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Mon ML, Romano N, Farace PD, Tortone CA, Oriani DS, Picariello G, Zumárraga MJ, Gioffré AK, Talia PM. Exploring the cellulolytic activity of environmental mycobacteria. Tuberculosis (Edinb) 2024; 147:102516. [PMID: 38735123 DOI: 10.1016/j.tube.2024.102516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Although studies on non-tuberculous mycobacteria have increased in recent years because they cause a considerable proportion of infections, their cellulolytic system is still poorly studied. This study presents a characterization of the cellulolytic activities of environmental mycobacterial isolates derived from soil and water samples from the central region of Argentina, aimed to evaluate the conservation of the mechanism for the degradation of cellulose in this group of bacteria. The molecular and genomic identification revealed identity with Mycolicibacterium septicum. The endoglucanase and total cellulase activities were assessed both qualitatively and quantitatively and the optimal enzymatic conditions were characterized. A specific protein of around 56 kDa with cellulolytic activity was detected in a zymogram. Protein sequences possibly arising from a cellulase were identified by mass spectrometry-based shotgun proteomics. Results showed that M. septicum encodes for cellulose- and hemicellulose-related degrading enzymes, including at least an active β-1,4 endoglucanase enzyme that could be useful to improve its survival in the environment. Given the important health issues related to mycobacteria, the results of the present study may contribute to the knowledge of their cellulolytic system, which could be important for their ability to survive in many different types of environments.
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Affiliation(s)
- María Laura Mon
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Nelson Romano
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Pablo Daniel Farace
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Claudia A Tortone
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Delia S Oriani
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Gianluca Picariello
- Istituto di Scienze Dell'Alimentazione, Consiglio Nazionale Delle Ricerche, Via Roma 64, 83100, Avellino, Italy.
| | - Martín José Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Andrea Karina Gioffré
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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2
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McManus WR, Schorey JS. Comparison of Ultrastructure, Extracellular Matrix, and Drug Susceptibility in M. avium subs. hominissuis Biofilms. Pathogens 2023; 12:1427. [PMID: 38133310 PMCID: PMC10747021 DOI: 10.3390/pathogens12121427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Pulmonary infections with Mycobacterium avium occur in susceptible individuals following exposure to the bacterium in the environment, where it often persists in biofilms. Many methods have been used to generate biofilms of M. avium, and it is unknown whether different approaches generate similar structures and cell phenotypes. To make a parallel comparison of in vitro biofilm ultrastructure, extracellular matrix (ECM) composition, and the drug susceptibility of biofilm resident bacteria, we used two published methods to generate M. avium biofilms: four-week incubation in M63 medium or 24 h exposure to dithiothreitol (DTT). Scanning electron microscopy revealed differences in the biofilm ultrastructure between the two methods, including variation in the appearance of ECM materials and morphology of resident cells, while light microscopy and staining with calcofluor white indicated that both biofilms contained polysaccharides characteristic of cellulose. Measuring the susceptibility of biofilms to degradation by enzymes suggested differences in structurally important ECM molecules, with DTT biofilms having important protein and, to a lesser extent, cellulose components, and M63 biofilms having moderate protein, cellulose, and DNA components. Both biofilms conferred resistance to the bactericidal effects of amikacin and clarithromycin, with resident cells being killed at greater than 10-fold lower rates than planktonic cells at almost all concentrations. These comparisons indicate differences in biofilm responses by M. avium under differing conditions, but also suggest common features of biofilm formation, including cellulose production and antimicrobial resistance.
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Affiliation(s)
| | - Jeffrey S. Schorey
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA;
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3
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Deng Y, Wang SY. Sorption of Cellulases in Biofilm Enhances Cellulose Degradation by Bacillus subtilis. Microorganisms 2022; 10:microorganisms10081505. [PMID: 35893563 PMCID: PMC9329931 DOI: 10.3390/microorganisms10081505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Biofilm commonly forms on the surfaces of cellulosic biomass but its roles in cellulose degradation remain largely unexplored. We used Bacillus subtilis to study possible mechanisms and the contributions of two major biofilm components, extracellular polysaccharides (EPS) and TasA protein, to submerged biofilm formation on cellulose and its degradation. We found that biofilm produced by B. subtilis is able to absorb exogenous cellulase added to the culture medium and also retain self-produced cellulase within the biofilm matrix. The bacteria that produced more biofilm degraded more cellulose compared to strains that produced less biofilm. Knockout strains that lacked both EPS and TasA formed a smaller amount of submerged biofilm on cellulose than the wild-type strain and also degraded less cellulose. Imaging of biofilm on cellulose suggests that bacteria, cellulose, and cellulases form cellulolytic biofilm complexes that facilitate synergistic cellulose degradation. This study brings additional insight into the important functions of biofilm in cellulose degradation and could potentiate the development of biofilm-based technology to enhance biomass degradation for biofuel production.
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4
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Hughes JM, Eberl HJ, Sonner S. A mathematical model of discrete attachment to a cellulolytic biofilm using random DEs. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:6582-6619. [PMID: 35730273 DOI: 10.3934/mbe.2022310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We propose a new mathematical framework for the addition of stochastic attachment to biofilm models, via the use of random ordinary differential equations. We focus our approach on a spatially explicit model of cellulolytic biofilm growth and formation that comprises a PDE-ODE coupled system to describe the biomass and carbon respectively. The model equations are discretized in space using a standard finite volume method. We introduce discrete attachment events into the discretized model via an impulse function with a standard stochastic process as input. We solve our model with an implicit ODE solver. We provide basic simulations to investigate the qualitative features of our model. We then perform a grid refinement study to investigate the spatial convergence of our model. We investigate model behaviour while varying key attachment parameters. Lastly, we use our attachment model to provide evidence for a stable travelling wave solution to the original PDE-ODE coupled system.
