secretion by saprotrophic basidiomycetes. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:6. [PMID: 35418096 PMCID: PMC8764865 DOI: 10.1186/s13068-022-02107-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/06/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Fungal saccharification of lignocellulosic biomass occurs concurrently with the secretion of a diverse collection of proteins, together functioning as a catalytic system to liberate soluble sugars from insoluble composite biomaterials. How different fungi respond to different substrates is of fundamental interest to the developing biomass saccharification industry. Among the cornerstones of fungal enzyme systems are the highly expressed cellulases (endo-β-glucanases and cellobiohydrolases). Recently, a cyclophellitol-derived activity-based probe (ABP-Cel) was shown to be a highly sensitive tool for the detection and identification of cellulases.
Results
Here we show that ABP-Cel enables endo-β-glucanase profiling in diverse fungal secretomes. In combination with established ABPs for β-xylanases and β-d-glucosidases, we collected multiplexed in-gel fluorescence activity-based protein profiles of 240 secretomes collected over ten days from biological replicates of ten different basidiomycete fungi grown on maltose, wheat straw, or aspen pulp. Our results reveal the remarkable dynamics and unique enzyme fingerprints associated with each species substrate combination. Chemical proteomic analysis identifies significant arsenals of cellulases secreted by each fungal species during growth on lignocellulosic biomass. Recombinant production and characterization of a collection of probe-reactive enzymes from GH5, GH10, and GH12 confirm that ABP-Cel shows broad selectivity towards enzymes with endo-β-glucanase activity.
Conclusion
Using small-volume samples with minimal sample preparation, the results presented here demonstrate the ready accessibility of sensitive direct evidence for fungal enzyme secretion during early stages of growth on complex lignocellulosic substrates.
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9
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Brown JL, Perisin MA, Swift CL, Benyamin M, Liu S, Singan V, Zhang Y, Savage E, Pennacchio C, Grigoriev IV, O'Malley MA. Co‑cultivation of anaerobic fungi with Clostridium acetobutylicum bolsters butyrate and butanol production from cellulose and lignocellulose. J Ind Microbiol Biotechnol 2022; 49:6823545. [PMID: 36367297 PMCID: PMC9923384 DOI: 10.1093/jimb/kuac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
A system for co-cultivation of anaerobic fungi with anaerobic bacteria was established based on lactate cross-feeding to produce butyrate and butanol from plant biomass. Several co-culture formulations were assembled that consisted of anaerobic fungi (Anaeromyces robustus, Neocallimastix californiae, or Caecomyces churrovis) with the bacterium Clostridium acetobutylicum. Co-cultures were grown simultaneously (e.g., 'one pot'), and compared to cultures where bacteria were cultured in fungal hydrolysate sequentially. Fungal hydrolysis of lignocellulose resulted in 7-11 mM amounts of glucose and xylose, as well as acetate, formate, ethanol, and lactate to support clostridial growth. Under these conditions, one-stage simultaneous co-culture of anaerobic fungi with C. acetobutylicum promoted the production of butyrate up to 30 mM. Alternatively, two-stage growth slightly promoted solventogenesis and elevated butanol levels (∼4-9 mM). Transcriptional regulation in the two-stage growth condition indicated that this cultivation method may decrease the time required to reach solventogenesis and induce the expression of cellulose-degrading genes in C. acetobutylicum due to relieved carbon-catabolite repression. Overall, this study demonstrates a proof of concept for biobutanol and bio-butyrate production from lignocellulose using an anaerobic fungal-bacterial co-culture system.
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Affiliation(s)
- Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Rm 3357 Engineering II, Santa Barbara, CA 93117, USA
| | - Matthew A Perisin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Rm 3357 Engineering II, Santa Barbara, CA 93117, USA
| | - Marcus Benyamin
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Sanchao Liu
- Biological and Biotechnology Sciences Division, DEVCOM Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christa Pennacchio
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
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10
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Wei Y, Yang H, Wang Z, Zhao J, Qi H, Wang C, Zhang J, Yang T. Roughage biodegradation by natural co-cultures of rumen fungi and methanogens from Qinghai yaks. AMB Express 2022; 12:123. [PMID: 36121525 PMCID: PMC9485394 DOI: 10.1186/s13568-022-01462-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Anaerobic fungus–methanogen co-cultures from rumen liquids and faeces can degrade lignocellulose efficiently. In this study, 31 fungus–methanogen co-cultures were first obtained from the rumen of yaks grazing in Qinghai Province, China, using the Hungate roll-tube technique. The fungi were identified according to morphological characteristics and internal transcribed spacer (ITS) sequences. The methanogens associated with each fungus were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA gene sequencing. They were five co-culture types: Neocallimastix frontalis + Methanobrevibacter ruminantium, Neocallimastix frontalis + Methanobrevibacter gottschalkii, Orpinomyces joyonii + Methanobrevibacter ruminantium, Caecomyces communis + Methanobrevibacter ruminantium, and Caecomyces communis + Methanobrevibacter millerae. Among the 31 co-cultures, during the 5-day incubation, the N. frontalis + M. gottschalkii co-culture YakQH5 degraded 59.0%–68.1% of the dry matter (DM) and 49.5%–59.7% of the neutral detergent fiber (NDF) of wheat straw, corn stalk, rice straw, oat straw and sorghum straw to produce CH4 (3.0–4.6 mmol/g DM) and acetate (7.3–8.6 mmol/g DM) as end-products. Ferulic acid (FA) released at 4.8 mg/g DM on corn stalk and p-coumaric acid (PCA) released at 11.7 mg/g DM on sorghum straw showed the highest values, with the following peak values of enzyme activities: xylanase at 12,910 mU/mL on wheat straw, ferulic acid esterase (FAE) at 10.5 mU/mL on corn stalk, and p-coumaric acid esterase (CAE) at 20.5 mU/mL on sorghum straw. The N. frontalis + M. gottschalkii co-culture YakQH5 from Qinghai yaks represents a new efficient combination for lignocellulose biodegradation, performing better than previously reported fungus–methanogen co-cultures from the digestive tract of ruminants.
