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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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Barragán-Trinidad M, Buitrón G. Pretreatment of agave bagasse with ruminal fluid to improve methane recovery. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 175:52-61. [PMID: 38159368 DOI: 10.1016/j.wasman.2023.12.041] [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: 09/06/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Agave bagasse, a lignocellulosic waste that results from the milling and juice extraction of Agave tequilana var azul pineapples, is a suitable substrate for the production of methane through anaerobic digestion. However, it is necessary to apply a pretreatment to convert the bagasse into energy. In this context, this paper proposes using ruminal microorganisms to hydrolyze agave bagasse. This study evaluated the effect of the initial agave bagasse to ruminal fluid (S0/X0) ratio (0.33, 0.5, 1, and 2) on the hydrolysis efficiency. Subsequently, the supernatant was used for methane production. The hydrolysis efficiency increased as the S0/X0 ratio decreased. A hydrolysis efficiency of 60 % was achieved using an S0/X0 ratio of 0.33. The S0/X0 ratio of 0.33 optimally improved the specific methane production and energy recovery (155 ± 2 mL CH4/g TS and 6.1 ± 0.1 kJ/g TS) compared to raw biomass. The most abundant hydrolytic bacteria were Prevotella, Ruminococcus and Fibrobacter, and Engyodontium was the most abundant proteolytic fungus.
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Affiliation(s)
- Martín Barragán-Trinidad
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico.
| | - Germán Buitrón
- Laboratory for Research on Advanced Processes for Water Treatment, Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, Querétaro 76230, Mexico.
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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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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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Silva JP, Ticona ARP, Hamann PRV, Quirino BF, Noronha EF. Deconstruction of Lignin: From Enzymes to Microorganisms. Molecules 2021; 26:2299. [PMID: 33921125 PMCID: PMC8071518 DOI: 10.3390/molecules26082299] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/20/2022] Open
Abstract
Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.
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Affiliation(s)
- Jéssica P. Silva
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Alonso R. P. Ticona
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Pedro R. V. Hamann
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Betania F. Quirino
- Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, 70770-901 Brasília, Brazil;
| | - Eliane F. Noronha
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
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Lahive CW, Kamer PCJ, Lancefield CS, Deuss PJ. An Introduction to Model Compounds of Lignin Linking Motifs; Synthesis and Selection Considerations for Reactivity Studies. CHEMSUSCHEM 2020; 13:4238-4265. [PMID: 32510817 PMCID: PMC7540175 DOI: 10.1002/cssc.202000989] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 05/31/2023]
Abstract
The development of fundamentally new valorization strategies for lignin plays a vital role in unlocking the true potential of lignocellulosic biomass as sustainable and economically compatible renewable carbon feedstock. In particular, new catalytic modification and depolymerization strategies are required. Progress in this field, past and future, relies for a large part on the application of synthetic model compounds that reduce the complexity of working with the lignin biopolymer. This aids the development of catalytic methodologies and in-depth mechanistic studies and guides structural characterization studies in the lignin field. However, due to the volume of literature and the piecemeal publication of methodology, the choice of suitable lignin model compounds is far from straight forward, especially for those outside the field and lacking a background in organic synthesis. For example, in catalytic depolymerization studies, a balance between synthetic effort and fidelity compared to the actual lignin of interest needs to be found. In this Review, we provide a broad overview of the model compounds available to study the chemistry of the main native linking motifs typically found in lignins from woody biomass, the synthetic routes and effort required to access them, and discuss to what extent these represent actual lignin structures. This overview can aid researchers in their selection of the most suitable lignin model systems for the development of emerging lignin modification and depolymerization technologies, maximizing their chances of successfully developing novel lignin valorization strategies.