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Affiliation(s)
- Jack M Hughes
- Department of Mathematics, University of British Columbia, 1984 Mathematics Rd., Vancouver, BC V6T 1Z2, Canada
| | - Hermann J Eberl
- Department of Mathematics and Statistics, University of Guelph, 50 Stone Rd E., Guelph, ON N1G 2W1, Canada
| | - Stefanie Sonner
- Radboud University, IMAPP - Mathematics, Postbus 9010, 6500 GL Nijmegen, The Netherlands
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5
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Zhang H, Yang P, Wang Z, Li M, Zhang J, Liu D, Chen Y, Ying H. Clostridium acetobutylicum Biofilm: Advances in Understanding the Basis. Front Bioeng Biotechnol 2021; 9:658568. [PMID: 34150727 PMCID: PMC8209462 DOI: 10.3389/fbioe.2021.658568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Clostridium acetobutylicum is an important industrial platform capable of producing a variety of biofuels and bulk chemicals. Biofilm of C. acetobutylicum renders many production advantages and has been long and extensively applied in fermentation. However, molecular and genetic mechanisms underlying the biofilm have been much less studied and remain largely unknown. Here, we review studies to date focusing on C. acetobutylicum biofilms, especially on its physiological and molecular aspects, summarizing the production advantages, cell physiological changes, extracellular matrix components and regulatory genes of the biofilm. This represents the first review dedicated to the biofilm of C. acetobutylicum. Hopefully, it will deepen our understanding toward C. acetobutylicum biofilm and inspire more research to learn and develop more efficient biofilm processes in this industrially important bacterium.
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Affiliation(s)
- Huifang Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Pengpeng Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Zhenyu Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Mengting Li
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China
| | - Jie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Dong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, China
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6
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Elter A, Bock T, Spiehl D, Russo G, Hinz SC, Bitsch S, Baum E, Langhans M, Meckel T, Dörsam E, Kolmar H, Schwall G. Carbohydrate binding module-fused antibodies improve the performance of cellulose-based lateral flow immunoassays. Sci Rep 2021; 11:7880. [PMID: 33846482 PMCID: PMC8042022 DOI: 10.1038/s41598-021-87072-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/23/2021] [Indexed: 01/24/2023] Open
Abstract
Since the pandemic outbreak of Covid-19 in December 2019, several lateral flow assay (LFA) devices were developed to enable the constant monitoring of regional and global infection processes. Additionally, innumerable lateral flow test devices are frequently used for determination of different clinical parameters, food safety, and environmental factors. Since common LFAs rely on non-biodegradable nitrocellulose membranes, we focused on their replacement by cellulose-composed, biodegradable papers. We report the development of cellulose paper-based lateral flow immunoassays using a carbohydrate-binding module-fused to detection antibodies. Studies regarding the protein binding capacity and potential protein wash-off effects on cellulose paper demonstrated a 2.7-fold protein binding capacity of CBM-fused antibody fragments compared to the sole antibody fragment. Furthermore, this strategy improved the spatial retention of CBM-fused detection antibodies to the test area, which resulted in an enhanced sensitivity and improved overall LFA-performance compared to the naked detection antibody. CBM-assisted antibodies were validated by implementation into two model lateral flow test devices (pregnancy detection and the detection of SARS-CoV-2 specific antibodies). The CBM-assisted pregnancy LFA demonstrated sensitive detection of human gonadotropin (hCG) in synthetic urine and the CBM-assisted Covid-19 antibody LFA was able to detect SARS-CoV-2 specific antibodies present in serum. Our findings pave the way to the more frequent use of cellulose-based papers instead of nitrocellulose in LFA devices and thus potentially improve the sustainability in the field of POC diagnostics.
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Affiliation(s)
- Adrian Elter
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany.,Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany
| | - Tina Bock
- Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany.,Sustainability, Science and Technology Relations, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany
| | - Dieter Spiehl
- Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany.,Institue of Printing Science and Technology, Technical University of Darmstadt, Magdalenenstrasse 2, 64289, Darmstadt, Germany
| | - Giulio Russo
- Department of Biotechnology, Technical University of Braunschweig, Spielmannstrasse 7, 38124, Braunschweig, Germany.,Abcalis GmbH, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany.,Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany
| | - Sebastian Bitsch
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany.,Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany
| | - Eva Baum
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany.,Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany
| | - Markus Langhans
- Macromolecular Chemistry and Paper Chemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany
| | - Tobias Meckel
- Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany.,Macromolecular Chemistry and Paper Chemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany
| | - Edgar Dörsam
- Institue of Printing Science and Technology, Technical University of Darmstadt, Magdalenenstrasse 2, 64289, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, 64287, Darmstadt, Germany. .,Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany.
| | - Gerhard Schwall
- Merck Lab, Technical University of Darmstadt, Alarich-Weiss-Strasse 8, 64287, Darmstadt, Germany. .,Sustainability, Science and Technology Relations, Merck KGaA, Frankfurter Strasse 250, 64293, Darmstadt, Germany.
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7
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Jiang Y, Liu Y, Zhang X, Gao H, Mou L, Wu M, Zhang W, Xin F, Jiang M. Biofilm application in the microbial biochemicals production process. Biotechnol Adv 2021; 48:107724. [PMID: 33640404 DOI: 10.1016/j.biotechadv.2021.107724] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022]
Abstract
Biofilms can be naturally formed through the attachment of microorganisms on the supporting materials. However, natural biofilms formed in the environment may cause some detrimental effects, such as the equipment contamination and food safety issues et al. On the contrary, biofilms mediated microbial fermentation provides a promising approach for the efficient biochemicals production owing to the properties of self-immobilization, high resistance to toxic reactants and maintenance of long-term cells activity. While few reviews have specifically addressed the biological application of biofilms in the microbial fermentation process. Accordingly, this review will comprehensively summarize the biofilms formation mechanism and potential functions in the microbial fermentation process. Furthermore, the construction strategies for the formation of stable biofilms through synthetic biology technology or the modification of suitable supporting materials will be also discussed. The application of biofilms mediated fermentation will provide an outlook for the biorefinery platform in the future.
