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Engel D, Hoffmann M, Kosfeld U, Mann M. Online monitoring of methane transfer rates unveils nitrogen fixation dynamics in Methylococcus capsulatus. Biotechnol Bioeng 2024. [PMID: 39392283 DOI: 10.1002/bit.28855] [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: 03/07/2024] [Revised: 09/09/2024] [Accepted: 09/20/2024] [Indexed: 10/12/2024]
Abstract
This study explores methane utilization by the methanotrophic microorganism Methylococcus capsulatus (Bath) for biomass production, presenting a promising approach to mitigate methane emissions and foster the development sustainable biomaterials. Traditional screening methods for gas cultivations involve either serum flasks without online monitoring or costly, low-throughput fermenters. To address these limitations, the Respiration Activity MOnitoring System was augmented with methane sensors for real-time methane transfer rate (MTR) monitoring in shake flasks. Utilizing online monitoring of the MTR in shake flasks results in enhanced throughput and cost-effectiveness for cultivating M. capsulatus. Simultaneous monitoring of transfer rates for oxygen, methane, and carbon dioxide was conducted in up to eight shake flasks, ensuring the success of the cultivation process. Alterations in methane-to-oxygen transfer rate ratios and carbon fixation rates reveal the impact of transfer limitations on microbial growth. Detection of gas transfer limitations, exploration of process parameter influences, and investigations of medium components were enabled by the introduced method. Optimal nitrogen concentrations could be determined to ensure optimal growth. This streamlined approach accelerates the screening process, offering efficient investigations into metabolic effects, limitations, and parameter influences in gas fermentations without the need for elaborate offline sampling, significantly reducing costs and enhanced reproducibility.
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Affiliation(s)
- Dominik Engel
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | | | - Udo Kosfeld
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Marcel Mann
- AVT-Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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Keitel L, Braun K, Finger M, Kosfeld U, Yordanov S, Büchs J. Carbon dioxide and trace oxygen concentrations impact growth and product formation of the gut bacterium Phocaeicola vulgatus. BMC Microbiol 2023; 23:391. [PMID: 38062358 PMCID: PMC10701953 DOI: 10.1186/s12866-023-03127-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The promising yet barely investigated anaerobic species Phocaeicola vulgatus (formerly Bacteroides vulgatus) plays a vital role for human gut health and effectively produces organic acids. Among them is succinate, a building block for high-value-added chemicals. Cultivating anaerobic bacteria is challenging, and a detailed understanding of P. vulgatus growth and metabolism is required to improve succinate production. One significant aspect is the influence of different gas concentrations. CO2 is required for the growth of P. vulgatus. However, it is a greenhouse gas that should not be wasted. Another highly interesting aspect is the sensitivity of P. vulgatus towards O2. In this work, the effects of varying concentrations of both gases were studied in the in-house developed Respiratory Activity MOnitoring System (RAMOS), which provides online monitoring of CO2, O2, and pressure under gassed conditions. The RAMOS was combined with a gas mixing system to test CO2 and O2 concentrations in a range of 0.25-15.0 vol% and 0.0-2.5 vol%, respectively. RESULTS Changing the CO2 concentration in the gas supply revealed a CO2 optimum of 3.0 vol% for total organic acid production and 15.0 vol% for succinate production. It was demonstrated that the organic acid composition changed depending on the CO2 concentration. Furthermore, unrestricted growth of P. vulgatus up to an O2 concentration of 0.7 vol% in the gas supply was proven. The viability decreased rapidly at concentrations larger than or equal to 1.3 vol% O2. CONCLUSIONS The study showed that P. vulgatus requires little CO2, has a distinct O2 tolerance and is therefore well suited for industrial applications.
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Affiliation(s)
- Laura Keitel
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Kristina Braun
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Maurice Finger
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Udo Kosfeld
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Stanislav Yordanov
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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Miebach K, Finger M, Scherer AMK, Maaß CA, Büchs J. Hydrogen online monitoring based on thermal conductivity for anaerobic microorganisms. Biotechnol Bioeng 2023; 120:2199-2213. [PMID: 37462090 DOI: 10.1002/bit.28502] [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: 06/06/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
H2 -producing microorganisms are a promising source of sustainable biohydrogen. However, most H2 -producing microorganisms are anaerobes, which are difficult to cultivate and characterize. While several methods for measuring H2 exist, common H2 sensors often require oxygen, making them unsuitable for anaerobic processes. Other sensors can often not be operated at high gas humidity. Thus, we applied thermal conductivity (TC) sensors and developed a parallelized, online H2 monitoring for time-efficient characterization of H2 production by anaerobes. Since TC sensors are nonspecific for H2 , the cross-sensitivity of the sensors was evaluated regarding temperature, gas humidity, and CO2 concentrations. The systems' measurement range was validated with two anaerobes: a high H2 -producer (Clostridium pasteurianum) and a low H2 -producer (Phocaeicola vulgatus). Online monitoring of H2 production in shake flask cultivations was demonstrated, and H2 transfer rates were derived. Combined with online CO2 and pressure measurements, molar gas balances of the cultivations were closed, and an anaerobic respiration quotient was calculated. Thus, insight into the effect of medium components and inhibitory cultivation conditions on H2 production with the model anaerobes was gained. The presented online H2 monitoring method can accelerate the characterization of anaerobes for biohydrogen production and reveal metabolic changes without expensive equipment and offline analysis.
