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Yang H, Ma L, Fu M, Li K, Li Y, Li Q. Mechanism analysis of humification coupling metabolic pathways based on cow dung composting with ionic liquids. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116426. [PMID: 36240639 DOI: 10.1016/j.jenvman.2022.116426] [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: 08/11/2022] [Revised: 09/22/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
This study focused on how adding ionic liquids (IL) affects composting humification. During the warming and thermophilic phases, addition of IL increased precursors content, and increased the polymerization of humus (HS) at later stages. Furthermore, the final HS and humic acid (HA) content of experimental groups (T) groups 129.79 mg/g and 79.91 mg/g were higher than in control group (CK) 118.57 mg/g and 74.53 mg/g, respectively (p < 0.05). IL up-regulated the gene abundance of metabolism for carbohydrate and amino acid (AA), and promoted the contributions of Actinobacteria and Proteobacteria, which affected humification. The redundancy analysis (RDA) results showed that the citrate-cycle (TCA cycle)(ko0020), pentose phosphate pathway (ko00030), pyruvate metabolism (ko00620), glyoxylate and dicarboxylate metabolism (ko00630), propanoate metabolism (ko00640), butanoate metabolism (ko00650) positively correlated with HA and HI. HA and humification index (HI) positively correlated with AA metabolic pathways, and fulvic acid (FA) was negatively correlated with these pathways. Overall, metabolism for carbohydrate and AA metabolism favored compost humification. ILs improved metabolism for carbohydrate and amino acid metabolism, thus enhancing humification.
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Affiliation(s)
- Hongxiang Yang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Liangcai Ma
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Mengxin Fu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Kecheng Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Yinzhong Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, 530004, China.
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2
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Sitepu I, Enriquez L, Nguyen V, Fry R, Simmons B, Singer S, Simmons C, Boundy-Mills KL. Ionic Liquid Tolerance of Yeasts in Family Dipodascaceae and Genus Wickerhamomyces. Appl Biochem Biotechnol 2020; 191:1580-1593. [PMID: 32185613 DOI: 10.1007/s12010-020-03293-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/13/2020] [Indexed: 11/26/2022]
Abstract
In previous studies of ionic liquid (IL) tolerance of numerous species of ascomycetous yeasts, two strains of Wickerhamomyces ciferrii and Galactomyces candidus had unusually high tolerance in media containing up to 5% (w/v) of the 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]). The study aimed at investigating whether additional strains of these species, and additional species in the Dipodascaceae family, also possess IL tolerance, and to compare sensitivity to the acetate and chloride versions of the ionic liquid. Fifty five yeast strains in the family Dipodascaceae, which encompasses genera Galactomyces, Geotrichum, and Dipodascus, and seven yeast strains of species Wickerhamomyces ciferrii were tested for ability to grow in laboratory medium containing no IL, 242 mM [C2C1Im][OAc], or 242 mM [C2C1Im]Cl, and in IL-pretreated switchgrass hydrolysate. Many yeasts exhibited tolerance of one or both ILs, with higher tolerance of the chloride anion than of the acetate anion. Different strains of the same species exhibited varying degrees of IL tolerance. Galactomyces candidus, UCDFSTs 52-260, and 50-64, had exceptionally robust growth in [C2C1Im][OAc], and also grew well in the switchgrass hydrolysate. Identification of IL tolerant and IL resistant yeast strains will facilitate studies of the mechanism of IL tolerance, which could include superior efflux, metabolism or exclusion.
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Affiliation(s)
- Irnayuli Sitepu
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Lauren Enriquez
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Valerie Nguyen
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Russell Fry
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Blake Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Steve Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Christopher Simmons
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Kyria L Boundy-Mills
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA.