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Affiliation(s)
- Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Yansong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Xiaoyu Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Hao Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Lu Mou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Mengdi Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
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8
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Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes. Nat Commun 2020; 11:4708. [PMID: 32948758 PMCID: PMC7501288 DOI: 10.1038/s41467-020-18543-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/28/2020] [Indexed: 11/08/2022] Open
Abstract
While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. Our analysis of this data reveals an absolute protein-to-RNA ratio of 102–104 for bacterial populations and 103–105 for an archaeon, which is more comparable to Eukaryotic representatives’ humans and yeast. Furthermore, we use the linearity between the metaproteome and metatranscriptome over time to identify core functional guilds, hence using a fundamental biological feature (i.e., RNA/protein levels) to highlight phenotypical complementarity. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function. Here, the authors perform a temporal multi-omic analysis of a minimalistic cellulose-degrading and methane-producing consortium at the strain level and estimate protein-to-RNA ratios and RNA-protein dynamics of the community simultaneously over time.
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9
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Brethauer S, Shahab RL, Studer MH. Impacts of biofilms on the conversion of cellulose. Appl Microbiol Biotechnol 2020; 104:5201-5212. [PMID: 32337627 PMCID: PMC7275028 DOI: 10.1007/s00253-020-10595-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/02/2022]
Abstract
Abstract Lignocellulose is a widely available renewable carbon source and a promising feedstock for the production of various chemicals in biorefineries. However, its recalcitrant nature is a major hurdle that must be overcome to enable economic conversion processes. Deconstruction of lignocellulose is part of the global carbon cycle, and efficient microbial degradation systems have evolved that might serve as models to improve commercial conversion processes. Biofilms—matrix encased, spatially organized clusters of microbial cells and the predominating lifestyle in nature—have been recognized for their essential role in the degradation of cellulose in nature, e.g., in soils or in the digestive tracts of ruminant animals. Cellulolytic biofilms allow for a high concentration of enzymes at the boundary layer between the solid substrate and the liquid phase and the more complete capture of hydrolysis products directly at the hydrolysis site, which is energetically favorable. Furthermore, enhanced expression of genes for carbohydrate active enzymes as a response to the attachment on solid substrate has been demonstrated for cellulolytic aerobic fungi and anerobic bacteria. In natural multispecies biofilms, the vicinity of different microbial species allows the creation of efficient food webs and synergistic interactions thereby, e.g., avoiding the accumulation of inhibiting metabolites. In this review, these topics are discussed and attempts to realize the benefits of biofilms in targeted applications such as the consolidated bioprocessing of lignocellulose are highlighted. Key Points Multispecies biofilms enable efficient lignocellulose destruction in the biosphere. Cellulose degradation by anaerobic bacteria often occurs by monolayered biofilms. Fungal biofilms immobilize enzymes and substrates in an external digestion system. Surface attached cultures typically show higher expression of cellulolytic enzymes.
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Affiliation(s)
- Simone Brethauer
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland
| | - Robert L Shahab
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland
| | - Michael H Studer
- School of Agricultural, Forest and Food Sciences, Laboratory of Biofuels and Biochemicals, Bern University of Applied Sciences (BFH), 3052, Zollikofen, Switzerland.
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10
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Sivadon P, Barnier C, Urios L, Grimaud R. Biofilm formation as a microbial strategy to assimilate particulate substrates. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:749-764. [PMID: 31342619 DOI: 10.1111/1758-2229.12785] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 07/15/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
In most ecosystems, a large part of the organic carbon is not solubilized in the water phase. Rather, it occurs as particles made of aggregated hydrophobic and/or polymeric natural or man-made organic compounds. These particulate substrates are degraded by extracellular digestion/solubilization implemented by heterotrophic bacteria that form biofilms on them. Organic particle-degrading biofilms are widespread and have been observed in aquatic and terrestrial natural ecosystems, in polluted and man-driven environments and in the digestive tracts of animals. They have central ecological functions as they are major players in carbon recycling and pollution removal. The aim of this review is to highlight bacterial adhesion and biofilm formation as central mechanisms to exploit the nutritive potential of organic particles. It focuses on the mechanisms that allow access and assimilation of non-dissolved organic carbon, and considers the advantage provided by biofilms for gaining a net benefit from feeding on particulate substrates. Cooperative and competitive interactions taking place in biofilms feeding on particulate substrates are also discussed.