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Affiliation(s)
- Yaqin Wei
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China.
| | - Hui Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Zhiye Wang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Jiang Zhao
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Hongshan Qi
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Chuan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730000, People's Republic of China
| | - Jingrong Zhang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
| | - Tao Yang
- Key Laboratory of Microbial Resources Exploitation and Application of Gansu Province, Institute of Biology, Gansu Academy of Sciences, Lanzhou, 730000, People's Republic of China.,Center for Anaerobic Microbes, Institute of Biology, Gansu Academy of Sciences, No. 197 Dingxi South Road, Lanzhou, 730000, Gansu, People's Republic of China
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11
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Leggieri PA, Valentine MT, O'Malley MA. Biofilm disruption enhances growth rate and carbohydrate-active enzyme production in anaerobic fungi. BIORESOURCE TECHNOLOGY 2022; 358:127361. [PMID: 35609749 DOI: 10.1016/j.biortech.2022.127361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/07/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic gut fungi (AGF) are lignocellulose degraders that naturally form biofilms in the rumen of large herbivores and in standard culture techniques. While biofilm formation enhances biomass degradation and carbohydrate-active enzyme (CAZyme) production in some bacteria and aerobic fungi, gene expression and metabolism in AGF biofilms have not been compared to non-biofilm cultures. Here, using the tunable morphology of the non-rhizoidal AGF, Caecomyces churrovis, the impacts of biofilm formation on AGF gene expression, metabolic flux, growth rate, and xylan degradation rate are quantified to inform future industrial scale-up efforts. Contrary to previous findings, C. churrovis upregulated catabolic CAZymes in stirred culture relative to biofilm culture. Using a de novo transcriptome, 197 new transcripts with predicted CAZyme function were identified. Stirred cultures grew and degraded xylan significantly faster than biofilm-forming cultures with negligible differences in primary metabolic flux, offering a way to accelerate AGF biomass valorization without altering the fermentation product profile. The rhizoidal AGF, Neocallimastix lanati, also grew faster with stirring on a solid plant substrate, suggesting that the advantages of stirred C. churrovis cultures may apply broadly to other AGF.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Megan T Valentine
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA.
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12
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Dowd B, McDonnell D, Tuohy MG. Current Progress in Optimising Sustainable Energy Recovery From Cattle Paunch Contents, a Slaughterhouse Waste Product. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.722424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Paunch contents are the recalcitrant, lignocellulose-rich, partially-digested feed present in the rumen of ruminant animals. Cattle forage in Europe is primarily from perennial and Italian ryegrasses and/or white clover, so paunch contents from forage-fed cattle in Europe is enriched in these feedstuffs. Globally, due to its underutilisation, the potential energy in cattle paunch contents annually represents an energy loss of 23,216,548,750–27,804,250,000 Megajoules (MJ) and financial loss of up to ~€800,000,000. Therefore, this review aims to describe progress made to-date in optimising sustainable energy recovery from paunch contents. Furthermore, analyses to determine the economic feasibility/potential of recovering sustainable energy from paunch contents was carried out. The primary method used to recover sustainable energy from paunch contents to-date has involved biomethane production through anaerobic digestion (AD). The major bottleneck in its utilisation through AD is its recalcitrance, resulting in build-up of fibrous material. Pre-treatments partially degrade the lignocellulose in lignocellulose-rich wastes, reducing their recalcitrance. Enzyme systems could be inexpensive and more environmentally compatible than conventional solvent pre-treatments. A potential source of enzyme systems is the rumen microbiome, whose efficiency in lignocellulose degradation is attracting significant research interest. Therefore, the application of rumen fluid (liquid derived from dewatering of paunch contents) to improve biomethane production from AD of lignocellulosic wastes is included in this review. Analysis of a study where rumen fluid was used to pre-treat paper sludge from a paper mill prior to AD for biomethane production suggested economic feasibility for CHP combustion, with potential savings of ~€11,000 annually. Meta-genomic studies of bacterial/archaeal populations have been carried out to understand their ruminal functions. However, despite their importance in degrading lignocellulose in nature, rumen fungi remain comparatively under-investigated. Further investigation of rumen microbes, their cultivation and their enzyme systems, and the role of rumen fluid in degrading lignocellulosic wastes, could provide efficient pre-treatments and co-digestion strategies to maximise biomethane yield from a range of lignocellulosic wastes. This review describes current progress in optimising sustainable energy recovery from paunch contents, and the potential of rumen fluid as a pre-treatment and co-substrate to recover sustainable energy from lignocellulosic wastes using AD.
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13
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Bhujbal SK, Ghosh P, Vijay VK, Rathour R, Kumar M, Singh L, Kapley A. Biotechnological potential of rumen microbiota for sustainable bioconversion of lignocellulosic waste to biofuels and value-added products. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152773. [PMID: 34979222 DOI: 10.1016/j.scitotenv.2021.152773] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/05/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Lignocellulosic biomass is an abundant resource with untapped potential for biofuel, enzymes, and chemical production. Its complex recalcitrant structure obstructs its bioconversion into biofuels and other value-added products. For improving its bioconversion efficiency, it is important to deconstruct its complex structure. In natural systems like rumen, diverse microbial communities carry out hydrolysis, acidogenesis, acetogenesis, and methanogenesis of lignocellulosic biomass through physical penetration, synergistic and enzymatic actions enhancing lignocellulose degradation activity. This review article aims to discuss comprehensively the rumen microbial ecosystem, their interactions, enzyme production, and applications for efficient bioconversion of lignocellulosic waste to biofuels. Furthermore, meta 'omics' approaches to elucidate the structure and functions of rumen microorganisms, fermentation mechanisms, microbe-microbe interactions, and host-microbe interactions have been discussed thoroughly. Additionally, feed additives' role in improving ruminal fermentation efficiency and reducing environmental nitrogen losses has been discussed. Finally, the current status of rumen microbiota applications and future perspectives for the development of rumen mimic bioreactors for efficient bioconversion of lignocellulosic wastes to biofuels and chemicals have been highlighted.
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Affiliation(s)
- Sachin Krushna Bhujbal
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Pooja Ghosh
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Virendra Kumar Vijay
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Rashmi Rathour
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Manish Kumar
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Lal Singh
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
| | - Atya Kapley
- CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nagpur 440020, India
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14
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Brown JL, Swift CL, Mondo SJ, Seppala S, Salamov A, Singan V, Henrissat B, Drula E, Henske JK, Lee S, LaButti K, He G, Yan M, Barry K, Grigoriev IV, O'Malley MA. Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:234. [PMID: 34893091 PMCID: PMC8665504 DOI: 10.1186/s13068-021-02083-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/19/2021] [Indexed: 05/12/2023]
Abstract
Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal-methanogen physical associations and fungal cell wall development and remodeling.
