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Wray AC, Downey AR, Nodal AA, Park KK, Gorman-Lewis D. Bioenergetic characterization of hyperthermophilic archaean Methanocaldococcus sp. FS406-22. Extremophiles 2024; 28:32. [PMID: 39023751 DOI: 10.1007/s00792-024-01349-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/28/2024] [Indexed: 07/20/2024]
Abstract
Hyperthermophilic archaean Methanocaldococcus sp. FS406-22 (hereafter FS406) is a hydrogenotrophic methanogen isolated from a deep-sea hydrothermal vent. To better understand the energetic requirements of hydrogen oxidation under extreme conditions, the thermodynamic characterization of FS406 incubations is necessary and notably underexplored. In this work, we quantified the bioenergetics of FS406 incubations at a range of temperatures (65, 76, and 85 ℃) and hydrogen concentrations (1.1, 1.4, and 2.1 mm). The biomass yields (C-mol of biomass per mol of H2 consumed) ranged from 0.02 to 0.19. Growth rates ranged from 0.4 to 1.5 h-1. Gibbs energies of incubation based on macrochemical equations of cell growth ranged from - 198 kJ/C-mol to - 1840 kJ/C-mol. Enthalpies of incubation determined from calorimetric measurements ranged from - 4150 kJ/C-mol to - 36333 kJ/C-mol. FS406 growth rates were most comparable to hyperthermophilic methanogen Methanocaldococcus jannaschii. Maintenance energy calculations from the thermodynamic parameters of FS406 and previously determined heterotrophic methanogen data revealed that temperature is a primary determinant rather than an electron donor. This work provides new insights into the thermodynamic underpinnings of a hyperthermophilic hydrothermal vent methanogen and helps to better constrain the energetic requirements of life in extreme environments.
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Affiliation(s)
- Addien C Wray
- Earth and Space Sciences, University of Washington, Seattle, WA, USA.
| | - Autum R Downey
- Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Andrea A Nodal
- Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Katherine K Park
- Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Drew Gorman-Lewis
- Earth and Space Sciences, University of Washington, Seattle, WA, USA
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He J, Li J, Gao Q, Shen W, Liu W, Xia M, Xiao H, Xiao D. In Vitro Evaluation of Chito-Oligosaccharides on Disappearance Rate of Nutrients, Rumen Fermentation Parameters, and Micro-Flora of Beef Cattle. Animals (Basel) 2024; 14:1657. [PMID: 38891704 PMCID: PMC11170994 DOI: 10.3390/ani14111657] [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: 05/06/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The study aimed to investigate the effect of dietary chitosan oligosaccharides (COS) meal levels on the nutrient disappearance rate, rumen fermentation, and microflora of beef cattle in vitro. A total of 24 fermentation tanks were randomly divided into four treatments containing 0% COS (CON), 0.02% COS, 0.04% COS, and 0.08% COS for an 8-day experiment period, with each treatment comprising six replicates. The disappear rates of DM, CP, EE, and total gas production were quadratically increased with increasing COS levels. The disappear rates of DM, CP, EE, and ADF were greatest, whereas the total gas production was lowest in the 0.08% COS group. The pH, NH3-N, MCP, the content of propionate, isobutyrate, butyrate, valerate, and the A/P were quadratically increased with increasing COS levels, while the A/P were linearly decreased. The pH, MCP, and the content of propionate, and butyrate were highest, whereas the NH3-N and the content of acetate, isobutyrate, valerate, and the A/P were lowest in the 0.08% COS group. Microbiomics analysis showed that the rumen microbial diversity was not altered between the CON and the 0.08% COS group. However, the relative abundance of Methanosphaera, Ruminococcus, Endomicrobium, and Eubacterium groups was increased, and the relative abundance of pathogenic bacteria Dorea and Escherichia-Shigella showed a decrease in the 0.08% COS group. Overall, the 0.08% COS was the most effective among the three addition levels, resulting in an increase in the disappearance rate of in vitro fermented nutrients and improvements in rumen fermentation indexes and microbial communities. This, in turn, led to the maintenance of rumen health.
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Affiliation(s)
- Jianfu He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Jing Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
| | - Qian Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
| | - Weijun Shen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
- Yuelushan Laboratory, Changsha 410128, China
| | - Wenchang Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
| | - Min Xia
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
| | - Haixiang Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
| | - Dingfu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (J.H.); (J.L.); (Q.G.); (W.S.); (W.L.); (M.X.); (H.X.)