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Affiliation(s)
- Pierre Sivadon
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
| | - Claudie Barnier
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
| | - Laurent Urios
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
| | - Régis Grimaud
- CNRS/Université de Pau et des Pays de l'Adour/E2S UPPA, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux UMR5254, Pau, 64000, France
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11
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Ichikawa S, Ogawa S, Nishida A, Kobayashi Y, Kurosawa T, Karita S. Cellulosomes localise on the surface of membrane vesicles from the cellulolytic bacterium Clostridium thermocellum. FEMS Microbiol Lett 2019; 366:5526221. [DOI: 10.1093/femsle/fnz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
ABSTRACTMembrane vesicles released from bacteria contribute to cell–cell communication by carrying various cargos such as proteins, nucleic acids and signaling molecules. Cellulolytic bacteria have been isolated from many environments, yet the function of membrane vesicles for cellulolytic ability has been rarely described. Here, we show that a Gram-positive cellulolytic bacterium Clostridium thermocellum released membrane vesicles, each approximately 50–300 nm in diameter, into the broth. The observations with immunoelectron microscopy also revealed that cellulosomes, which are carbohydrate-active enzyme complexes that give C. thermocellum high cellulolytic activity, localized on the surface of the membrane vesicles. The membrane vesicles collected by ultracentrifugation maintained the cellulolytic activity. Supplementation with the biosurfactant surfactin or sonication treatment disrupted the membrane vesicles in the exoproteome of C. thermocellum and significantly decreased the degradation activity of the exoproteome for microcrystalline cellulose. However, these did not affect the degradation activity for soluble carboxymethyl cellulose. These results suggest a novel function of membrane vesicles: C. thermocellum releases cellulolytic enzymes on the surface of membrane vesicles to enhance the cellulolytic activity of C. thermocellum for crystalline cellulose.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Satoru Ogawa
- Faculty of Medicine, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Ayami Nishida
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Yuzuki Kobayashi
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Toshihito Kurosawa
- Advanced Science Research Promotion Center, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
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Microfluidic study of effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength in the flowing and no-flowing microchannels. ACTA ACUST UNITED AC 2019; 46:855-868. [DOI: 10.1007/s10295-019-02161-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/05/2019] [Indexed: 01/12/2023]
Abstract
Abstract
Biofilm accumulation in porous media can cause pore plugging and change many of the physical properties of porous media. Engineering bioplugging may have significant applications for many industrial processes, while improved knowledge on biofilm accumulation in porous media at porescale in general has broad relevance for a range of industries as well as environmental and water research. The experimental results by means of microscopic imaging over a T-shape microchannel clearly show that increase in fluid velocity could facilitate biofilm growth, but that above a velocity threshold, biofilm detachment and inhibition of biofilm formation due to high shear stress were observed. High nutrient concentration prompts the biofilm growth; however, the generated biofilm displays a weak adhesive strength. This paper provides an overview of biofilm development in a hydrodynamic environment for better prediction and modelling of bioplugging processes associated with porous systems in petroleum industry, hydrogeology and water purification.
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13
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Bomble YJ, Lin CY, Amore A, Wei H, Holwerda EK, Ciesielski PN, Donohoe BS, Decker SR, Lynd LR, Himmel ME. Lignocellulose deconstruction in the biosphere. Curr Opin Chem Biol 2017; 41:61-70. [DOI: 10.1016/j.cbpa.2017.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022]
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14
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Verbeke TJ, Garcia GM, Elkins JG. The effect of switchgrass loadings on feedstock solubilization and biofuel production by Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:233. [PMID: 29213307 PMCID: PMC5708108 DOI: 10.1186/s13068-017-0917-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/08/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Efficient deconstruction and bioconversion of solids at high mass loadings is necessary to produce industrially relevant titers of biofuels from lignocellulosic biomass. To date, only a few studies have investigated the effect of solids loadings on microorganisms of interest for consolidated bioprocessing. Here, the effects that various switchgrass loadings have on Clostridium thermocellum solubilization and bioconversion are investigated. RESULTS Clostridium thermocellum was grown for 10 days on 10, 25, or 50 g/L switchgrass or Avicel at equivalent glucan loadings. Avicel was completely consumed at all loadings, but total cellulose solubilization decreased from 63 to 37% as switchgrass loadings increased from 10 to 50 g/L. Washed, spent switchgrass could be additionally hydrolyzed and fermented in second-round fermentations suggesting that access to fermentable substrates was not the limiting factor at higher feedstock loadings. Results from fermentations on Avicel or cellobiose using culture medium supplemented with 50% spent fermentation broth demonstrated that compounds present in the supernatants from the 25 or 50 g/L switchgrass loadings were the most inhibitory to continued fermentation. CONCLUSIONS Recalcitrance alone cannot fully account for differences in solubilization and end-product formation between switchgrass and Avicel at increased substrate loadings. Experiments aimed at separating metabolic inhibition from inhibition of hydrolysis suggest that C. thermocellum's hydrolytic machinery is more vulnerable to inhibition from switchgrass-derived compounds than its fermentative metabolism.
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Affiliation(s)
- Tobin J. Verbeke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Present Address: Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4 Canada
| | - Gabriela M. Garcia
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
| | - James G. Elkins
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038 USA
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15
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Eberl H, Jalbert E, Dumitrache A, Wolfaardt G. A spatially explicit model of inverse colony formation of cellulolytic biofilms. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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16
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Van Wyk N, Navarro D, Blaise M, Berrin JG, Henrissat B, Drancourt M, Kremer L. Characterization of a mycobacterial cellulase and its impact on biofilm- and drug-induced cellulose production. Glycobiology 2017; 27:392-399. [DOI: 10.1093/glycob/cwx014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/01/2017] [Indexed: 12/20/2022] Open
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17
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Dumitrache A, Klingeman DM, Natzke J, Rodriguez M, Giannone RJ, Hettich RL, Davison BH, Brown SD. Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells. Sci Rep 2017; 7:43583. [PMID: 28240279 PMCID: PMC5327387 DOI: 10.1038/srep43583] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/25/2017] [Indexed: 01/01/2023] Open
Abstract
Clostridium (Ruminiclostridium) thermocellum is a model organism for its ability to deconstruct plant biomass and convert the cellulose into ethanol. The bacterium forms biofilms adherent to lignocellulosic feedstocks in a continuous cell-monolayer in order to efficiently break down and uptake cellulose hydrolysates. We developed a novel bioreactor design to generate separate sessile and planktonic cell populations for omics studies. Sessile cells had significantly greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division consistent with substrate replete conditions. Planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. This study demonstrates that microbial attachment to cellulose substrate produces widespread gene expression changes for critical functions of this organism and provides physiological insights for two cells populations relevant for engineering of industrially-ready phenotypes.