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Sivapragasam M, Moniruzzaman M, Goto M. An Overview on the Toxicological Properties of Ionic Liquids toward Microorganisms. Biotechnol J 2020; 15:e1900073. [PMID: 31864234 DOI: 10.1002/biot.201900073] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 11/21/2019] [Indexed: 12/27/2022]
Abstract
Ionic liquids (ILs), a class of materials with unique physicochemical properties, have been used extensively in the fields of chemical engineering, biotechnology, material sciences, pharmaceutics, and many others. Because ILs are very polar by nature, they can migrate into the environment with the possibility of inclusion in the food chain and bioaccumulation in living organisms. However, the chemical natures of ILs are not quintessentially biocompatible. Therefore, the practical uses of ILs must be preceded by suitable toxicological assessments. Among different methods, the use of microorganisms to evaluate IL toxicity provides many advantages including short generation time, rapid growth, and environmental and industrial relevance. This article reviews the recent research progress on the toxicological properties of ILs toward microorganisms and highlights the computational prediction of various toxicity models.
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Affiliation(s)
- Magaret Sivapragasam
- Biotechnology Department, QUEST International University Perak, 30250, Ipoh, Perak, Malaysia
| | - Muhammad Moniruzzaman
- Chemical Engineering Department, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Malaysia.,Center of Researches in Ionic Liquids (CORIL), Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Malaysia
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Fukuoka, 819-0395, Japan.,Center for Future Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
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Kluyveromyces marxianus, an Attractive Yeast for Ethanolic Fermentation in the Presence of Imidazolium Ionic Liquids. Int J Mol Sci 2018; 19:ijms19030887. [PMID: 29547579 PMCID: PMC5877748 DOI: 10.3390/ijms19030887] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/11/2018] [Accepted: 03/14/2018] [Indexed: 11/25/2022] Open
Abstract
Imidazolium ionic liquids (ILs) are promising solvents for lignocellulosic biomass (LCB) pretreatment and allow the achievement of higher ethanolic yields after enzymatic hydrolysis and ethanolic fermentation. However, residual ILs entrapped in pretreated biomass are often toxic for fermentative microorganisms, but interaction mechanisms between ILs and cells are still unknown. Here we studied the effects of 1-ethyl-3-methylimidazolium acetate [Emim][OAc] and 1-ethyl-3-methylimidazolium methylphosphonate [Emim][MeO(H)PO2] on Kluyveromyces marxianus, a thermotolerant ethanologenic yeast. Morphological impacts induced by ILs on K. marxianus were characterized by Scanning Electron Microscopy analysis and showed wrinkled, softened, and holed shapes. In Yeast-Malt-Dextrose (YMD) medium, K. marxianus tolerated IL additions up to 2% for [Emim][OAc] and 6% for [Emim][MeO(H)PO2]. Below these thresholds, some IL concentrations enhanced ethanolic yields up to +34% by switching the metabolic status from respiratory to fermentative. Finally, K. marxianus fermentation was applied on several substrates pretreated with [Emim][OAc] or [Emim][MeO(H)PO2] and enzymatically hydrolyzed: a model long fiber cellulose and two industrial LCBs, softwood (spruce) and hardwood (oak) sawdusts. The maximum ethanolic yields obtained were 1.8 to 3.9 times higher when substrates were pretreated with imidazolium ILs. Therefore K. marxianus is an interesting fermentative yeast in a second-generation bioethanol process implying IL pretreatment.