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Affiliation(s)
- Ciaran W. Lahive
- Department of Chemical Engineering (ENTEG)University of GroningenNijenborgh 49747 AGGroningenNetherlands
- School of Chemistry and Biomedical Science Research ComplexUniversity of St. Andrews and EaStCHEMNorth HaughSt. AndrewsFifeKY16 9STUnited Kingdom
| | - Paul C. J. Kamer
- School of Chemistry and Biomedical Science Research ComplexUniversity of St. Andrews and EaStCHEMNorth HaughSt. AndrewsFifeKY16 9STUnited Kingdom
- Leibniz-Institut für Katalyse e.V.Albert-Einstein-Straße 29a18059RostockGermany
| | - Christopher S. Lancefield
- School of Chemistry and Biomedical Science Research ComplexUniversity of St. Andrews and EaStCHEMNorth HaughSt. AndrewsFifeKY16 9STUnited Kingdom
| | - Peter J. Deuss
- Department of Chemical Engineering (ENTEG)University of GroningenNijenborgh 49747 AGGroningenNetherlands
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Ianni A, Bennato F, Martino C, Grotta L, Martino G. Volatile Flavor Compounds in Cheese as Affected by Ruminant Diet. Molecules 2020; 25:E461. [PMID: 31979062 PMCID: PMC7037034 DOI: 10.3390/molecules25030461] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 11/16/2022] Open
Abstract
Extensive research has been conducted concerning the determination and characterization of volatile compounds contributing to aroma and flavor in cheese. Considerable knowledge has been accumulated on the understanding of the mechanisms through which these compounds are formed during ripening, as well as on the optimization of the methodological approaches which lead to their detection. More recently, particular attention has been given to the aromatic properties of milk and cheeses obtained from lactating dairy ruminants fed experimental diets, characterized, for instance, by the addition of trace elements, natural supplements, or agricultural by-products rich in bioactive compounds. The purpose of this review is to summarize the major families of volatile compounds most commonly found in these types of dairy products at various ripening stages, describing in greater detail the role of animal diet in influencing the synthesis mechanisms most commonly responsible for cheese flavor determination. A large number of volatile compounds, including carboxylic acids, lactones, ketones, alcohols, and aldehydes, can be detected in cheese. The relative percentage of each compound depends on the biochemical processes that occur during ripening, and these are mainly mediated by endogenous enzymes and factors of bacterial origin whose function can be strongly influenced by the bioactive compounds taken by animals with the diet and released in milk through the mammary gland. Further evaluations on the interactions between volatile compounds and cheese matrix would be necessary in order to improve the knowledge on the synthesis mechanisms of such compounds; in addition to this, more should be done with respect to the determination of synergistic effects of flavor compounds, correlating such compounds to the aroma of dairy products.
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Affiliation(s)
- Andrea Ianni
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy; (A.I.); (F.B.); (L.G.)
| | - Francesca Bennato
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy; (A.I.); (F.B.); (L.G.)
| | - Camillo Martino
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, 64100 Teramo, Italy;
| | - Lisa Grotta
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy; (A.I.); (F.B.); (L.G.)
| | - Giuseppe Martino
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via R. Balzarini 1, 64100 Teramo, Italy; (A.I.); (F.B.); (L.G.)
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He B, Jin S, Cao J, Mi L, Wang J. Metatranscriptomics of the Hu sheep rumen microbiome reveals novel cellulases. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:153. [PMID: 31249617 PMCID: PMC6587244 DOI: 10.1186/s13068-019-1498-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/14/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cellulosic biomass has great potential as a renewable biofuel resource. Robust, high-performance enzymes are needed to effectively utilize this valuable resource. In this study, metatranscriptomics was used to explore the carbohydrate-active enzymes (CAZymes), especially glycoside hydrolases (GHs), present in the rumen microbiome of Hu sheep. Select CAZymes were experimentally verified and characterized after cloning and expression in E. coli. RESULTS The metatranscriptomes of six Hu sheep rumen microbiomes yielded 42.3 Gbp of quality-checked sequence data that represented in total 2,380,783 unigenes after de novo assembling using Trinity and clustered with CD-HIT-EST. Annotation using the CAZy database revealed that 2.65% of the unigenes encoded GHs, which were assigned to 111 different CAZymes families. Firmicutes (18.7%) and Bacteroidetes (13.8%) were the major phyla to which the unigenes were taxonomically assigned. In total, 14,489 unigenes were annotated to 15 cellulase-containing GH families, with GH3, GH5 and GH9 being the predominant. From these putative cellulase-encoding unigenes, 4225 open reading frames (ORFs) were predicted to contain 2151 potential cellulase catalytic modules. Additionally, 147 ORFs were found to encode proteins that contain carbohydrate-binding modules (CBMs). Heterogeneous expression of 30 candidate cDNAs from the GH5 family in E. coli BL21 showed that 17 of the tested proteins had endoglucanase activity, while 7 exhibited exoglucanase activity. Interestingly, two of the GH5 proteins (Cel5A-h28 and Cel5A-h11) showed high specific activity against carboxymethylcellulose (CMC) and p-nitrophenyl-β-d-cellobioside (pNPC) (222.2 and 142.8 U/mg), respectively. The optimal pH value for activity of Cel5A-h11 and Cel5A-h28 was 6.0 for both enzymes, and optimal temperatures were 40 and 50 °C, respectively. Both enzymes retained over 70 and 60%, respectively, of their original activities after incubation at 40 °C for 60 min. However, their activities were rapidly diminished upon exposure to higher temperatures. Cel5A-h11 and Cel5A-h28 retained more than 80 and 60% of their maximal enzymatic activities after incubation for 16 h in buffered solutions in the pH range from 4.0 to 9.0. CONCLUSION The metatranscriptomic results revealed that the rumen microbiome of Hu sheep encoded a repertoire of new enzymes capable of cellulose degradation and metatranscriptomics was an effective method to discover novel cellulases for biotechnological applications.