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Affiliation(s)
- Katharina Miebach
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | - Maurice Finger
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
| | | | | | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Aachen, Germany
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Finger M, Schröder E, Berg C, Dinger R, Büchs J. Toward standardized solid medium cultivations: Online microbial monitoring based on respiration activity. Biotechnol J 2023; 18:e2200627. [PMID: 37183352 DOI: 10.1002/biot.202200627] [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: 12/14/2022] [Revised: 03/31/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
Cultivating microorganisms on solid agar media is a fundamental technique in microbiology and other related disciplines. For the evaluation, most often, a subjective visual examination is performed. Crucial information, such as metabolic activity, is not assessed. Thus, time-resolved monitoring of the respiration activity in agar cultivations is presented to provide additional insightful data on the metabolism. A modified version of the Respiration Activity MOnitoring System (RAMOS) was used to determine area-specific oxygen and carbon dioxide transfer rates and the resulting respiratory quotients of agar cultivations. Therewith, information on growth, substrate consumption, and product formation was obtained. The validity of the presented method was tested for different prokaryotic and eukaryotic organisms on agar, such as Escherichia coli BL21, Pseudomonas putida KT2440, Streptomyces coelicolor A3(2), Saccharomyces cerevisiae WT, Pichia pastoris WT, and Trichoderma reesei RUT-C30. Furthermore, it is showcased that several potential applications, including the determination of colony forming units, antibiotic diffusion tests, quality control for spore production or for pre-cultures and media optimization, can be quantitatively evaluated by interpretation of the respiration activity.
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Affiliation(s)
- Maurice Finger
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Eliot Schröder
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Christoph Berg
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Robert Dinger
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany
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Harahap BM, Ahring BK. Acetate Production from Syngas Produced from Lignocellulosic Biomass Materials along with Gaseous Fermentation of the Syngas: A Review. Microorganisms 2023; 11:microorganisms11040995. [PMID: 37110418 PMCID: PMC10143712 DOI: 10.3390/microorganisms11040995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Biotransformation of lignocellulose-derived synthetic gas (syngas) into acetic acid is a promising way of creating biochemicals from lignocellulosic waste materials. Acetic acid has a growing market with applications within food, plastics and for upgrading into a wide range of biofuels and bio-products. In this paper, we will review the microbial conversion of syngas to acetic acid. This will include the presentation of acetate-producing bacterial strains and their optimal fermentation conditions, such as pH, temperature, media composition, and syngas composition, to enhance acetate production. The influence of syngas impurities generated from lignocellulose gasification will further be covered along with the means to alleviate impurity problems through gas purification. The problem with mass transfer limitation of gaseous fermentation will further be discussed as well as ways to improve gas uptake during the fermentation.
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Affiliation(s)
- Budi Mandra Harahap
- Bioproducts, Science, and Engineering Laboratory, Washington State University Tri-Cities, 2710, Crimson Way, Richland, WA 99354, USA
- Department of Biological System Engineering, Washington State University, L. J. Smith Hall, Pullman, WA 99164, USA
| | - Birgitte K Ahring
- Bioproducts, Science, and Engineering Laboratory, Washington State University Tri-Cities, 2710, Crimson Way, Richland, WA 99354, USA
- Department of Biological System Engineering, Washington State University, L. J. Smith Hall, Pullman, WA 99164, USA
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Wegner Hall, Pullman, WA 99164, USA
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Wollborn D, Munkler LP, Horstmann R, Germer A, Blank LM, Büchs J. Predicting high recombinant protein producer strains of Pichia pastoris Mut S using the oxygen transfer rate as an indicator of metabolic burden. Sci Rep 2022; 12:11225. [PMID: 35780248 PMCID: PMC9250517 DOI: 10.1038/s41598-022-15086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/17/2022] [Indexed: 11/09/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is a widely used host for recombinant protein production. In this study, a clonal library of P. pastoris MutS strains (S indicates slow methanol utilization) was screened for high green fluorescent protein (GFP) production. The expression cassette was under the control of the methanol inducible AOX promoter. The growth behavior was online-monitored in 48-well and 96-well microtiter plates by measuring the oxygen transfer rate (OTR). By comparing the different GFP producing strains, a correlation was established between the slope of the cumulative oxygen transfer during the methanol metabolization phase and the strain’s production performance. The correlation corresponds to metabolic burden during methanol induction. The findings were validated using a pre-selected strain library (7 strains) of high, medium, and low GFP producers. For those strains, the gene copy number was determined via Whole Genome Sequencing. The results were consistent with the described OTR correlation. Additionally, a larger clone library (45 strains) was tested to validate the applicability of the proposed method. The results from this study suggest that the cumulative oxygen transfer can be used as a screening criterion for protein production performance that allows for a simple primary screening process, facilitating the pre-selection of high producing strains.