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Auer L, Lazuka A, Sillam-Dussès D, Miambi E, O'Donohue M, Hernandez-Raquet G. Uncovering the Potential of Termite Gut Microbiome for Lignocellulose Bioconversion in Anaerobic Batch Bioreactors. Front Microbiol 2017; 8:2623. [PMID: 29312279 PMCID: PMC5744482 DOI: 10.3389/fmicb.2017.02623] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/15/2017] [Indexed: 11/16/2022] Open
Abstract
Termites are xylophages, being able to digest a wide variety of lignocellulosic biomass including wood with high lignin content. This ability to feed on recalcitrant plant material is the result of complex symbiotic relationships, which involve termite-specific gut microbiomes. Therefore, these represent a potential source of microorganisms for the bioconversion of lignocellulose in bioprocesses targeting the production of carboxylates. In this study, gut microbiomes of four termite species were studied for their capacity to degrade wheat straw and produce carboxylates in controlled bioreactors. All of the gut microbiomes successfully degraded lignocellulose and up to 45% w/w of wheat straw degradation was observed, with the Nasutitermes ephratae gut-microbiome displaying the highest levels of wheat straw degradation, carboxylate production and enzymatic activity. Comparing the 16S rRNA gene diversity of the initial gut inocula to the bacterial communities in lignocellulose degradation bioreactors revealed important changes in community diversity. In particular, taxa such as Spirochaetes and Fibrobacteres that were highly abundant in the initial gut inocula were replaced by Firmicutes and Proteobacteria at the end of incubation in wheat straw bioreactors. Overall, this study demonstrates that termite-gut microbiomes constitute a reservoir of lignocellulose-degrading bacteria that can be harnessed in artificial conditions for biomass conversion processes that lead to the production of useful molecules.
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Affiliation(s)
- Lucas Auer
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - Adèle Lazuka
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - David Sillam-Dussès
- Laboratoire d'Éthologie Expérimentale et Comparée, Université Paris 13 - Sorbonne Paris Cité, Villetaneuse, France
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Institut de Recherche Pour le Développement – Sorbonne Universités, Bondy, France
| | - Edouard Miambi
- Institut d'Ecologie et des Sciences de l'Environnement de Paris, Université Paris-Est Créteil, Créteil, France
| | - Michael O'Donohue
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
| | - Guillermina Hernandez-Raquet
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INSA, Toulouse, France
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Ceballos SJ, Yu C, Claypool JT, Singer SW, Simmons BA, Thelen MP, Simmons CW, VanderGheynst JS. Development and characterization of a thermophilic, lignin degrading microbiota. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist AM. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microb Cell Fact 2017; 16:204. [PMID: 29145855 PMCID: PMC5691611 DOI: 10.1186/s12934-017-0819-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/09/2017] [Indexed: 11/13/2022] Open
Abstract
Background There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass. Methods To generate strains capable of tolerating residual ILs present in treated feedstocks, a tolerance adaptive laboratory evolution (TALE) approach was developed and utilized to improve growth of two different Escherichia coli strains, DH1 and K-12 MG1655, in the presence of two different ionic liquids, 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]) and 1-butyl-3-methylimidazolium chloride ([C4C1Im]Cl). For multiple parallel replicate populations of E. coli, cells were repeatedly passed to select for improved fitness over the course of approximately 40 days. Clonal isolates were screened and the best performing isolates were subjected to whole genome sequencing. Results The most prevalent mutations in tolerant clones occurred in transport processes related to the functions of mdtJI, a multidrug efflux pump, and yhdP, an uncharacterized transporter. Additional mutations were enriched in processes such as transcriptional regulation and nucleotide biosynthesis. Finally, the best-performing strains were compared to previously characterized tolerant strains and showed superior performance in tolerance of different IL and media combinations (i.e., cross tolerance) with robust growth at 8.5% (w/v) and detectable growth up to 11.9% (w/v) [C2C1Im][OAc]. Conclusion The generated strains thus represent the best performing platform strains available for bioproduction utilizing IL-treated renewable substrates, and the TALE method was highly successful in overcoming the general issue of substrate toxicity and has great promise for use in tolerance engineering. Electronic supplementary material The online version of this article (10.1186/s12934-017-0819-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elsayed T Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Shizeng Wang
- Joint Bioenergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Rebecca M Lennen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - 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
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark. .,Department of Bioengineering, University of California, 9500 Gilman Drive La Jolla, San Diego, CA, 92093, USA.