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Affiliation(s)
- Alexandru Dumitrache
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Dawn M Klingeman
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Jace Natzke
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Miguel Rodriguez
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Richard J Giannone
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Robert L Hettich
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Brian H Davison
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
| | - Steven D Brown
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A
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Willson BJ, Kovács K, Wilding-Steele T, Markus R, Winzer K, Minton NP. Production of a functional cell wall-anchored minicellulosome by recombinant Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:109. [PMID: 27222664 PMCID: PMC4877998 DOI: 10.1186/s13068-016-0526-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/10/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The use of fossil fuels is no longer tenable. Not only are they a finite resource, their use is damaging the environment through pollution and global warming. Alternative, environmentally friendly, renewable sources of chemicals and fuels are required. To date, the focus has been on using lignocellulose as a feedstock for microbial fermentation. However, its recalcitrance to deconstruction is making the development of economic processes extremely challenging. One solution is the generation of an organism suitable for use in consolidated bioprocessing (CBP), i.e. one able to both hydrolyse lignocellulose and ferment the released sugars, and this represents an important goal for synthetic biology. We aim to use synthetic biology to develop the solventogenic bacterium C. acetobutylicum as a CBP organism through the introduction of a cellulosome, a complex of cellulolytic enzymes bound to a scaffold protein called a scaffoldin. In previous work, we were able to demonstrate the in vivo production of a C. thermocellum-derived minicellulosome by recombinant strains of C. acetobutylicum, and aim to develop on this success, addressing potential issues with the previous strategy. RESULTS The genes for the cellulosomal enzymes Cel9G, Cel48F, and Xyn10A from C. cellulolyticum were integrated into the C. acetobutylicum genome using Allele-Coupled Exchange (ACE) technology, along with a miniscaffoldin derived from C. cellulolyticum CipC. The possibility of anchoring the recombinant cellulosome to the cell surface using the native sortase system was assessed, and the cellulolytic properties of the recombinant strains were assayed via plate growth, batch fermentation and sugar release assays. CONCLUSIONS We have been able to demonstrate the synthesis and in vivo assembly of a four-component minicellulosome by recombinant C. acetobutylicum strains. Furthermore, we have been able to anchor a minicellulosome to the C. acetobutylicum cell wall by the use of the native sortase system. The recombinant strains display an improved growth phenotype on xylan and an increase in released reducing sugar from several substrates including untreated powdered wheat straw. This constitutes an important milestone towards the development of a truly cellulolytic strain suitable for CBP.
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Affiliation(s)
- Benjamin J. Willson
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Katalin Kovács
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Tom Wilding-Steele
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Robert Markus
- />SLIM Imaging Unit, Faculty of Medicine and Health Sciences, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Klaus Winzer
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Nigel P. Minton
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
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Direct Image-Based Enumeration of Clostridium phytofermentans Cells on Insoluble Plant Biomass Growth Substrates. Appl Environ Microbiol 2016; 82:972-8. [PMID: 26637592 DOI: 10.1128/aem.03119-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/15/2015] [Indexed: 11/20/2022] Open
Abstract
A dual-fluorescent-dye protocol to visualize and quantify Clostridium phytofermentans ISDg (ATCC 700394) cells growing on insoluble cellulosic substrates was developed by combining calcofluor white staining of the growth substrate with cell staining using the nucleic acid dye Syto 9. Cell growth, cell substrate attachment, and fermentation product formation were investigated in cultures containing either Whatman no. 1 filter paper, wild-type Sorghum bicolor, or a reduced-lignin S. bicolor double mutant (bmr-6 bmr-12 double mutant) as the growth substrate. After 3 days of growth, cell numbers in cultures grown on filter paper as the substrate were 6.0- and 2.2-fold higher than cell numbers in cultures with wild-type sorghum and double mutant sorghum, respectively. However, cells produced more ethanol per cell when grown with either sorghum substrate than with filter paper as the substrate. Ethanol yields of cultures were significantly higher with double mutant sorghum than with wild-type sorghum or filter paper as the substrate. Moreover, ethanol production correlated with cell attachment in sorghum cultures: 90% of cells were directly attached to the double mutant sorghum substrate, while only 76% of cells were attached to wild-type sorghum substrate. With filter paper as the growth substrate, ethanol production was correlated with cell number; however, with either wild-type or mutant sorghum, ethanol production did not correlate with cell number, suggesting that only a portion of the microbial cell population was active during growth on sorghum. The dual-staining procedure described here may be used to visualize and enumerate cells directly on insoluble cellulosic substrates, enabling in-depth studies of interactions of microbes with plant biomass.