- Yuelushan Laboratory, Changsha 410128, China
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Gao Q, He J, Wang J, Yan Y, Liu L, Wang Z, Shen W, Wan F. Effects of dietary D-lactate levels on rumen fermentation, microflora and metabolomics of beef cattle. Front Microbiol 2024; 15:1348729. [PMID: 38380091 PMCID: PMC10877051 DOI: 10.3389/fmicb.2024.1348729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Introduction Excessive intake of lactate caused by improper use of silage in animal husbandry has adverse effects on rumen fermentation, such as rumen acidosis. The speed of absorption and metabolism of D-lactate in rumen epithelial cells was slower than that of L-lactate, making D-lactate more prone to accumulate and induce rumen acidosis. Therefore, this study was conducted to explore the effects of dietary D-lactate levels on rumen fermentation of beef cattle and its mechanism in an in vitro system. Methods This experiment was adopted in single-factor random trial design, with 5 days for adaptation and 3 days for sample collection. Three treatments (n = 8/treatment) were used: (1) D-LA (0.3%), basal fermentation substrate with 0.3% (dry matter, DM basis) D-lactate; (2) D-LA (0.75%), basal fermentation substrate with 0.75% (DM basis) D-lactate; and (3) D-LA (1.2%), basal fermentation substrate with 1.2% (DM basis) D-lactate. Results With the dietary D-lactate levels increased, the daily production of total gas, hydrogen and methane, as well as the ruminal concentrations of acetate, propionate, butyrate, isobutyrate, valerate, isovalerate, total volatile fatty acid and D-lactate increased (p < 0.05), but the ruminal pH and acetate/propionate ratios decreased (p < 0.05). Principle coordinate analysis based on Bray-Curtis distance showed that increasing dietary D-lactate levels could significantly affect the structure of rumen bacterial community (p < 0.05), but had no significant effect on the structure of rumen eukaryotic community (p > 0.05). NK4A214_group, Ruminococcus_gauvreauii_group, Eubacterium_oxidoreducens_group, Escherichia-Shigella, Marvinbryantia and Entodinium were enriched in D-LA (1.2%) group (p < 0.05), as well as WCHB1-41, vadinBE97, Clostridium_sensu_stricto_1, Anaeroplasma and Ruminococcus were enriched in D-LA (0.3%) group (p < 0.05). Changes in the composition of ruminal microorganisms affected rumen metabolism, mainly focus on the biosynthesis of glycosaminoglycans (p < 0.05). Discussion Overall, feeding whole-plant corn silage with high D-lactate content could not induce rumen acidosis, and the metabolization of dietary D-lactate into volatile fatty acids increased the energy supply of beef cattle. However, it also increased the ruminal CH4 emissions and the relative abundance of opportunistic pathogen Escherichia-Shigella in beef cattle. The relative abundance of Verrucomicrobiota and Escherichia-Shigella may be influenced by glycosaminoglycans, reflecting the interaction between rumen microorganisms and metabolites.
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Affiliation(s)
- Qian Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jianfu He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jin Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Yonghui Yan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Lei Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, China
| | - Zuo Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Weijun Shen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Fachun Wan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
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Popovic M. SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants. MICROBIAL RISK ANALYSIS 2023; 24:100260. [PMID: 36974134 PMCID: PMC10032061 DOI: 10.1016/j.mran.2023.100260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 06/11/2023]
Abstract
SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.
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Affiliation(s)
- Marko Popovic
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
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Hart C, Gorman-Lewis D. Energetics of Acidianus ambivalens growth in response to oxygen availability. GEOBIOLOGY 2021; 19:48-62. [PMID: 32902110 DOI: 10.1111/gbi.12413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/30/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
All life requires energy to drive metabolic reactions such as growth and cell maintenance; therefore, fluctuations in energy availability can alter microbial activity. There is a gap in our knowledge concerning how energy availability affects the growth of extreme chemolithoautotrophs. Toward this end, we investigated the growth of thermoacidophile Acidianus ambivalens during sulfur oxidation under aerobic to microaerophilic conditions. Calorimetry was used to measure enthalpy (ΔHinc ) of microbial activity, and chemical changes in growth media were measured to calculate Gibbs energy change (ΔGinc ) during incubation. In all experiments, Gibbs energy was primarily dissipated through the release of heat, which suggests enthalpy-driven growth. In microaerophilic conditions, growth was significantly more efficient in terms of biomass yield (defined as C-mol biomass per mole sulfur consumed) and resulted in lower ΔGinc and ΔHinc . ΔGinc in oxygen-limited (OL) and oxygen- and CO2 -limited (OCL) microaerophilic growth conditions resulted in averages of -1.44 × 103 kJ/C-mol and -7.56 × 102 kJ/C-mol, respectively, and average ΔHinc values of -1.11 × 105 kJ/C-mol and -4.43 × 104 kJ/C-mol, respectively. High-oxygen experiments resulted in lower biomass yield values, an increase in ΔGinc to -1.71 × 104 kJ/C-mol, and more exothermic ΔHinc values of -4.71 × 105 kJ/C-mol. The observed inefficiency in high-oxygen conditions may suggest larger maintenance energy demands due to oxidative stresses and a preference for growth in microaerophilic environments.