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Affiliation(s)
- David Wollborn
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Lara Pauline Munkler
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Rebekka Horstmann
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany
| | - Andrea Germer
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, 52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB - Institute of Applied Microbiology, RWTH Aachen University, 52074, Aachen, Germany
| | - Jochen Büchs
- Chair of Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074, Aachen, Germany.
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Marcel M, Darina E, Patrick K, Aline H, Gabriele P, Stefan J, Jochen B. Impact of different trace elements on metabolic routes during heterotrophic growth of C. ljungdahlii investigated through online measurement of the carbon dioxide transfer rate. Biotechnol Prog 2022; 38:e3263. [PMID: 35434968 DOI: 10.1002/btpr.3263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/30/2022] [Accepted: 04/15/2022] [Indexed: 11/09/2022]
Abstract
Synthesis gas fermentation using acetogenic clostridia is a rapidly increasing research area. It offers the possibility to produce platform chemicals from sustainable C1 carbon sources. The Wood-Ljungdahl pathway (WLP), which allows acetogens to grow autotrophically, is also active during heterotrophic growth. It acts as an electron sink and allows for the utilization of a wide variety of soluble substrates and increases ATP yields during heterotrophic growth. While glycolysis leads to CO2 evolution, WLP activity results in CO2 fixation. Thus, a reduction of net CO2 emissions during growth with sugars is an indicator of WLP activity. To study the effect of trace elements and ventilation rates on the interaction between glycolysis and the WLP, the model acetogen Clostridium ljungdahlii was cultivated in YTF medium, a complex medium generally employed for heterotrophic growth, with fructose as growth substrate. The recently reported anaRAMOS device was used for online measurement of metabolic activity, in form of CO2 evolution. The addition of multiple trace elements (iron, cobalt, manganese, zinc, nickel, copper, selenium, and tungsten) was tested, to study the interaction between glycolysis and the Wood ljungdahl pathway. While the addition of iron(II) increased growth rates and ethanol production, added nickel(II) increased WLP activity and acetate formation, reducing net CO2 production by 28%. Also, higher CO2 availability through reduced volumetric gas flow resulted in 25% reduction of CO2 evolution. These online metabolic data demonstrate that the anaRAMOS is a valuable tool in the investigation of metabolic responses i.e. to determine nutrient requirements that results in reduced CO2 production. Thereby the media composition can be optimized depending on the specific goal. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mann Marcel
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
| | - Effert Darina
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
| | - Kottenhahn Patrick
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany.,Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, Aachen, Germany
| | - Hüser Aline
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
| | - Philipps Gabriele
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, Aachen, Germany
| | - Jennewein Stefan
- Department for Industrial Biotechnology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstr. 6, Aachen, Germany
| | - Büchs Jochen
- RWTH Aachen University, AVT - Biochemical Engineering, Aachen, Germany
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Heffernan JK, Mahamkali V, Valgepea K, Marcellin E, Nielsen LK. Analytical tools for unravelling the metabolism of gas-fermenting Clostridia. Curr Opin Biotechnol 2022; 75:102700. [PMID: 35240422 DOI: 10.1016/j.copbio.2022.102700] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/24/2022] [Accepted: 02/05/2022] [Indexed: 12/23/2022]
Abstract
Acetogens harness the Wood-Ljungdahl Pathway, a unique metabolic pathway for C1 capture close to the thermodynamic limit. Gas fermentation using acetogens is already used for CO-to-ethanol conversion at industrial-scale and has the potential to valorise a range of C1 and waste substrates to short-chain and medium-chain carboxylic acids and alcohols. Advances in analytical quantification and metabolic modelling have helped guide industrial gas fermentation designs. Further advances in the measurements of difficult to measure metabolites are required to improve kinetic modelling and understand the regulation of acetogen metabolism. This will help guide future synthetic biology designs needed to realise the full potential of gas fermentation in stimulating a circular bioeconomy.
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Affiliation(s)
- James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Vishnu Mahamkali
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
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