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20
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Sun L, Liu T, Müller B, Schnürer A. The microbial community structure in industrial biogas plants influences the degradation rate of straw and cellulose in batch tests. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:128. [PMID: 27330562 PMCID: PMC4912747 DOI: 10.1186/s13068-016-0543-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 06/02/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Materials rich in lignocellulose, such as straw, are abundant, cheap and highly interesting for biogas production. However, the complex structure of lignocellulose is difficult for microbial cellulolytic enzymes to access, limiting degradation. The rate of degradation depends on the activity of members of the microbial community, but the knowledge of this community in the biogas process is rather limited. This study, therefore, investigated the degradation rate of cellulose and straw in batch cultivation test initiated with inoculums from four co-digestion biogas plants (CD) and six wastewater treatment plants (WWTP). The results were correlated to the bacterial community by 454-pyrosequencing targeting 16S rRNA gene and by T-RFLP analysis targeting genes of glycoside hydrolase families 5 (cel5) and 48 (cel48), combined with construction of clone libraries. RESULTS UniFrac principal coordinate analysis of 16S rRNA gene amplicons revealed a clustering of WWTPs, while the CDs were more separated from each other. Bacteroidetes and Firmicutes dominated the community with a comparably higher abundance of the latter in the processes operating at high ammonia levels. Sequences obtained from the cel5 and cel 48 clone libraries were also mainly related to the phyla Firmicutes and Bacteroidetes and here ammonia was a parameter with a strong impact on the cel5 community. The results from the batch cultivation showed similar degradation pattern for eight of the biogas plants, while two characterised by high ammonia level and low bacterial diversity, showed a clear lower degradation rate. Interestingly, two T-RFs from the cel5 community were positively correlated to high degradation rates of both straw and cellulose. One of the respective partial cel5 sequences shared 100 % identity to Clostridium cellulolyticum. CONCLUSION The degradation rate of cellulose and straw varied in the batch tests dependent on the origin of the inoculum and was negatively correlated with the ammonia level. The cellulose-degrading community, targeted by analysis of the glycoside hydrolase families 5 (cel5) and 48 (cel48), showed a dominance of bacteria belonging the Firmicutes and Bacteriodetes, and a positive correlation was found between the cellulose degradation rate of wheat straw with the level of C. cellulolyticum.
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Affiliation(s)
- Li Sun
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Tong Liu
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Bettina Müller
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
| | - Anna Schnürer
- />Department of Microbiology, Swedish University of Agricultural Science, Uppsala BioCenter, P.O. Box 7025, 750 07 Uppsala, Sweden
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Science, 1432 Ås, Norway
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Dumitrache A, Eberl HJ, Allen DG, Wolfaardt GM. Mathematical modeling to validate on-line CO2 measurements as a metric for cellulolytic biofilm activity in continuous-flow bioreactors. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Progress and challenges in the engineering of non-cellulolytic microorganisms for consolidated bioprocessing. Curr Opin Biotechnol 2015; 33:32-8. [DOI: 10.1016/j.copbio.2014.10.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/06/2014] [Accepted: 10/11/2014] [Indexed: 11/23/2022]
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23
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Weller C, Wu M. A generation-time effect on the rate of molecular evolution in bacteria. Evolution 2015; 69:643-52. [PMID: 25564727 DOI: 10.1111/evo.12597] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/17/2014] [Indexed: 12/31/2022]
Abstract
Molecular evolutionary rate varies significantly among species and a strict global molecular clock has been rejected across the tree of life. Generation time is one primary life-history trait that influences the molecular evolutionary rate. Theory predicts that organisms with shorter generation times evolve faster because of the accumulation of more DNA replication errors per unit time. Although the generation-time effect has been demonstrated consistently in plants and animals, the evidence of its existence in bacteria is lacking. The bacterial phylum Firmicutes offers an excellent system for testing generation-time effect because some of its members can enter a dormant, nonreproductive endospore state in response to harsh environmental conditions. It follows that spore-forming bacteria would--with their longer generation times--evolve more slowly than their nonspore-forming relatives. It is therefore surprising that a previous study found no generation-time effect in Firmicutes. Using a phylogenetic comparative approach and leveraging on a large number of Firmicutes genomes, we found sporulation significantly reduces the genome-wide spontaneous DNA mutation rate and protein evolutionary rate. Contrary to the previous study, our results provide strong evidence that the evolutionary rates of bacteria, like those of plants and animals, are influenced by generation time.
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Affiliation(s)
- Cory Weller
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904
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24
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Biofilms of Clostridium species. Anaerobe 2014; 30:193-8. [DOI: 10.1016/j.anaerobe.2014.09.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/10/2014] [Accepted: 09/14/2014] [Indexed: 12/30/2022]
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25
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Yang YC, Liu X, Wan C, Sun S, Lee DJ. Accelerated aerobic granulation using alternating feed loadings: alginate-like exopolysaccharides. BIORESOURCE TECHNOLOGY 2014; 171:360-366. [PMID: 25218208 DOI: 10.1016/j.biortech.2014.08.092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 06/03/2023]
Abstract
Alginate-like exopolysaccharides (ALE) likely contribute markedly to strength of aerobic granules. This study cultivated aerobic granules from propionate wastewaters using strategies with different organic loading rates (OLRs) (4.4-17.4 kg/m(3)-d). When the OLR increased suddenly, the constituent cells (Pseudomonas, Clostridium, Thauera and Arthrobacter) were stimulated to secret extracellular cyclic diguanylate (c-di-GMP) and produced excess ALE, which formed a large quantity of sticky materials that served as the precursor of aerobic granules. Formation of excess ALE was the prerequisite for accelerated granulation. Conversely, this study observed no enrichment of poly guluronic acid blocks in ALE during granulation.
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Affiliation(s)
- Ya-Chun Yang
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan
| | - Xiang Liu
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Chunli Wan
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Supu Sun
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan.
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26
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Akinosho H, Yee K, Close D, Ragauskas A. The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Front Chem 2014; 2:66. [PMID: 25207268 PMCID: PMC4143619 DOI: 10.3389/fchem.2014.00066] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/28/2014] [Indexed: 01/25/2023] Open
Abstract
First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.