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Affiliation(s)
- Chloe Hart
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA
| | - Drew Gorman-Lewis
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA
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Katla S, Pavan SS, Mohan N, Sivaprakasam S. Biocalorimetric monitoring of glycoengineered P. pastoris cultivation for the production of recombinant huIFNα2b: A quantitative study based on mixed feeding strategies. Biotechnol Prog 2020; 36:e2971. [PMID: 31990134 DOI: 10.1002/btpr.2971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 11/05/2022]
Abstract
Real-time monitoring of glycoengineered Pichia pastoris by employing process analytical technology (PAT) tools is vital for gaining deeper insights into the therapeutic protein production process. The present study focuses on influence of mixed feed carbon substrates during the induction phases of glycoengineered P. pastoris cultivation, for recombinant human interferon α2b (huIFNα2b) production by employing calorimetric (biological heat rate, q B ) and respirometric (oxygen uptake rate and carbon dioxide evolution rate) measurements. Mixed feed stream of carbon substrates (methanol + glycerol, methanol + sorbitol) at a predetermined "C-molar ratios" were added during the induction phases. Methanol- and sorbitol-based mixed feeding approach resulted in an improved huIFNα2b titer of 288 mg/L by channeling of methanol predominantly towards an optimal functioning of AOX expression system. A stand-off between biomass yield Y X S and biomass heat yield Y Q X coefficient, degree of reduction of methanol and its cosubstrate (glycerol and sorbitol) determines the fraction of carbon energy channeled toward biomass and protein production, under strict aerobic conditions. Calorespirometric monitoring and assessment of thermal yields enables a reliable prediction of process variables, leading to futuristic efficient PAT-based feed rate control.
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Affiliation(s)
- Srikanth Katla
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Satya Sai Pavan
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Naresh Mohan
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Senthilkumar Sivaprakasam
- BioPAT Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Muñoz-Tamayo R, Popova M, Tillier M, Morgavi DP, Morel JP, Fonty G, Morel-Desrosiers N. Hydrogenotrophic methanogens of the mammalian gut: Functionally similar, thermodynamically different-A modelling approach. PLoS One 2019; 14:e0226243. [PMID: 31826000 PMCID: PMC6905546 DOI: 10.1371/journal.pone.0226243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 12/11/2022] Open
Abstract
Methanogenic archaea occupy a functionally important niche in the gut microbial ecosystem of mammals. Our purpose was to quantitatively characterize the dynamics of methanogenesis by integrating microbiology, thermodynamics and mathematical modelling. For that, in vitro growth experiments were performed with pure cultures of key methanogens from the human and ruminant gut, namely Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanobacterium formicium. Microcalorimetric experiments were performed to quantify the methanogenesis heat flux. We constructed an energetic-based mathematical model of methanogenesis. Our model captured efficiently the dynamics of methanogenesis with average concordance correlation coefficients of 0.95 for CO2, 0.98 for H2 and 0.97 for CH4. Together, experimental data and model enabled us to quantify metabolism kinetics and energetic patterns that were specific and distinct for each species despite their use of analogous methane-producing pathways. Then, we tested in silico the interactions between these methanogens under an in vivo simulation scenario using a theoretical modelling exercise. In silico simulations suggest that the classical competitive exclusion principle is inapplicable to gut ecosystems and that kinetic information alone cannot explain gut ecological aspects such as microbial coexistence. We suggest that ecological models of gut ecosystems require the integration of microbial kinetics with nonlinear behaviours related to spatial and temporal variations taking place in mammalian guts. Our work provides novel information on the thermodynamics and dynamics of methanogens. This understanding will be useful to construct new gut models with enhanced prediction capabilities and could have practical applications for promoting gut health in mammals and mitigating ruminant methane emissions.