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8
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Abstract
The purpose of this review is to delineate means of decontaminating soil. This information might be used to mitigate soil-associated risks of foodborne pathogens. The majority of the research in the published literature involves inactivation of plant pathogens in soil, i.e., those pathogens harmful to fruit and vegetable production and ornamental plants. Very little has been published regarding the inactivation of foodborne human pathogens in crop soil. Nevertheless, because decontamination techniques for plant pathogens might also be useful methods for eliminating foodborne pathogens, this review also includes inactivation of plant pathogens, with appropriate discussion and comparisons, in the hopes that these methods may one day be validated against foodborne pathogens. Some of the major soil decontamination methods that have been investigated and are covered include chemical decontamination (chemigation), solarization, steaming, biofumigation, bacterial competitive exclusion, torch flaming, microwave treatment, and amendment with biochar. Other innovative means of inactivating foodborne pathogens in soils may be discovered and explored in the future, provided that these techniques are economically feasible in terms of chemicals, equipment, and labor. Food microbiology and food safety researchers should reach out to soil scientists and plant pathologists to create links where they do not currently exist and strengthen relationships where they do exist to take advantage of multidisciplinary skills. In time, agricultural output and the demand for fresh produce will increase. With advances in the sensitivity of pathogen testing and epidemiological tracebacks, the need to mitigate preharvest bacterial contamination of fresh produce will become paramount. Hence, soil decontamination technologies may become more economically feasible and practical in light of increasing the microbial safety of fresh produce.
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Affiliation(s)
- Joshua B Gurtler
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Food Safety and Intervention Technologies Research Unit, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038-8551, USA
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Egorova KS, Gordeev EG, Ananikov VP. Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine. Chem Rev 2017; 117:7132-7189. [PMID: 28125212 DOI: 10.1021/acs.chemrev.6b00562] [Citation(s) in RCA: 902] [Impact Index Per Article: 128.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.
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Affiliation(s)
- Ksenia S Egorova
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Evgeniy G Gordeev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia
| | - Valentine P Ananikov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Leninsky prospect 47, Moscow 119991, Russia.,Department of Chemistry, Saint Petersburg State University , Stary Petergof 198504, Russia
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Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis. mSystems 2016; 1:mSystems00120-16. [PMID: 27981239 PMCID: PMC5155067 DOI: 10.1128/msystems.00120-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/15/2016] [Indexed: 01/12/2023] Open
Abstract
Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes. Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified. Increasing the level of IL to 0.1% (wt) led to increased levels of relative abundance and transcription in organisms of the phylum Firmicutes. Interestingly, IL concentrations of up to 1% (wt) also resulted in greater xylanase transcription and enzyme activity as well as increased transcription of endoglucanase, beta-glucosidase, and IL tolerance genes compared to communities without IL. IL levels above 1% (wt) resulted in decreased enzyme activity and transcription of genes involved in lignocellulose hydrolysis. The results indicate that moderate levels of IL select for thermophilic microorganisms that not only tolerate IL but also effectively hydrolyze lignocellulose from switchgrass. Discovery of IL-tolerant organisms and enzymes is critical for the development of biological processes that convert IL-pretreated biomass to biofuels and chemicals. Employing metatranscriptomic analysis of enrichment cultures can facilitate the discovery of microorganisms and enzymes that may be active in the presence of toxic compounds such as ionic liquids. IMPORTANCE Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes.
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Yu C, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS. Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts. Appl Microbiol Biotechnol 2016; 100:10237-10249. [PMID: 27838839 DOI: 10.1007/s00253-016-7955-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/26/2022]
Abstract
Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.