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Affiliation(s)
- Hannah Akinosho
- School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology Atlanta, GA, USA ; Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA
| | - Kelsey Yee
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dan Close
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Arthur Ragauskas
- Oak Ridge National Laboratory, BioEnergy Science Center Oak Ridge, TN, USA ; Department of Chemical and Biomolecular Engineering and Department of Forestry, Wildlife, and Fisheries, University of Tennessee Knoxville, TN, USA
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27
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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28
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Zuroff TR, Gu W, Fore RL, Leschine SB, Curtis WR. Insights into Clostridium phytofermentans biofilm formation: aggregation, microcolony development and the role of extracellular DNA. MICROBIOLOGY-SGM 2014; 160:1134-1143. [PMID: 24625451 DOI: 10.1099/mic.0.078014-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biofilm formation is a critical component to the lifestyle of many naturally occurring cellulose-degrading microbes. In this work, cellular aggregation and biofilm formation of Clostridium phytofermentans, a cellulolytic anaerobic bacterium, was investigated using a combination of microscopy and analytical techniques. Aggregates included thread-like linkages and a DNA/protein-rich extracellular matrix when grown on soluble cellobiose. Similar dense biofilms formed on the surface of the model cellulosic substrate Whatman no. 1 filter paper. Following initially dispersed attachment, microcolonies of ~500 µm diameter formed on the filter paper after 6 days. Enzymic treatment of both the biofilm and cellular aggregates with DNase and proteinase resulted in significant loss of rigidity, pointing to the key role of extracellular DNA and proteins in the biofilm structure. A high-throughput biofilm assay was adapted for studying potential regulators of biofilm formation. Various media manipulations were shown to greatly impact biofilm formation, including repression in the presence of glucose but not the β(1→4)-linked disaccharide cellobiose, implicating a balance of hydrolytic activity and assimilation to maintain biofilm integrity. Using the microtitre plate biofilm assay, DNase and proteinase dispersed ~60 and 30 % of mature biofilms, respectively, whilst RNase had no impact. This work suggests that Clostridium phytofermentans has evolved a DNA/protein-rich biofilm matrix complementing its cellulolytic nature. These insights add to our current understanding of natural ecosystems as well as strategies for efficient bioprocess design.
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Affiliation(s)
- Trevor R Zuroff
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Weimin Gu
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Rachel L Fore
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Susan B Leschine
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Wayne R Curtis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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Prawitwong P, Waeonukul R, Tachaapaikoon C, Pason P, Ratanakhanokchai K, Deng L, Sermsathanaswadi J, Septiningrum K, Mori Y, Kosugi A. Direct glucose production from lignocellulose using Clostridium thermocellum cultures supplemented with a thermostable β-glucosidase. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:184. [PMID: 24359557 PMCID: PMC3878107 DOI: 10.1186/1754-6834-6-184] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/05/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cellulases continue to be one of the major costs associated with the lignocellulose hydrolysis process. Clostridium thermocellum is an anaerobic, thermophilic, cellulolytic bacterium that produces cellulosomes capable of efficiently degrading plant cell walls. The end-product cellobiose, however, inhibits degradation. To maximize the cellulolytic ability of C. thermocellum, it is important to eliminate this end-product inhibition. RESULTS This work describes a system for biological saccharification that leads to glucose production following hydrolysis of lignocellulosic biomass. C. thermocellum cultures supplemented with thermostable beta-glucosidases make up this system. This approach does not require any supplementation with cellulases and hemicellulases. When C. thermocellum strain S14 was cultured with a Thermoanaerobacter brockii beta-glucosidase (CglT with activity 30 U/g cellulose) in medium containing 100 g/L cellulose (617 mM initial glucose equivalents), we observed not only high degradation of cellulose, but also accumulation of 426 mM glucose in the culture broth. In contrast, cultures without CglT, or with less thermostable beta-glucosidases, did not efficiently hydrolyze cellulose and accumulated high levels of glucose. Glucose production required a cellulose load of over 10 g/L. When alkali-pretreated rice straw containing 100 g/L glucan was used as the lignocellulosic biomass, approximately 72% of the glucan was saccharified, and glucose accumulated to 446 mM in the culture broth. The hydrolysate slurry containing glucose was directly fermented to 694 mM ethanol by addition of Saccharomyces cerevisiae, giving an 85% theoretical yield without any inhibition. CONCLUSIONS Our process is the first instance of biological saccharification with exclusive production and accumulation of glucose from lignocellulosic biomass. The key to its success was the use of C. thermocellum supplemented with a thermostable beta-glucosidase and cultured under a high cellulose load. We named this approach biological simultaneous enzyme production and saccharification (BSES). BSES may resolve a significant barrier to economical production by providing a platform for production of fermentable sugars with reduced enzyme amounts.