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Affiliation(s)
- Jennifer L Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Candice L Swift
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Susanna Seppala
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vasanth Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elodie Drula
- Architecture Et Fonction Des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
- INRAE USC1408, AFMB, 13009, Marseille, France
| | - John K Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Samantha Lee
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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15
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Leggieri PA, Kerdman-Andrade C, Lankiewicz TS, Valentine MT, O’Malley MA. Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture. Microb Cell Fact 2021; 20:199. [PMID: 34663313 PMCID: PMC8522008 DOI: 10.1186/s12934-021-01684-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate species or measure species-specific attributes in most multi-species systems. Anaerobic gut fungi (AGF) (Neocallimastigomycetes) are native to the rumen of large herbivores, where they exist as minority members among a wealth of prokaryotes. AGF have significant biotechnological potential owing to their diverse repertoire of potent lignocellulose-degrading carbohydrate-active enzymes (CAZymes), which indirectly bolsters activity of other rumen microbes through metabolic exchange. While decades of literature suggest that polysaccharide degradation and AGF growth are accelerated in co-culture with prokaryotes, particularly methanogens, methods have not been available to measure concentrations of individual species in co-culture. New methods to disentangle the contributions of AGF and rumen prokaryotes are sorely needed to calculate AGF growth rates and metabolic fluxes to prove this hypothesis and understand its causality for predictable co-culture design. RESULTS We present a simple, microplate-based method to measure AGF and methanogen concentrations in co-culture based on fluorescence and absorbance spectroscopies. Using samples of < 2% of the co-culture volume, we demonstrate significant increases in AGF growth rate and xylan and glucose degradation rates in co-culture with methanogens relative to mono-culture. Further, we calculate significant differences in AGF metabolic fluxes in co-culture relative to mono-culture, namely increased flux through the energy-generating hydrogenosome organelle. While calculated fluxes highlight uncertainties in AGF primary metabolism that preclude definitive explanations for this shift, our method will enable steady-state fluxomic experiments to probe AGF metabolism in greater detail. CONCLUSIONS The method we present to measure AGF and methanogen concentrations enables direct growth measurements and calculation of metabolic fluxes in co-culture. These metrics are critical to develop a quantitative understanding of interwoven rumen metabolism, as well as the impact of co-culture on polysaccharide degradation and metabolite production. The framework presented here can inspire new methods to probe systems beyond AGF and methanogens. Simple modifications to the method will likely extend its utility to co-cultures with more than two organisms or those grown on solid substrates to facilitate the design and deployment of microbial communities for bioproduction and beyond.
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Affiliation(s)
- Patrick A. Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Corey Kerdman-Andrade
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Thomas S. Lankiewicz
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106 USA
- Joint BioEnergy Institute (JBEI), Emeryville, CA 94608 USA
| | - Megan T. Valentine
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
- Joint BioEnergy Institute (JBEI), Emeryville, CA 94608 USA
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16
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Anaerobic Fungal Mevalonate Pathway Genomic Biases Lead to Heterologous Toxicity Underpredicted by Codon Adaptation Indices. Microorganisms 2021; 9:microorganisms9091986. [PMID: 34576881 PMCID: PMC8468974 DOI: 10.3390/microorganisms9091986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/19/2022] Open
Abstract
Anaerobic fungi are emerging biotechnology platforms with genomes rich in biosynthetic potential. Yet, the heterologous expression of their biosynthetic pathways has had limited success in model hosts like E. coli. We find one reason for this is that the genome composition of anaerobic fungi like P. indianae are extremely AT-biased with a particular preference for rare and semi-rare AT-rich tRNAs in E coli, which are not explicitly predicted by standard codon adaptation indices (CAI). Native P. indianae genes with these extreme biases create drastic growth defects in E. coli (up to 69% reduction in growth), which is not seen in genes from other organisms with similar CAIs. However, codon optimization rescues growth, allowing for gene evaluation. In this manner, we demonstrate that anaerobic fungal homologs such as PI.atoB are more active than S. cerevisiae homologs in a hybrid pathway, increasing the production of mevalonate up to 2.5 g/L (more than two-fold) and reducing waste carbon to acetate by ~90% under the conditions tested. This work demonstrates the bioproduction potential of anaerobic fungal enzyme homologs and how the analysis of codon utilization enables the study of otherwise difficult to express genes that have applications in biocatalysis and natural product discovery.
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17
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Podolsky IA, Schauer EE, Seppälä S, O'Malley MA. Identification of novel membrane proteins for improved lignocellulose conversion. Curr Opin Biotechnol 2021; 73:198-204. [PMID: 34482155 DOI: 10.1016/j.copbio.2021.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 11/28/2022]
Abstract
Lignocellulose processing yields a heterogeneous mixture of substances, which are poorly utilized by current industrial strains. For efficient valorization of recalcitrant biomass, it is critical to identify and engineer new membrane proteins that enable the broad uptake of hydrolyzed substrates. Whereas glucose consumption rarely presents a bottleneck for cell factories, there is also a lack of transporters that allow co-consumption of glucose with other abundant biomass sugars such as xylose. This review discusses recent efforts to bioinformatically identify membrane proteins of high biotech potential for lignocellulose conversion and metabolic engineering in both model and nonconventional organisms. Of particular interest are transporters sourced from anaerobic gut fungi resident to large herbivores, which produce Sugars Will Eventually be Exported Transporters (SWEETs) that enhance xylose transport in the yeast Saccharomyces cerevisiae and enable glucose and xylose co-utilization. Additionally, recently identified fungal cellodextrin transporters are valuable alternatives to mitigate glucose repression and transporter inhibition.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elizabeth E Schauer
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA 94608, USA.
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18
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Swift CL, Malinov NG, Mondo SJ, Salamov A, Grigoriev IV, O'Malley MA. A Genomic Catalog of Stress Response Genes in Anaerobic Fungi for Applications in Bioproduction. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:708358. [PMID: 37744151 PMCID: PMC10512342 DOI: 10.3389/ffunb.2021.708358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 09/26/2023]
Abstract
Anaerobic fungi are a potential biotechnology platform to produce biomass-degrading enzymes. Unlike model fungi such as yeasts, stress responses that are relevant during bioprocessing have not yet been established for anaerobic fungi. In this work, we characterize both the heat shock and unfolded protein responses of four strains of anaerobic fungi (Anaeromyces robustus, Caecomyces churrovis, Neocallimastix californiae, and Piromyces finnis). The inositol-requiring 1 (Ire1) stress sensor, which typically initiates the fungal UPR, was conserved in all four genomes. However, these genomes also encode putative transmembrane kinases with catalytic domains that are similar to the metazoan stress-sensing enzyme PKR-like endoplasmic reticulum kinase (PERK), although whether they function in the UPR of anaerobic fungi remains unclear. Furthermore, we characterized the global transcriptional responses of Anaeromyces robustus and Neocallimastix californiae to a transient heat shock. Both fungi exhibited the hallmarks of ER stress, including upregulation of genes with functions in protein folding, ER-associated degradation, and intracellular protein trafficking. Relative to other fungi, the genomes of Neocallimastigomycetes contained the greatest gene percentage of HSP20 and HSP70 chaperones, which may serve to stabilize their asparagine-rich genomes. Taken together, these results delineate the unique stress response of anaerobic fungi, which is an important step toward their development as a biotechnology platform to produce enzymes and valuable biomolecules.