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Affiliation(s)
- Chaowei Yu
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis, CA, 95616, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Michael P Thelen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Biosciences Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Jean S VanderGheynst
- Department of Biological and Agricultural Engineering, University of California, One Shields Ave., Davis, CA, 95616, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
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Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate. Appl Microbiol Biotechnol 2016; 100:5639-52. [DOI: 10.1007/s00253-016-7525-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/21/2016] [Accepted: 04/05/2016] [Indexed: 10/21/2022]
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13
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Xu J, Wang X, Hu L, Xia J, Wu Z, Xu N, Dai B, Wu B. A novel ionic liquid-tolerant Fusarium oxysporum BN secreting ionic liquid-stable cellulase: consolidated bioprocessing of pretreated lignocellulose containing residual ionic liquid. BIORESOURCE TECHNOLOGY 2015; 181:18-25. [PMID: 25625459 DOI: 10.1016/j.biortech.2014.12.080] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
In this study, microbial communities from chemicals polluted microhabitats were cultured with the addition of imidazolium-based ionic liquid (IL) to enrich for IL-tolerant microbes. A strain of Fusarium oxysporum BN producing cellulase from these enrichments was capable of growing in 10% (w/v) 1-ethyl-3-methylimidazolium phosphinate, much higher than the normal IL concentrations in the lignocellulose regenerated from ILs. Cellulase secreted by the strain showed high resistance to ILs based on phosphate and sulfate radicals, evidencing of a high conformational stability in relevant media. Gratifyingly, F. oxysporum BN can directly convert IL-pretreated rice straw to bioethanol via consolidated bioprocessing (I-CBP). At optimum fermentation condition, a maximum ethanol yield of 0.125 g ethanol g(-1) of rice straw was finally obtained, corresponding to 64.2% of the theoretical yield.
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Affiliation(s)
- Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Xinfeng Wang
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China; Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huaian 223300, China
| | - Lei Hu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Jun Xia
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Zhen Wu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Ning Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Benlin Dai
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiangxi Road, Huaian 223300, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing 210000, China.
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Sitepu IR, Shi S, Simmons BA, Singer SW, Boundy-Mills K, Simmons CW. Yeast tolerance to the ionic liquid 1-ethyl-3-methylimidazolium acetate. FEMS Yeast Res 2014; 14:1286-94. [DOI: 10.1111/1567-1364.12224] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/17/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Irnayuli R. Sitepu
- Department of Food Science and Technology; University of California; Davis CA USA
- Forestry Research and Development Agency (FORDA); The Ministry of Forestry; Bogor Indonesia
| | - Shuang Shi
- Department of Food Science and Technology; University of California; Davis CA USA
| | - Blake A. Simmons
- Deconstruction Division; Joint BioEnergy Institute; Emeryville CA USA
- Biological and Materials Sciences Center; Sandia National Laboratories; Livermore CA USA
| | - Steven W. Singer
- Deconstruction Division; Joint BioEnergy Institute; Emeryville CA USA
- Earth Sciences Division; Lawrence Berkeley National Laboratory; Berkeley CA USA
| | - Kyria Boundy-Mills
- Department of Food Science and Technology; University of California; Davis CA USA
| | - Christopher W. Simmons
- Department of Food Science and Technology; University of California; Davis CA USA
- Deconstruction Division; Joint BioEnergy Institute; Emeryville CA USA
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15
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Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chem Biol 2014; 9:1470-9. [PMID: 24819174 DOI: 10.1021/cb5000289] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycoside hydrolases (GHs) are critical to cycling of plant biomass in the environment, digestion of complex polysaccharides by the human gut microbiome, and industrial activities such as deployment of cellulosic biofuels. High-throughput sequencing methods show tremendous sequence diversity among GHs, yet relatively few examples from the over 150,000 unique domain arrangements containing GHs have been functionally characterized. Here, we show how cell-free expression, bioconjugate chemistry, and surface-based mass spectrometry can be used to study glycoside hydrolase reactions with plant biomass. Detection of soluble products is achieved by coupling a unique chemical probe to the reducing end of oligosaccharides in a stable oxime linkage, while the use of (13)C-labeled monosaccharide standards (xylose and glucose) allows quantitation of the derivatized glycans. We apply this oxime-based nanostructure-initiator mass spectrometry (NIMS) method to characterize the functional diversity of GHs secreted by Clostridium thermocellum, a model cellulolytic organism. New reaction specificities are identified, and differences in rates and yields of individual enzymes are demonstrated in reactions with biomass substrates. Numerical analyses of time series data suggests that synergistic combinations of mono- and multifunctional GHs can decrease the complexity of enzymes needed for the hydrolysis of plant biomass during the production of biofuels.