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Affiliation(s)
- Rafael Muñoz-Tamayo
- UMR Modélisation Systémique Appliquée aux Ruminants, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
- * E-mail:
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Maxence Tillier
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Diego P. Morgavi
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | | | - Gérard Fonty
- Université Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France
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Mohan N, Pavan SS, Achar A, Swaminathan N, Sivaprakasam S. Calorespirometric investigation of Streptococcus zooepidemicus metabolism: Thermodynamics of anabolic payload contribution by growth and hyaluronic acid synthesis. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations. Curr Opin Chem Eng 2016. [DOI: 10.1016/j.coche.2016.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Ferry JG. Acetate Metabolism in Anaerobes from the Domain Archaea. Life (Basel) 2015; 5:1454-71. [PMID: 26068860 PMCID: PMC4500148 DOI: 10.3390/life5021454] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/01/2015] [Indexed: 01/26/2023] Open
Abstract
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth's biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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The Application of Dielectric Spectroscopy and Biocalorimetry for the Monitoring of Biomass in Immobilized Mammalian Cell Cultures. Processes (Basel) 2015. [DOI: 10.3390/pr3020384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Biocalorimetric Studies of the Metabolic Activity ofPseudomonas aeruginosaAerobically Grown in a Glucose-Limited Complex Growth Medium. Biosci Biotechnol Biochem 2014; 72:936-42. [DOI: 10.1271/bbb.70476] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Biotechnol J 2013; 8:1070-9. [PMID: 23420771 DOI: 10.1002/biot.201200266] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/15/2013] [Accepted: 02/13/2013] [Indexed: 11/11/2022]
Abstract
Methanosarcina barkeri is an Archaeon that produces methane anaerobically as the primary byproduct of its metabolism. M. barkeri can utilize several substrates for ATP and biomass production including methanol, acetate, methyl amines, and a combination of hydrogen and carbon dioxide. In 2006, a metabolic reconstruction of M. barkeri, iAF692, was generated based on a draft genome annotation. The iAF692 reconstruction enabled the first genome-Scale simulations for Archaea. Since the publication of the first metabolic reconstruction of M. barkeri, additional genomic, biochemical, and phenotypic data have clarified several metabolic pathways. We have used this newly available data to improve the M. barkeri metabolic reconstruction. Modeling simulations using the updated model, iMG746, have led to increased accuracy in predicting gene knockout phenotypes and simulations of batch growth behavior. We used the model to examine knockout lethality data and make predictions about metabolic regulation under different growth conditions. Thus, the updated metabolic reconstruction of M. barkeri metabolism is a useful tool for predicting cellular behavior, studying the methanogenic lifestyle, guiding experimental studies, and making predictions relevant to metabolic engineering applications.
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Affiliation(s)
- Matthew C Gonnerman
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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The Choice of Suitable Online Analytical Techniques and Data Processing for Monitoring of Bioprocesses. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012. [DOI: 10.1007/10_2012_175] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Karthikeyan R, Surianarayanan M, Sudharshan S, Gunasekaran P, Asit Baran M. Biocalorimetric and respirometric studies on production of Penicillin G acylase from Bacillus badius pac in E. coli DH5α. Biochem Eng J 2011. [DOI: 10.1016/j.bej.2011.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Methane produced in the biosphere is derived from two major pathways. Conversion of the methyl group of acetate to CH(4) in the aceticlastic pathway accounts for at least two-thirds, and reduction of CO(2) with electrons derived from H(2), formate, or CO accounts for approximately one-third. Although both pathways have terminal steps in common, they diverge considerably in the initial steps and energy conservation mechanisms. Steps and enzymes unique to the CO(2) reduction pathway are confined to methanogens and the domain Archaea. On the other hand, steps and enzymes unique to the aceticlastic pathway are widely distributed in the domain Bacteria, the understanding of which has contributed to a broader understanding of prokaryotic biology.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16801, USA.
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Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. J Theor Biol 2010; 264:683-92. [PMID: 20230840 DOI: 10.1016/j.jtbi.2010.02.044] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/15/2010] [Accepted: 02/24/2010] [Indexed: 01/05/2023]
Abstract
The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in Escherichia coli and compare favourably with in silico prediction by flux balance analysis.