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Affiliation(s)
- Candice L. Swift
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nikola G. Malinov
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Michelle A. O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
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19
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Stabel M, Schweitzer T, Haack K, Gorenflo P, Aliyu H, Ochsenreither K. Isolation and Biochemical Characterization of Six Anaerobic Fungal Strains from Zoo Animal Feces. Microorganisms 2021; 9:1655. [PMID: 34442734 PMCID: PMC8399178 DOI: 10.3390/microorganisms9081655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022] Open
Abstract
Anaerobic fungi are prime candidates for the conversion of agricultural waste products to biofuels. Despite the increasing interest in these organisms, their growth requirements and metabolism remain largely unknown. The isolation of five strains of anaerobic fungi and their identification as Neocallimastix cameroonii, Caecomyces spec., Orpinomyces joyonii, Pecoramyces ruminantium, and Khoyollomyces ramosus, is described. The phylogeny supports the reassignment of Neocallimastix californiae and Neocallimastix lanati to Neocallimastix cameroonii and points towards the redesignation of Cyllamyces as a species of Caecomyces. All isolated strains including strain A252, which was described previously as Aestipascuomyces dubliciliberans, were further grown on different carbon sources and the produced metabolites were analyzed; hydrogen, acetate, formate, lactate, and succinate were the main products. Orpinomyces joyonii was lacking succinate production and Khoyollomyces ramosus was not able to produce lactate under the studied conditions. The results further suggested a sequential production of metabolites with a preference for hydrogen, acetate, and formate. By comparing fungal growth on monosaccharides or on the straw, a higher hydrogen production was noticed on the latter. Possible reactions to elevated sugar concentrations by anaerobic fungi are discussed.
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Affiliation(s)
- Marcus Stabel
- Process Engineering in Life Sciences 2: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (T.S.); (K.H.); (P.G.); (H.A.); (K.O.)
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20
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Abstract
Anaerobic fungi (Neocallimastigomycota) isolated from the guts of herbivores are powerful biomass-degrading organisms that enhance their degradative ability through the formation of cellulosomes, multienzyme complexes that synergistically colocalize enzymes to extract sugars from recalcitrant plant matter. However, a functional understanding of how fungal cellulosomes are deployed in vivo to orchestrate plant matter degradation is lacking, as is knowledge of how cellulosome production and function vary throughout the morphologically diverse life cycle of anaerobic fungi. In this work, we generated antibodies against three major fungal cellulosome protein domains, a dockerin, scaffoldin, and glycoside hydrolase (GH) 48 protein, and used them in conjunction with helium ion and immunofluorescence microscopy to characterize cellulosome localization patterns throughout the life cycle of Piromyces finnis when grown on simple sugars and complex cellulosic carbon sources. Our analyses reveal that fungal cellulosomes are cell-localized entities specifically targeted to the rhizoids of mature fungal cells and bodies of zoospores. Examination of cellulosome localization patterns across life stages also revealed that cellulosome production is independent of growth substrate in zoospores but repressed by simple sugars in mature cells. This suggests that further exploration of gene regulation patterns in zoospores is needed and can inform potential strategies for derepressing cellulosome expression and boosting hydrolytic enzyme yields from fungal cultures. Collectively, these findings underscore how life cycle-dependent cell morphology and regulation of cellulosome production impact biomass degradation by anaerobic fungi, insights that will benefit ongoing efforts to develop these organisms and their cellulosomes into platforms for converting waste biomass into valuable bioproducts.
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21
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Hillman ET, Li M, Hooker CA, Englaender JA, Wheeldon I, Solomon KV. Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus. Biotechnol Prog 2021; 37:e3172. [PMID: 33960738 DOI: 10.1002/btpr.3172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/06/2021] [Accepted: 05/03/2021] [Indexed: 12/12/2022]
Abstract
Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.
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Affiliation(s)
- Ethan T Hillman
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA
| | - Mengwan Li
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Casey A Hooker
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
| | - Jacob A Englaender
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Ian Wheeldon
- Department of Chemical & Environmental Engineering, University of California Riverside, Riverside, California, USA
| | - Kevin V Solomon
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA.,Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, West Lafayette, Indiana, USA.,Laboratory of Renewable Resources Engineering (LORRE), Purdue University, West Lafayette, Indiana, USA
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22
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Podolsky IA, Seppälä S, Xu H, Jin YS, O'Malley MA. A SWEET surprise: Anaerobic fungal sugar transporters and chimeras enhance sugar uptake in yeast. Metab Eng 2021; 66:137-147. [PMID: 33887459 DOI: 10.1016/j.ymben.2021.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/23/2021] [Accepted: 04/12/2021] [Indexed: 01/08/2023]
Abstract
In the yeast Saccharomyces cerevisiae, microbial fuels and chemicals production on lignocellulosic hydrolysates is constrained by poor sugar transport. For biotechnological applications, it is desirable to source transporters with novel or enhanced function from nonconventional organisms in complement to engineering known transporters. Here, we identified and functionally screened genes from three strains of early-branching anaerobic fungi (Neocallimastigomycota) that encode sugar transporters from the recently discovered Sugars Will Eventually be Exported Transporter (SWEET) superfamily in Saccharomyces cerevisiae. A novel fungal SWEET, NcSWEET1, was identified that localized to the plasma membrane and complemented growth in a hexose transporter-deficient yeast strain. Single cross-over chimeras were constructed from a leading NcSWEET1 expression-enabling domain paired with all other candidate SWEETs to broadly scan the sequence and functional space for enhanced variants. This led to the identification of a chimera, NcSW1/PfSW2:TM5-7, that enhanced the growth rate significantly on glucose, fructose, and mannose. Additional chimeras with varied cross-over junctions identified residues in TM1 that affect substrate selectivity. Furthermore, we demonstrate that NcSWEET1 and the enhanced NcSW1/PfSW2:TM5-7 variant facilitated novel co-consumption of glucose and xylose in S. cerevisiae. NcSWEET1 utilized 40.1% of both sugars, exceeding the 17.3% utilization demonstrated by the control HXT7(F79S) strain. Our results suggest that SWEETs from anaerobic fungi are beneficial tools for enhancing glucose and xylose co-utilization and offers a promising step towards biotechnological application of SWEETs in S. cerevisiae.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Haiqing Xu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Center for Advanced Bioenergy and Bioproduct Innovation (CABBI), Urbana, IL, 61801, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA; Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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23
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Saye LMG, Navaratna TA, Chong JPJ, O’Malley MA, Theodorou MK, Reilly M. The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production. Microorganisms 2021; 9:694. [PMID: 33801700 PMCID: PMC8065543 DOI: 10.3390/microorganisms9040694] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose is a promising feedstock for biofuel production as a renewable, carbohydrate-rich and globally abundant source of biomass. However, challenges faced include environmental and/or financial costs associated with typical lignocellulose pretreatments needed to overcome the natural recalcitrance of the material before conversion to biofuel. Anaerobic fungi are a group of underexplored microorganisms belonging to the early diverging phylum Neocallimastigomycota and are native to the intricately evolved digestive system of mammalian herbivores. Anaerobic fungi have promising potential for application in biofuel production processes due to the combination of their highly effective ability to hydrolyse lignocellulose and capability to convert this substrate to H2 and ethanol. Furthermore, they can produce volatile fatty acid precursors for subsequent biological conversion to H2 or CH4 by other microorganisms. The complex biological characteristics of their natural habitat are described, and these features are contextualised towards the development of suitable industrial systems for in vitro growth. Moreover, progress towards achieving that goal is reviewed in terms of process and genetic engineering. In addition, emerging opportunities are presented for the use of anaerobic fungi for lignocellulose pretreatment; dark fermentation; bioethanol production; and the potential for integration with methanogenesis, microbial electrolysis cells and photofermentation.