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Affiliation(s)
- Bo He
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Shuwen Jin
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jiawen Cao
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Lan Mi
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
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Mulat DG, Dibdiakova J, Horn SJ. Microbial biogas production from hydrolysis lignin: insight into lignin structural changes. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:61. [PMID: 29541158 PMCID: PMC5844095 DOI: 10.1186/s13068-018-1054-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND The emerging cellulosic bioethanol industry will generate huge amounts of lignin-rich residues that may be converted into biogas by anaerobic digestion (AD) to increase the output of energy carriers from the biorefinery plants. The carbohydrates fraction of lignocellulosic biomass is degradable, whereas the lignin fraction is generally considered difficult to degrade during AD. The objective of this study was to investigate the feasibility of biogas production by AD from hydrolysis lignin (HL), prepared by steam explosion (SE) and enzymatic saccharification of birch. A novel nylon bag technique together with two-dimensional nuclear magnetic resonance spectroscopy, pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS), and Fourier transform infrared (FTIR) spectroscopy was used to identify recalcitrant and degradable structures in the lignin during AD. RESULTS The HL had a lignin content of 80% which included pseudo-lignin and condensed-lignin structures resulting from the SE pretreatment. The obtained methane yield from HL was almost twofold higher than the theoretical methane from the carbohydrate fraction alone, indicating that part of the lignin was converted to methane. Characterization of the undegradable material after AD revealed a substantial loss of signals characteristic for carbohydrates and lignin-carbohydrate complexes (LCC), indicating conversion of these chemical components to methane during AD. The β-O-4' linkage and resinol were not modified as such in AD, but major change was seen for the S/G ratio from 5.8 to 2.6, phenylcoumaran from 4.9 to 1.0%, and pseudo-lignin and condensed-lignin were clearly degraded. Scanning electron microscopy and simultaneous thermal analysis measurements demonstrated changes in morphology and thermal properties following SE pretreatment and AD. Our results showed that carbohydrate, LCC, pseudo-lignin, and condensed-lignin degradation had contributed to methane production. The energy yield for the combined ethanol production and biogas production was 8.1 MJ fuel per kg DM of substrate (4.9 MJ/kg from ethanol and 3.2 MJ/kg from methane). CONCLUSION This study shows the benefit of using a novel bag technique together with advanced analytical techniques to investigate the degradation mechanisms of lignin during AD, and also points to a possible application of HL produced in cellulosic bioethanol plants.
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Affiliation(s)
- Daniel Girma Mulat
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Janka Dibdiakova
- Norwegian Institute of Bioeconomy Research, P.O. Box 115, 1432 Ås, Norway
| | - Svein Jarle Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
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Hu X, Liu G, Shafer ABA, Wei Y, Zhou J, Lin S, Wu H, Zhou M, Hu D, Liu S. Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing. Front Microbiol 2017; 8:572. [PMID: 28421061 PMCID: PMC5376572 DOI: 10.3389/fmicb.2017.00572] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/20/2017] [Indexed: 12/31/2022] Open
Abstract
The gut ecosystem is characterized by dynamic and reciprocal interactions between the host and bacteria. Although characterizing microbiota for herbivores has become recognized as important tool for gauging species health, no study to date has investigated the bacterial communities and evaluated the age-related bacterial dynamics of musk deer. Moreover, gastrointestinal diseases have been hypothesized to be a limiting factor of population growth in captive musk deer. Here, high-throughput sequencing of the bacterial 16S rRNA gene was used to profile the fecal bacterial communities in juvenile and adult alpine and forest musk deer. The two musk deer species harbored similar bacterial communities at the phylum level, whereas the key genera for the two species were distinct. The bacterial communities were dominated by Firmicutes and Bacteroidetes, with the bacterial diversity being higher in forest musk deer. The Firmicutes to Bacteroidetes ratio also increased from juvenile to adult, while the bacterial diversity, within-group and between-group similarity, all increased with age. This work serves as the first sequence-based analysis of variation in bacterial communities within and between musk deer species, and demonstrates how the gut microbial community dynamics vary among closely related species and shift with age. As gastrointestinal diseases have been observed in captive populations, this study provides valuable data that might benefit captive management and future reintroduction programs.