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Affiliation(s)
- Panida Prawitwong
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Lan Deng
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Junjarus Sermsathanaswadi
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, Thailand
| | - Krisna Septiningrum
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- University of Tsukuba Graduate School of Life and Environmental Sciences, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yutaka Mori
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- University of Tsukuba Graduate School of Life and Environmental Sciences, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8572, Japan
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Dumitrache A, Wolfaardt GM, Allen DG, Liss SN, Lynd LR. Tracking the cellulolytic activity of Clostridium thermocellum biofilms. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:175. [PMID: 24286524 PMCID: PMC4176736 DOI: 10.1186/1754-6834-6-175] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/02/2013] [Indexed: 05/10/2023]
Abstract
BACKGROUND Microbial cellulose conversion by Clostridium thermocellum 27405 occurs predominantly through the activity of substrate-adherent bacteria organized in thin, primarily single cell-layered biofilms. The importance of cellulosic surface exposure to microbial hydrolysis has received little attention despite its implied impact on conversion kinetics. RESULTS We showed the spatial heterogeneity of fiber distribution in pure cellulosic sheets, which made direct measurements of biofilm colonization and surface penetration impossible. Therefore, we utilized on-line measurements of carbon dioxide (CO2) production in continuous-flow reactors, in conjunction with confocal imaging, to observe patterns of biofilm invasion and to indirectly estimate microbial accessibility to the substrate's surface and the resulting limitations on conversion kinetics. A strong positive correlation was found between cellulose consumption and CO2 production (R2 = 0.996) and between surface area and maximum biofilm activity (R2 = 0.981). We observed an initial biofilm development rate (0.46 h-1, 0.34 h-1 and 0.33 h-1) on Whatman sheets (#1, #598 and #3, respectively) that stabilized when the accessible surface was maximally colonized. The results suggest that cellulose conversion kinetics is initially subject to a microbial limitation period where the substrate is in excess, followed by a substrate limitation period where cellular mass, in the form of biofilms, is not limiting. Accessible surface area acts as an important determinant of the respective lengths of these two distinct periods. At end-point fermentation, all sheets were digested predominantly under substrate accessibility limitations (e.g., up to 81% of total CO2 production for Whatman #1). Integration of CO2 production rates over time showed Whatman #3 underwent the fastest conversion efficiency under microbial limitation, suggestive of best biofilm penetration, while Whatman #1 exhibited the least recalcitrance and the faster degradation during the substrate limitation period. CONCLUSION The results showed that the specific biofilm development rate of cellulolytic bacteria such as C. thermocellum has a notable effect on overall reactor kinetics during the period of microbial limitation, when ca. 20% of cellulose conversion occurs. The study further demonstrated the utility of on-line CO2 measurements as a method to assess biofilm development and substrate digestibility pertaining to microbial solubilization of cellulose, which is relevant when considering feedstock pre-treatment options.
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Affiliation(s)
- Alexandru Dumitrache
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St., Toronto, ON M5S 3E1, Canada
| | - Gideon M Wolfaardt
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto, ON M5B 2K3, Canada
- Stellenbosch Institute for Advanced Study Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa
| | - David Grant Allen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St., Toronto, ON M5S 3E1, Canada
| | - Steven N Liss
- School of Environmental Studies and Department of Chemical Engineering, Queen’s University, 99 University Ave., Kingston, ON K7L 3N6, Canada
| | - Lee R Lynd
- Thayer School of Engineering, Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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Ferdinand PH, Borne R, Trotter V, Pagès S, Tardif C, Fierobe HP, Perret S. Are cellulosome scaffolding protein CipC and CBM3-containing protein HycP, involved in adherence of Clostridium cellulolyticum to cellulose? PLoS One 2013; 8:e69360. [PMID: 23935995 PMCID: PMC3723904 DOI: 10.1371/journal.pone.0069360] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/07/2013] [Indexed: 01/09/2023] Open
Abstract
Clostridium cellulolyticum, a mesophilic anaerobic bacterium, produces highly active enzymatic complexes called cellulosomes. This strain was already shown to bind to cellulose, however the molecular mechanism(s) involved is not known. In this context we focused on the gene named hycP, encoding a 250-kDa protein of unknown function, containing a Family-3 Carbohydrate Binding Module (CBM3) along with 23 hyaline repeat modules (HYR modules). In the microbial kingdom the gene hycP is only found in C. cellulolyticum and the very close strain recently sequenced Clostridium sp BNL1100. Its presence in C. cellulolyticum guided us to analyze its function and its putative role in adhesion of the cells to cellulose. The CBM3 of HycP was shown to bind to crystalline cellulose and was assigned to the CBM3b subfamily. No hydrolytic activity on cellulose was found with a mini-protein displaying representative domains of HycP. A C. cellulolyticum inactivated hycP mutant strain was constructed, and we found that HycP is neither involved in binding of the cells to cellulose nor that the protein has an obvious role in cell growth on cellulose. We also characterized the role of the cellulosome scaffolding protein CipC in adhesion of C. cellulolyticum to cellulose, since cellulosome scaffolding protein has been proposed to mediate binding of other cellulolytic bacteria to cellulose. A second mutant was constructed, where cipC was inactivated. We unexpectedly found that CipC is only partly involved in binding of C. cellulolyticum to cellulose. Other mechanisms for cellulose adhesion may therefore exist in C. cellulolyticum. In addition, no cellulosomal protuberances were observed at the cellular surface of C. cellulolyticum, what is in contrast to reports from several other cellulosomes producing strains. These findings may suggest that C. cellulolyticum has no dedicated molecular mechanism to aggregate the cellulosomes at the cellular surface.
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Wang ZW, Lee SH, Elkins JG, Li Y, Hamilton-Brehm S, Morrell-Falvey JL. Continuous live cell imaging of cellulose attachment by microbes under anaerobic and thermophilic conditions using confocal microscopy. J Environ Sci (China) 2013; 25:849-56. [PMID: 24218813 DOI: 10.1016/s1001-0742(12)60104-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Live cell imaging methods provide important insights into the dynamics of cellular processes that cannot be derived easily from population-averaged datasets. In the bioenergy field, much research is focused on fermentation of cellulosic biomass by thermophilic microbes to produce biofuels; however, little effort is dedicated to the development of imaging tools to monitor this dynamic biological process. This is, in part, due to the experimental challenges of imaging cells under both anaerobic and thermophilic conditions. Here an imaging system is described that integrates confocal microscopy, a flow cell device, and a lipophilic dye to visualize cells. Solutions to technical obstacles regarding suitable fluorescent markers, photodamage during imaging, and maintenance of environmental conditions during imaging are presented. This system was utilized to observe cellulose colonization by Clostridium thermocellum under anaerobic conditions at 60 degrees C. This method enables live cell imaging of bacterial growth under anaerobic and thermophilic conditions and should be widely applicable to visualizing different cell types or processes in real time.
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Affiliation(s)
- Zhi-Wu Wang
- BioEnergy Science Center Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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