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Affiliation(s)
- Luke M. G. Saye
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Tejas A. Navaratna
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - James P. J. Chong
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA; (T.A.N.); (M.A.O.)
| | - Michael K. Theodorou
- Department of Agriculture and the Environment, Harper Adams University, Newport TF10 8NB, UK
| | - Matthew Reilly
- Department of Biology, University of York, York YO10 5DD, UK; (L.M.G.S.); (J.P.J.C.)
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24
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Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. mSystems 2021; 6:6/1/e00002-21. [PMID: 33594000 PMCID: PMC8561657 DOI: 10.1128/msystems.00002-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus Neocallimastix lanati from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the 1,788 lignocellulolytic enzymes annotated in the genome, 585 are associated with the fungal cellulosome, underscoring the powerful lignocellulolytic potential of N. lanati. The genome-scale metabolic model captures the primary metabolism of N. lanati and accurately predicts experimentally validated substrate utilization requirements. Additionally, metabolic flux predictions are verified by 13C metabolic flux analysis, demonstrating that the model faithfully describes the underlying fungal metabolism. Furthermore, the model clarifies key aspects of the hydrogenosomal metabolism and can be used as a platform to quantitatively study these biotechnologically important yet poorly understood early-branching fungi. IMPORTANCE Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements. Currently, there is no framework that can be used to combine multi-omic data sets to understand their physiology. Here, we introduce a high-quality PacBio-sequenced genome of the anaerobic gut fungus Neocallimastix lanati. Beyond identifying a trove of lignocellulolytic enzymes, we use this genome to construct the first genome-scale metabolic model of an anaerobic gut fungus. The model is experimentally validated and sheds light on unresolved metabolic features common to gut fungi. Model-guided analysis will pave the way for deepening our understanding of anaerobic gut fungi and provides a systematic framework to guide strain engineering efforts of these organisms for biotechnological use.
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25
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Li Y, Meng Z, Xu Y, Shi Q, Ma Y, Aung M, Cheng Y, Zhu W. Interactions between Anaerobic Fungi and Methanogens in the Rumen and Their Biotechnological Potential in Biogas Production from Lignocellulosic Materials. Microorganisms 2021; 9:190. [PMID: 33477342 PMCID: PMC7830786 DOI: 10.3390/microorganisms9010190] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/29/2022] Open
Abstract
Anaerobic fungi in the digestive tract of herbivores are one of the critical types of fiber-degrading microorganisms present in the rumen. They degrade lignocellulosic materials using unique rhizoid structures and a diverse range of fiber-degrading enzymes, producing metabolic products such as H2/CO2, formate, lactate, acetate, and ethanol. Methanogens in the rumen utilize some of these products (e.g., H2 and formate) to produce methane. An investigation of the interactions between anaerobic fungi and methanogens is helpful as it provides valuable insight into the microbial interactions within the rumen. During the last few decades, research has demonstrated that anaerobic fungi stimulate the growth of methanogens and maintain methanogenic diversity. Meanwhile, methanogens increase the fiber-degrading capability of anaerobic fungi and stimulate metabolic pathways in the fungal hydrogenosome. The ability of co-cultures of anaerobic fungi and methanogens to degrade fiber and produce methane could potentially be a valuable method for the degradation of lignocellulosic materials and methane production.
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Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Zhenxiang Meng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yao Xu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Yuping Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (Y.L.); (Z.M.); (Y.X.); (Q.S.); (Y.M.); (M.A.); (W.Z.)
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26
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Cut-Lengths of Perennial Ryegrass Leaf-Blades Influences In Vitro Fermentation by the Anaerobic Fungus Neocallimastix frontalis. Microorganisms 2020; 8:microorganisms8111774. [PMID: 33187375 PMCID: PMC7696013 DOI: 10.3390/microorganisms8111774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 11/17/2022] Open
Abstract
Anaerobic fungi in the gut of domesticated and wild mammalian herbivores play a key role in the host's ability to utilize plant biomass. Due to their highly effective ability to enzymatically degrade lignocellulose, anaerobic fungi are biotechnologically interesting. Numerous factors have been shown to affect the ability of anaerobic fungi to break down plant biomass. However, methods to reduce the non-productive lag time in batch cultures and the effect of leaf-blade cut-length and condition on the fungal fermentation are not known. Therefore, experimentation using a novel gas production approach with pre-grown, axenic cultures of Neocallimastix frontalis was performed using both fresh and air-dried perennial ryegrass leaf-blades of different cut-lengths. The methodology adopted removed the lag-phase and demonstrated the digestion of un-autoclaved leaf-blades. Fermentation of leaf-blades of 4.0 cm cut-length produced 18.4% more gas yet retained 11.2% more apparent DM relative to 0.5 cm cut-length leaf-blades. Drying did not affect fermentation by N. frontalis, although an interaction between drying and leaf-blade cut-length was noted. Removal of the lag phase and the use of un-autoclaved substrates are important when considering the biotechnological potential of anaerobic fungi. A hypothesis based upon sporulation at cut surfaces is proposed to describe the experimental results.
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27
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Hess M, Paul SS, Puniya AK, van der Giezen M, Shaw C, Edwards JE, Fliegerová K. Anaerobic Fungi: Past, Present, and Future. Front Microbiol 2020; 11:584893. [PMID: 33193229 PMCID: PMC7609409 DOI: 10.3389/fmicb.2020.584893] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/29/2020] [Indexed: 11/13/2022] Open
Abstract
Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.
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Affiliation(s)
- Matthias Hess
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shyam S. Paul
- Gut Microbiome Lab, ICAR-Directorate of Poultry Research, Indian Council of Agricultural Research, Hyderabad, India
| | - Anil K. Puniya
- Anaerobic Microbiology Lab, ICAR-National Dairy Research Institute, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Claire Shaw
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Joan E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Kateřina Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Prague, Czechia
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28
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Hagen LH, Brooke CG, Shaw CA, Norbeck AD, Piao H, Arntzen MØ, Olson HM, Copeland A, Isern N, Shukla A, Roux S, Lombard V, Henrissat B, O'Malley MA, Grigoriev IV, Tringe SG, Mackie RI, Pasa-Tolic L, Pope PB, Hess M. Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber. ISME JOURNAL 2020; 15:421-434. [PMID: 32929206 PMCID: PMC8026616 DOI: 10.1038/s41396-020-00769-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa, and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 h in nylon bags within the rumen of cannulated dairy cows. Across a gene catalog covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of hemicelluloses, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo- and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8, and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryote-selected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggest that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.