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Affiliation(s)
- Xiaolong Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Gang Liu
- Institute of Wetland Research – Chinese Academy of ForestryBeijing, China
| | - Aaron B. A. Shafer
- Forensic Science and Environmental & Life Sciences, Trent University, PeterboroughON, Canada
| | - Yuting Wei
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Juntong Zhou
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Shaobi Lin
- Zhangzhou Pien Tze Huang Pharmaceutical Co., LtdZhangzhou, China
| | - Haibin Wu
- Zhangzhou Pien Tze Huang Pharmaceutical Co., LtdZhangzhou, China
| | - Mi Zhou
- Breeding Centre of Alpine Musk Deer in FengchunLanzhou, China
| | - Defu Hu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
| | - Shuqiang Liu
- Laboratory of Non-invasive Research Technology for Endangered Species, College of Nature Conservation, Beijing Forestry UniversityBeijing, China
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11
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Baba Y, Matsuki Y, Mori Y, Suyama Y, Tada C, Fukuda Y, Saito M, Nakai Y. Pretreatment of lignocellulosic biomass by cattle rumen fluid for methane production: Bacterial flora and enzyme activity analysis. J Biosci Bioeng 2017; 123:489-496. [DOI: 10.1016/j.jbiosc.2016.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/18/2016] [Accepted: 11/19/2016] [Indexed: 01/19/2023]
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12
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Valdez-Vazquez I, Morales AL, Escalante AE. History of adaptation determines short-term shifts in performance and community structure of hydrogen-producing microbial communities degrading wheat straw. Microb Biotechnol 2017; 10:1569-1580. [PMID: 28296150 PMCID: PMC5658582 DOI: 10.1111/1751-7915.12678] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/17/2017] [Indexed: 11/26/2022] Open
Abstract
This study addresses the question of ecological interest for the determination of structure and diversity of microbial communities that degrade lignocellulosic biomasses to produce biofuels. Two microbial consortia with different history, native of wheat straw (NWS) and from a methanogenic digester (MD) fed with cow manure, were contrasted in terms of hydrogen performance, substrate disintegration and microbial diversity. NWS outperformed the hydrogen production rate of MD. Microscopic images revealed that NWS acted on the cuticle and epidermis, generating cellulose strands with high crystallinity, while MD degraded deeper layers, equally affecting all polysaccharides. The bacterial composition markedly differed according to the inocula origin. NWS almost solely comprised hydrogen producers of the phyla Firmicutes and Proteobacteria, with 38% members of Enterococcus. After hydrogen fermentation, NWS comprised 8% Syntrophococcus, an acetogen that cleaves aryl ethers of constituent groups on the aromatic components of lignin. Conversely, MD comprised thirteen phyla, primarily including Firmicutes with H2‐producing members, and Bacteroidetes with non‐H2‐producing members, which reduced the hydrogen performance. Overall, the results of this study provide clear evidence that the history of adaptation of NWS enhanced the hydrogen performance from untreated wheat straw. Further, native wheat straw communities have the potential to refine cellulose fibers and produce biofuels simultaneously.