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Affiliation(s)
- Kai Deng
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Taichi E. Takasuka
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Richard Heins
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Xiaoliang Cheng
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lai F. Bergeman
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Jian Shi
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Ryan Aschenbrener
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Sam Deutsch
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Seema Singh
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Kenneth L. Sale
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
- University of
California, Berkeley, California 94720, United States
| | - Anup K. Singh
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Sandia
National Laboratories, Livermore, California 94551, United States
| | - Brian G. Fox
- Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Trent R. Northen
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
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16
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Xu J, He B, Wu B, Wang B, Wang C, Hu L. An ionic liquid tolerant cellulase derived from chemically polluted microhabitats and its application in in situ saccharification of rice straw. BIORESOURCE TECHNOLOGY 2014; 157:166-173. [PMID: 24549238 DOI: 10.1016/j.biortech.2014.01.102] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/20/2014] [Accepted: 01/24/2014] [Indexed: 06/03/2023]
Abstract
A cellulase-producing fungus was isolated from chemically polluted microhabitats by [Amim][Cl] enrichment and identified as Aspergillus fumigatus. The maximum activity of the cellulase in 30% (v/v) ionic liquids (ILs) was detected in [Emim][DMP], [Amim][Cl] and [Emim][MA] as 127%, 111% and 109%, respectively, of its activity in buffer, suggesting its superior performance in high concentration ILs. Strikingly, although its initial activity varied in each IL, its half-life was longer in most ILs than in buffer, evidence of a high conformational stability of the enzyme that is essential for maintaining the remaining activity in relevant media. It noteworthy that 1-3M NaCl can activate the cellulase somewhat. More gratifyingly, a compatible IL-cellulase system based on the cellulase was developed, and its use significantly improved the saccharification rate of rice straw from 53% to 88% versus the control, demonstrating its potential for efficient transformation of lignocellulose to glucose in a single-step process.
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Affiliation(s)
- Jiaxing Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huaian 223300, China.
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing 210000, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing 210000, China
| | - Bin Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing 210000, China
| | - Chenghua Wang
- College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Lei Hu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huaian 223300, China
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17
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Portillo MDC, Saadeddin A. Recent trends in ionic liquid (IL) tolerant enzymes and microorganisms for biomass conversion. Crit Rev Biotechnol 2014; 35:294-301. [DOI: 10.3109/07388551.2013.843069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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18
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Simmons CW, Reddy AP, VanderGheynst JS, Simmons BA, Singer SW. Bacillus coagulanstolerance to 1-ethyl-3-methylimidazolium-based ionic liquids in aqueous and solid-state thermophilic culture. Biotechnol Prog 2014; 30:311-6. [DOI: 10.1002/btpr.1859] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/01/2013] [Accepted: 11/28/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Christopher W. Simmons
- Joint BioEnergy Inst., Deconstruction Division; Emeryville CA
- Biological and Agricultural Engineering; University of California-Davis; Davis CA
- Food Science and Technology; University of California-Davis; Davis CA
| | - Amitha P. Reddy
- Joint BioEnergy Inst., Deconstruction Division; Emeryville CA
- Biological and Agricultural Engineering; University of California-Davis; Davis CA
| | - Jean S. VanderGheynst
- Joint BioEnergy Inst., Deconstruction Division; Emeryville CA
- Biological and Agricultural Engineering; University of California-Davis; Davis CA
| | - Blake A. Simmons
- Joint BioEnergy Inst., Deconstruction Division; Emeryville CA
- Physical and Life Sciences Directorate; Lawrence Livermore National Laboratory; Livermore CA
| | - Steven W. Singer
- Joint BioEnergy Inst., Deconstruction Division; Emeryville CA
- Dept. of Biomass Science and Conversion Technology; Sandia National Laboratories; Livermore CA
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19
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