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Affiliation(s)
- Live H Hagen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.
| | | | | | | | - Hailan Piao
- Washington State University, Richland, WA, USA
| | - Magnus Ø Arntzen
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Heather M Olson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nancy Isern
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Anil Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Simon Roux
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR 7257, Université Aix-Marseille, 13288, Marseille, France.,Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Susannah G Tringe
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois, Urbana-Champaign, IL, USA
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, CA, USA
| | - Phillip B Pope
- Faculty of Biotechnology, Chemistry and Food Science, Norwegian University of Life Sciences, Aas, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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29
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Hanafy RA, Johnson B, Youssef NH, Elshahed MS. Assessing anaerobic gut fungal diversity in herbivores using D1/D2 large ribosomal subunit sequencing and multi-year isolation. Environ Microbiol 2020; 22:3883-3908. [PMID: 32656919 DOI: 10.1111/1462-2920.15164] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/22/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
The anaerobic gut fungi (AGF, Neocallimastigomycota) reside in the alimentary tracts of herbivores where they play a central role in the breakdown of plant material. Here, we report on the development of the hypervariable domains D1/D2 of the large ribosomal subunit (D1/D2 LSU) as a barcoding marker for the AGF. We generated a reference D1/D2 LSU database for all cultured AGF genera, as well as the majority of candidate genera encountered in prior internal transcribed spacer 1 (ITS1)-based surveys. Subsequently, a D1/D2 LSU-based diversity survey using long read PacBio SMRT sequencing was conducted on faecal samples from 21 wild and domesticated herbivores. Twenty-eight genera and candidate genera were identified, including multiple novel lineages that were predominantly, but not exclusively, identified in wild herbivores. Association between certain AGF genera and animal lifestyles, or animal host family was observed. Finally, to address the current paucity of AGF isolates, concurrent isolation efforts utilizing multiple approaches to maximize recovery yielded 216 isolates belonging to 12 different genera, several of which have no prior cultured-representatives. Our results establish the utility of D1/D2 LSU and PacBio sequencing for AGF diversity surveys, the culturability of multiple AGF taxa, and demonstrate that wild herbivores represent a yet-untapped reservoir of AGF diversity.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Britny Johnson
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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30
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An Arduino based automatic pressure evaluation system to quantify growth of non‐model anaerobes in culture. AIChE J 2020. [DOI: 10.1002/aic.16540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Wilken SE, Seppälä S, Lankiewicz TS, Saxena M, Henske JK, Salamov AA, Grigoriev IV, O’Malley MA. Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi. Metab Eng Commun 2020; 10:e00107. [PMID: 31799118 PMCID: PMC6883316 DOI: 10.1016/j.mec.2019.e00107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022] Open
Abstract
Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi.
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Affiliation(s)
- St. Elmo Wilken
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
- Department of Evolution Ecology and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Mohan Saxena
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - John K. Henske
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
| | - Asaf A. Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, 93106, USA
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32
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Vinzelj J, Joshi A, Insam H, Podmirseg SM. Employing anaerobic fungi in biogas production: challenges & opportunities. BIORESOURCE TECHNOLOGY 2020; 300:122687. [PMID: 31926794 DOI: 10.1016/j.biortech.2019.122687] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 05/24/2023]
Abstract
Anaerobic fungi (AF, phylum Neocallimastigomycota) are best known for their ability to efficiently break down lignocellulosic biomass. Their unique combination of mechanical and enzymatic attacks on recalcitrant plant structures bears great potential for enhancement of the anaerobic digestion (AD) process. Although scientists in this field have long agreed upon the potential of AF for biotechnology, research is only recently gaining traction. This delay was largely due to difficulties in culture-dependent and culture-independent analysis of those high-maintenance organisms with their still unknown complex growth requirements. In this review, we will summarize current research efforts on bioaugmentation with AF and further point out, how the lack of basic knowledge on AF nutritional needs hampers their implementation on an industrial scale. Through this, we hope to further kindle interest into basic research on AF in order to advance their stable integration into biotechnological processes.
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Affiliation(s)
- Julia Vinzelj
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Akshay Joshi
- ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, CH-8820 Wädenswil, Switzerland
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
| | - Sabine Marie Podmirseg
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, A-6020 Innsbruck, Austria
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Lillington SP, Leggieri PA, Heom KA, O'Malley MA. Nature's recyclers: anaerobic microbial communities drive crude biomass deconstruction. Curr Opin Biotechnol 2019; 62:38-47. [PMID: 31593910 DOI: 10.1016/j.copbio.2019.08.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022]
Abstract
Microbial communities within anaerobic ecosystems have evolved to degrade and recycle carbon throughout the earth. A number of strains have been isolated from anaerobic microbial communities, which are rich in carbohydrate active enzymes (CAZymes) to liberate fermentable sugars from crude plant biomass (lignocellulose). However, natural anaerobic communities host a wealth of microbial diversity that has yet to be harnessed for biotechnological applications to hydrolyze crude biomass into sugars and value-added products. This review highlights recent advances in 'omics' techniques to sequence anaerobic microbial genomes, decipher microbial membership, and characterize CAZyme diversity in anaerobic microbiomes. With a focus on the herbivore rumen, we further discuss methods to discover new CAZymes, including those found within multi-enzyme fungal cellulosomes. Emerging techniques to characterize the interwoven metabolism and spatial interactions between anaerobes are also reviewed, which will prove critical to developing a predictive understanding of anaerobic communities to guide in microbiome engineering.
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Affiliation(s)
- Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Kellie A Heom
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, United States.
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Leveraging anaerobic fungi for biotechnology. Curr Opin Biotechnol 2019; 59:103-110. [DOI: 10.1016/j.copbio.2019.03.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/19/2019] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
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Shi Q, Li Y, Li Y, Cheng Y, Zhu W. Effects of steam explosion on lignocellulosic degradation of, and methane production from, corn stover by a co-cultured anaerobic fungus and methanogen. BIORESOURCE TECHNOLOGY 2019; 290:121796. [PMID: 31319215 DOI: 10.1016/j.biortech.2019.121796] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 05/23/2023]
Abstract
The aim of this study was to investigate the effects of steam explosion on lignocellulose digestibility of, and methane production from corn stover by a co-culture of anaerobic fungus and methanogen. The cumulative methane production at 72 h of incubation from the steam-exploded corn stover was 32.2 ± 1.74 mL, which not significantly different (P > 0.05) from that of the untreated corn stover (37.1 ± 1.09 mL). However, steam explosion decreased the hemicellulose contents of corn stover by 28.0 ± 0.39% and increased the neutral detergent solute by 23.5 ± 0.25%. While this treatment did not affect the dry matter digestibility (64.1 ± 0.26%, and 64.1 ± 0.28%, respectively). In conclusion, the co-culture of anaerobic fungus and methanogen can degrade the crude fibrous portion of corn stover without any pretreatments. It possesses promising biotechnological prospects for conversion of crop residue based straw resources to obtain biofuel in the form of methane.
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Affiliation(s)
- Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanfei Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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Gilmore SP, Lankiewicz TS, Wilken SE, Brown JL, Sexton JA, Henske JK, Theodorou MK, Valentine DL, O’Malley MA. Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation. ACS Synth Biol 2019; 8:2174-2185. [PMID: 31461261 DOI: 10.1021/acssynbio.9b00271] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.