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Affiliation(s)
- Idania Valdez-Vazquez
- Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, C.P 76230, Querétaro, Qro., Mexico
| | - Ana L Morales
- Unidad Académica Juriquilla, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Blvd. Juriquilla 3001, C.P 76230, Querétaro, Qro., Mexico
| | - Ana E Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria Coyoacán, C.P. 04510, Mexico City, D.F, Mexico
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13
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Brown ME, Chang MCY. Exploring bacterial lignin degradation. Curr Opin Chem Biol 2013; 19:1-7. [PMID: 24780273 DOI: 10.1016/j.cbpa.2013.11.015] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/26/2013] [Accepted: 11/29/2013] [Indexed: 12/18/2022]
Abstract
Plant biomass represents a renewable carbon feedstock that could potentially be used to replace a significant level of petroleum-derived chemicals. One major challenge in its utilization is that the majority of this carbon is trapped in the recalcitrant structural polymers of the plant cell wall. Deconstruction of lignin is a key step in the processing of biomass to useful monomers but remains challenging. Microbial systems can provide molecular information on lignin depolymerization as they have evolved to break lignin down using metalloenzyme-dependent radical pathways. Both fungi and bacteria have been observed to metabolize lignin; however, their differential reactivity with this substrate indicates that they may utilize different chemical strategies for its breakdown. This review will discuss recent advances in studying bacterial lignin degradation as an approach to exploring greater diversity in the environment.
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Affiliation(s)
- Margaret E Brown
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
| | - Michelle C Y Chang
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-1460, USA.
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14
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Scully ED, Hoover K, Carlson J, Tien M, Geib SM. Proteomic analysis of Fusarium solani isolated from the Asian longhorned beetle, Anoplophora glabripennis. PLoS One 2012; 7:e32990. [PMID: 22496740 PMCID: PMC3322136 DOI: 10.1371/journal.pone.0032990] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 02/05/2012] [Indexed: 11/20/2022] Open
Abstract
Wood is a highly intractable food source, yet many insects successfully colonize and thrive in this challenging niche. Overcoming the lignin barrier of wood is a key challenge in nutrient acquisition, but full depolymerization of intact lignin polymers has only been conclusively demonstrated in fungi and is not known to occur by enzymes produced by insects or bacteria. Previous research validated that lignocellulose and hemicellulose degradation occur within the gut of the wood boring insect, Anoplophora glabripennis (Asian longhorned beetle), and that a fungal species, Fusarium solani (ATCC MYA 4552), is consistently associated with the larval stage. While the nature of this relationship is unresolved, we sought to assess this fungal isolate's ability to degrade lignocellulose and cell wall polysaccharides and to extract nutrients from woody tissue. This gut-derived fungal isolate was inoculated onto a wood-based substrate and shotgun proteomics using Multidimensional Protein Identification Technology (MudPIT) was employed to identify 400 expressed proteins. Through this approach, we detected proteins responsible for plant cell wall polysaccharide degradation, including proteins belonging to 28 glycosyl hydrolase families and several cutinases, esterases, lipases, pectate lyases, and polysaccharide deacetylases. Proteinases with broad substrate specificities and ureases were observed, indicating that this isolate has the capability to digest plant cell wall proteins and recycle nitrogenous waste under periods of nutrient limitation. Additionally, several laccases, peroxidases, and enzymes involved in extracellular hydrogen peroxide production previously implicated in lignin depolymerization were detected. In vitro biochemical assays were conducted to corroborate MudPIT results and confirmed that cellulases, glycosyl hydrolases, xylanases, laccases, and Mn- independent peroxidases were active in culture; however, lignin- and Mn- dependent peroxidase activities were not detected While little is known about the role of filamentous fungi and their associations with insects, these findings suggest that this isolate has the endogenous potential to degrade lignocellulose and extract nutrients from woody tissue.
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Affiliation(s)
- Erin D. Scully
- Intercollege Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kelli Hoover
- Department of Entomology, Center for Chemical Ecology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - John Carlson
- School of Forest Resources, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Bioenergy Science and Technology (World Class University), Chonnam National University, Buk-Gu, Gwangju, Korea
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research Unit, USDA-ARS Pacific Basin Agricultural Research Center, Hilo, Hawaii, United States of America
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15
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Ko JJ, Shimizu Y, Ikeda K, Kim SK, Park CH, Matsui S. Biodegradation of high molecular weight lignin under sulfate reducing conditions: lignin degradability and degradation by-products. BIORESOURCE TECHNOLOGY 2009; 100:1622-7. [PMID: 18977138 DOI: 10.1016/j.biortech.2008.09.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 09/12/2008] [Accepted: 09/17/2008] [Indexed: 05/11/2023]
Abstract
This study is designed to investigate the biodegradation of high molecular weight (HMW) lignin under sulfate reducing conditions. With a continuously mesophilic operated reactor in the presence of co-substrates of cellulose, the changes in HMW lignin concentration and chemical structure were analyzed. The acid precipitable polymeric lignin (APPL) and lignin monomers, which are known as degradation by-products, were isolated and detected. The results showed that HMW lignin decreased and showed a maximum degradation capacity of 3.49 mg/l/day. APPL was confirmed as a polymeric degradation by-product and was accumulated in accordance with HMW lignin reduction. We also observed non-linear accumulation of aromatic lignin monomers such as hydrocinnamic acid. Through our experimental results, it was determined that HMW lignin, when provided with a co-substrate of cellulose, is biodegraded through production of APPL and aromatic monomers under anaerobic sulfate reducing conditions with a co-substrate of cellulose.