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Affiliation(s)
- Sean P. Gilmore
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Thomas S. Lankiewicz
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - St. Elmo Wilken
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jennifer L. Brown
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jessica A. Sexton
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - John K. Henske
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael K. Theodorou
- Harper Adams University, Agriculture Centre for Sustainable Energy Systems, Newport, Shropshire TF10 8NB, United Kingdom
| | - David L. Valentine
- Department of Earth Science and Marine Science Institute, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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Wang D, Zhao C, Liu S, Zhang T, Yao J, Cao Y. Effects of Piromyces sp. CN6 CGMCC 14449 on fermentation quality, nutrient composition and the in vitro degradation rate of whole crop maize silage. AMB Express 2019; 9:121. [PMID: 31359220 PMCID: PMC6663944 DOI: 10.1186/s13568-019-0846-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/23/2019] [Indexed: 11/28/2022] Open
Abstract
This study investigated the effects of the rumen fungus Piromyces sp. CN6 CGMCC 14449 as a silage additive on the fermentation quality, nutrient composition and in vitro digestibility of whole crop maize silage. Whole crop maize served as the silage material and was vacuum packed in polyethylene bags. Three ensiling treatments were applied: a control (CK), addition of a fungus (FU) at 105 thallus-forming units per gram, and addition of compound enzyme (EN) at 0.033 mg/g (containing cellulase and xylanase at activities of 90 filter paper units and 6000 IU per gram, respectively). Compared with the CK, the FU and EN treatments decreased the pH after 30 days fermentation (P <0.05). Both FU and EN treatments increased the lactate, crude protein, and water-soluble carbohydrate contents (P <0.05), whereas reduced the acetate, ADF and NDF contents as well as the ammonia nitrogen to total nitrogen ratio in silage after 30 days of ensilaging (P <0.05), compared with those for the CK, while no changes were found in the dry matter and dry matter recovery (P > 0.05). The fungal inoculant increased the in vitro digestibility of dry matter, NDF and ADF in silage after 30 days fermentation (P <0.05). In conclusion, the rumen fungus Piromyces sp. CN6 CGMCC 14449 can improve the quality and nutrient composition of whole crop maize silage and increase the crude fibre digestibility.
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Gordon V, Bakhtiari L, Kovach K. From molecules to multispecies ecosystems: the roles of structure in bacterial biofilms. Phys Biol 2019; 16:041001. [PMID: 30913545 DOI: 10.1088/1478-3975/ab1384] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Biofilms are communities of sessile microbes that are bound to each other by a matrix made of biopolymers and proteins. Spatial structure is present in biofilms on many lengthscales. These range from the nanometer scale of molecular motifs to the hundred-micron scale of multicellular aggregates. Spatial structure is a physical property that impacts the biology of biofilms in many ways. The molecular structure of matrix components controls their interaction with each other (thereby impacting biofilm mechanics) and with diffusing molecules such as antibiotics and immune factors (thereby impacting antibiotic tolerance and evasion of the immune system). The size and structure of multicellular aggregates, combined with microbial consumption of growth substrate, give rise to differentiated microenvironments with different patterns of metabolism and gene expression. Spatial association of more than one species can benefit one or both species, while distances between species can both determine and result from the transport of diffusible factors between species. Thus, a widespread theme in the biological importance of spatial structure in biofilms is the effect of structure on transport. We survey what is known about this and other effects of spatial structure in biofilms, from molecules up to multispecies ecosystems. We conclude with an overview of what experimental approaches have been developed to control spatial structure in biofilms and how these and other experiments can be complemented with computational work.
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Affiliation(s)
- Vernita Gordon
- Department of Physics, University of Texas at Austin, Austin TX 78712, United States of America. Center for Nonlinear Dynamics, University of Texas at Austin, Austin TX 78712, United States of America. Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin TX 78712, United States of America. Author to whom any correspondence should be addressed
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Wilken SE, Swift CL, Podolsky IA, Lankiewicz TS, Seppälä S, O'Malley MA. Linking ‘omics’ to function unlocks the biotech potential of non-model fungi. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Podolsky IA, Seppälä S, Lankiewicz TS, Brown JL, Swift CL, O'Malley MA. Harnessing Nature's Anaerobes for Biotechnology and Bioprocessing. Annu Rev Chem Biomol Eng 2019; 10:105-128. [PMID: 30883214 DOI: 10.1146/annurev-chembioeng-060718-030340] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Industrial biotechnology has the potential to decrease our reliance on petroleum for fuel and bio-based chemical production and also enable valorization of waste streams. Anaerobic microorganisms thrive in resource-limited environments and offer an array of novel bioactivities in this regard that could revolutionize biomanufacturing. However, they have not been adopted for widespread industrial use owing to their strict growth requirements, limited number of available strains, difficulty in scale-up, and genetic intractability. This review provides an overview of current and future uses for anaerobes in biotechnology and bioprocessing in the postgenomic era. We focus on the recently characterized anaerobic fungi (Neocallimastigomycota) native to the digestive tract of large herbivores, which possess a trove of enzymes, pathways, transporters, and other biomolecules that can be harnessed for numerous biotechnological applications. Resolving current genetic intractability, scale-up, and cultivation challenges will unlock the potential of these lignocellulolytic fungi and other nonmodel micro-organisms to accelerate bio-based production.
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Affiliation(s)
- Igor A Podolsky
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Thomas S Lankiewicz
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Candice L Swift
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA; , , , , ,
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Hooker CA, Hillman ET, Overton JC, Ortiz-Velez A, Schacht M, Hunnicutt A, Mosier NS, Solomon KV. Hydrolysis of untreated lignocellulosic feedstock is independent of S-lignin composition in newly classified anaerobic fungal isolate, Piromyces sp. UH3-1. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:293. [PMID: 30386430 PMCID: PMC6203967 DOI: 10.1186/s13068-018-1292-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/15/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plant biomass is an abundant but underused feedstock for bioenergy production due to its complex and variable composition, which resists breakdown into fermentable sugars. These feedstocks, however, are routinely degraded by many uncommercialized microbes such as anaerobic gut fungi. These gut fungi express a broad range of carbohydrate active enzymes and are native to the digestive tracts of ruminants and hindgut fermenters. In this study, we examine gut fungal performance on these substrates as a function of composition, and the ability of this isolate to degrade inhibitory high syringyl lignin-containing forestry residues. RESULTS We isolated a novel fungal specimen from a donkey in Independence, Indiana, United States. Phylogenetic analysis of the Internal Transcribed Spacer 1 sequence classified the isolate as a member of the genus Piromyces within the phylum Neocallimastigomycota (Piromyces sp. UH3-1, strain UH3-1). The isolate penetrates the substrate with an extensive rhizomycelial network and secretes many cellulose-binding enzymes, which are active on various components of lignocellulose. These activities enable the fungus to hydrolyze at least 58% of the glucan and 28% of the available xylan in untreated corn stover within 168 h and support growth on crude agricultural residues, food waste, and energy crops. Importantly, UH3-1 hydrolyzes high syringyl lignin-containing poplar that is inhibitory to many fungi with efficiencies equal to that of low syringyl lignin-containing poplar with no reduction in fungal growth. This behavior is correlated with slight remodeling of the fungal secretome whose composition adapts with substrate to express an enzyme cocktail optimized to degrade the available biomass. CONCLUSIONS Piromyces sp. UH3-1, a newly isolated anaerobic gut fungus, grows on diverse untreated substrates through production of a broad range of carbohydrate active enzymes that are robust to variations in substrate composition. Additionally, UH3-1 and potentially other anaerobic fungi are resistant to inhibitory lignin composition possibly due to changes in enzyme secretion with substrate. Thus, anaerobic fungi are an attractive platform for the production of enzymes that efficiently use mixed feedstocks of variable composition for second generation biofuels. More importantly, our work suggests that the study of anaerobic fungi may reveal naturally evolved strategies to circumvent common hydrolytic inhibitors that hinder biomass usage.