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Affiliation(s)
- Jae-Jung Ko
- Korea Institute of Construction Technology, 2311, Daehwa-Dong, Ilsanseo-Gu, Goyang-Si, Gyeonggi-Do 411-712, Republic of Korea.
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16
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Baurhoo B, Ruiz-Feria C, Zhao X. Purified lignin: Nutritional and health impacts on farm animals—A review. Anim Feed Sci Technol 2008. [DOI: 10.1016/j.anifeedsci.2007.10.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Gidh AV, Decker SR, Vinzant TB, Himmel ME, Williford C. Determination of lignin by size exclusion chromatography using multi angle laser light scattering. J Chromatogr A 2006; 1114:102-10. [PMID: 16566937 DOI: 10.1016/j.chroma.2006.02.044] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Revised: 02/14/2006] [Accepted: 02/17/2006] [Indexed: 10/24/2022]
Abstract
A method was developed using high-performance size exclusion liquid chromatography (HPSEC) with multi-angle laser light scattering (MALLS), quasi-elastic light scattering (QELS), interferometric refractometry (RI) and UV detection to characterize and monitor lignin. The combination proved very effective at tracking changes in molecular conformation of lignin molecules over time; i.e. changes in molecular weight distribution, radius of gyration, and hydrodynamic radius. Until this study, UV detection (280 nm) had been the primary lignin determination method for chromatography. Three different HPLC columns were used to study the effects of pH, flow conditions, and mobile phase compositions (dimethyl sulphoxide, water, 0.1M NaOH, and lithium bromide) on the chromatography of lignin. Since light scattering accuracy is highly dependent on solute concentration, both the UV and RI detectors were calibrated for use as concentration detectors. Shodex Asahipak GS-320 HQ column with 0.1M NaOH (pH 12.0) run at 0.5 ml/min was found to give the highest separation and most consistent recovery. The study also revealed that the lignin aggregated at pH below 8.5. This aggregation was detected only by MALLS and was not observed on UV or RI detectors. It is very important to take this loss in apparent concentration due to aggregation into consideration before collecting reliable depolymerization data.
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Affiliation(s)
- Aarti V Gidh
- National Bioenergy Center, National Renewable Energy Laboratory, 1617 Cole Blvd., Golden, CO 80401, USA.
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18
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Kim YH, Engesser KH. Degradation of alkyl ethers, aralkyl ethers, and dibenzyl ether by Rhodococcus sp. strain DEE5151, isolated from diethyl ether-containing enrichment cultures. Appl Environ Microbiol 2004; 70:4398-401. [PMID: 15240329 PMCID: PMC444782 DOI: 10.1128/aem.70.7.4398-4401.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty strains isolated from sewage sludge were found to degrade various ethers, including alkyl ethers, aralkyl ethers, and dibenzyl ether. In Rhodococcus strain DEE5151, induction of ether degradation needed substrates exhibiting at least one unsubstituted Calpha-methylene moiety as the main structural prerequisite. The cleavage reaction observed with anisole, phenetole, and dibenzyl ether indicates that the initial oxidation occurs at such respective Calpha positions. Diethyl ether-induced strain DEE5151 degraded dibenzyl ether via intermediately accumulated benzoic acid. Phenetole seems to be subject also to another ether-cleaving enzyme. Other strains of this group showed different enzymatic activities towards the substrate classes investigated.
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Affiliation(s)
- Yong-Hak Kim
- Institut für Siedlungswasserbau, Wassergüte- und Abfallwirtschaft, Universität Stuttgart, Abteilung Biologische Abluftreinigung, Bandtäle 2, D-70569 Stuttgart (Büsnau), Germany
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