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Affiliation(s)
- Casey A. Hooker
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Ethan T. Hillman
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
| | - Jonathan C. Overton
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Adrian Ortiz-Velez
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Makayla Schacht
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054 USA
| | - Abigail Hunnicutt
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
| | - Nathan S. Mosier
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
| | - Kevin V. Solomon
- Department of Agricultural and Biological Engineering, Purdue University, 225 South University Street, West Lafayette, IN 47907-2093 USA
- Laboratory of Renewable Resources Engineering (LORRE), Purdue University, 500 Central Drive, West Lafayette, IN 47907-2022 USA
- Purdue University Interdisciplinary Life Sciences (PULSe) Program, Purdue University, 155 South Grant Street, West Lafayette, IN 47907-2114 USA
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Henske JK, Gilmore SP, Haitjema CH, Solomon KV, O'Malley MA. Biomass‐degrading enzymes are catabolite repressed in anaerobic gut fungi. AIChE J 2018. [DOI: 10.1002/aic.16395] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- John K. Henske
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
| | - Sean P. Gilmore
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
| | - Charles H. Haitjema
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
| | - Kevin V. Solomon
- Dept. of Chemical Engineering University of California Santa Barbara CA, 93106
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Catabolic repression in early-diverging anaerobic fungi is partially mediated by natural antisense transcripts. Fungal Genet Biol 2018; 121:1-9. [PMID: 30223087 DOI: 10.1016/j.fgb.2018.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/16/2022]
Abstract
Early-diverging anaerobic fungi (order: Neocallimastigomycota), lignocelluolytic chytrid-like fungi central to fiber degradation in the digestive tracts of large herbivores, are attractive sources of cellulases and hemicellulases for biotechnology. Enzyme expression is tightly regulated and coordinated through mechanisms that remain unelucidated to optimize hydrolytic efficiency. Our analysis of anaerobic fungal transcriptomes reveals hundreds of cis-natural antisense transcripts (cis-NATs), which we hypothesize play an integral role in this regulation. Through integrated genomic and transcriptomic sequencing on a range of catabolic substrates, we validate these NATs in three species (Anaeromyces robustus, Neocallimasix californiae, and Piromyces finnis), and analyze their expression patterns and prevalence to gain insight into their function. NAT function was diverse and conserved across the three fungal genomes studied, with 10% of all metabolic process NATs associated with lignocellulose hydrolysis. Despite these similarities, however, only eleven gene targets were conserved orthologs. Several NATs were dynamically regulated by lignocellulosic substrates while their gene targets were unregulated. This observation is consistent with a hypothesized, but untested, regulatory mechanism where selected genes are exclusively regulated at the transcriptional/post-transcriptional level by NATs. However, only genes with high NAT relative expression levels displayed this phenomenon, suggesting a selection mechanism that favors larger dynamic ranges for more precise control of gene expression. In addition to this mode, we observed two other possible regulatory fates: canonical transcriptional regulation with no NAT response, and positive co-regulation of target mRNA and cognate NAT, which we hypothesize is a fine-tuning strategy to locally negate control outputs from global regulators. Our work reveals the complex contributions of antisense RNA to the catabolic response in anaerobic fungi, highlighting its importance in understanding lignocellulolytic activity for bioenergy applications. More importantly, the relative expression of NAT to target may form a critical determinant of transcriptional vs post-transcriptional (NAT) control of gene expression in primitive anaerobic fungi.
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In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi. Processes (Basel) 2018. [DOI: 10.3390/pr6010007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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Henske JK, Gilmore SP, Knop D, Cunningham FJ, Sexton JA, Smallwood CR, Shutthanandan V, Evans JE, Theodorou MK, O’Malley MA. Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:305. [PMID: 29270219 PMCID: PMC5737911 DOI: 10.1186/s13068-017-0997-4] [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: 08/03/2017] [Accepted: 12/12/2017] [Indexed: 05/19/2023]
Abstract
Anaerobic gut fungi are the primary colonizers of plant material in the rumen microbiome, but are poorly studied due to a lack of characterized isolates. While most genera of gut fungi form extensive rhizoidal networks, which likely participate in mechanical disruption of plant cell walls, fungi within the Caecomyces genus do not possess these rhizoids. Here, we describe a novel fungal isolate, Caecomyces churrovis, which forms spherical sporangia with a limited rhizoidal network yet secretes a diverse set of carbohydrate active enzymes (CAZymes) for plant cell wall hydrolysis. Despite lacking an extensive rhizoidal system, C. churrovis is capable of growth on fibrous substrates like switchgrass, reed canary grass, and corn stover, although faster growth is observed on soluble sugars. Gut fungi have been shown to use enzyme complexes (fungal cellulosomes) in which CAZymes bind to non-catalytic scaffoldins to improve biomass degradation efficiency. However, transcriptomic analysis and enzyme activity assays reveal that C. churrovis relies more on free enzymes compared to other gut fungal isolates. Only 15% of CAZyme transcripts contain non-catalytic dockerin domains in C. churrovis, compared to 30% in rhizoid-forming fungi. Furthermore, C. churrovis is enriched in GH43 enzymes that provide complementary hemicellulose degrading activities, suggesting that a wider variety of these activities are required to degrade plant biomass in the absence of an extensive fungal rhizoid network. Overall, molecular characterization of a non-rhizoid-forming anaerobic fungus fills a gap in understanding the roles of CAZyme abundance and associated degradation mechanisms during lignocellulose breakdown within the rumen microbiome.
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Affiliation(s)
- John K. Henske
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Sean P. Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Doriv Knop
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Francis J. Cunningham
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Jessica A. Sexton
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Chuck R. Smallwood
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | | | - James E. Evans
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354 USA
| | - Michael K. Theodorou
- Agriculture Centre for Sustainable Energy Systems (ACSES), Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB UK
| | - Michelle A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
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