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Virdis B, Rabaey K, Yuan Z, Rozendal RA, Keller J. Electron fluxes in a microbial fuel cell performing carbon and nitrogen removal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2009; 43:5144-9. [PMID: 19673320 DOI: 10.1021/es8036302] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The electron recovery in microbial fuel cells (MFCs) is decreased by processes like methanogenesis, bacterial growth, and the accumulation of intermediates. Using a suite of analytical techniques, including electrochemical monitoring, chemical analysis, microsensor analysis, and Titration and Off-Gas Analysis (TOGA), this study aimed to (a) identify and quantify the electron losses occurring at the anode and the cathode of a MFC removing acetate and nitrate (NO3-), respectively, and (b) to investigate the impact of the operational characteristics of the cathode on the denitrification process. Our results show that methane (CH4) production and estimated biomass formation at the anode and nitrous oxide (N2O) accumulation at the cathode were responsible for the reduction of Coulombic efficiency (epsilon) during continuous feeding conditions. At the anode, up to 40.1% of the acetate consumed was released as methane at closed circuit. At the cathode, N2O accumulation represented instead the main loss accounting for up to 10.0 +/- 2.1% of the oxidation capacity of the electron acceptor provided as NO3-. Batch experiments at controlled potentials and currents revealed that for a given current the fraction of electron transferred and released as N2O is significantly reduced by low cathodic potentials.
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Affiliation(s)
- Bernardino Virdis
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
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Maskow T, Kemp R, Buchholz F, Schubert T, Kiesel B, Harms H. What heat is telling us about microbial conversions in nature and technology: from chip- to megacalorimetry. Microb Biotechnol 2009; 3:269-84. [PMID: 21255327 PMCID: PMC3815370 DOI: 10.1111/j.1751-7915.2009.00121.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The exploitation of microorganisms in natural or technological systems calls for monitoring tools that reflect their metabolic activity in real time and, if necessary, are flexible enough for field application. The Gibbs energy dissipation of assimilated substrates or photons often in the form of heat is a general feature of life processes and thus, in principle, available to monitor and control microbial dynamics. Furthermore, the combination of measured heat fluxes with material fluxes allows the application of Hess' law to either prove expected growth stoichiometries and kinetics or identify and estimate unexpected side reactions. The combination of calorimetry with respirometry is theoretically suited for the quantification of the degree of coupling between catabolic and anabolic reactions. New calorimeter developments overcome the weaknesses of conventional devices, which hitherto limited the full exploitation of this powerful analytical tool. Calorimetric systems can be integrated easily into natural and technological systems of interest. They are potentially suited for high‐throughput measurements and are robust enough for field deployment. This review explains what information calorimetric analyses provide; it introduces newly emerging calorimetric techniques and it exemplifies the application of calorimetry in different fields of microbial research.
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Affiliation(s)
- Thomas Maskow
- UFZ, Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany.
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22
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Russell JB. The energy spilling reactions of bacteria and other organisms. J Mol Microbiol Biotechnol 2007; 13:1-11. [PMID: 17693707 DOI: 10.1159/000103591] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
For many years it was assumed that living organisms always utilized ATP in a highly efficient manner, but simple growth studies with bacteria indicated that the efficiency of biomass production was often at least 3-fold lower than the amount that would be predicted from standard biosynthetic pathways. The utilization of energy for maintenance could only explain a small portion of this discrepancy particularly when the growth rate was high. These ideas and thermodynamic arguments indicated that cells might have another avenue of energy utilization. This phenomenon has also been called 'uncoupling', 'spillage' and 'overflow metabolism', but 'energy spilling' is probably the most descriptive term. It appears that many bacteria spill energy, and the few that do not can be killed (large and often rapid decrease in viability), if the growth medium is nitrogen-limited and the energy source is in 'excess'. The lactic acid bacterium, Streptococcus bovis, is an ideal bacterium for the study of energy spilling. Because it only uses substrate level phosphorylation to generate ATP, ATP generation can be calculated with a high degree of certainty. It does not store glucose as glycogen, and its cell membrane can be easily accessed. Comparative analysis of heat production, membrane voltage, ATP production and Ohm's law indicated that the energy spilling reaction of S. bovis is mediated by a futile cycle of protons through the cell membrane. Less is known about Escherichia coli, but in this bacterium energy spilling could be mediated by a futile cycle of potassium or ammonium ions. Energy spilling is not restricted to prokaryotes and appears to occur in yeasts and in higher organisms. In man, energy spilling may be related to cancer, ageing, ischemia and cardiac failure.
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Affiliation(s)
- James B Russell
- US Plant, Soil and Nutrition Laboratory, Agricultural Research Service, USDA, Ithaca, NY 14853, USA.
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Sousa T, Mota R, Domingos T, Kooijman SALM. Thermodynamics of organisms in the context of dynamic energy budget theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:051901. [PMID: 17279933 DOI: 10.1103/physreve.74.051901] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 08/10/2006] [Indexed: 05/13/2023]
Abstract
We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.
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Affiliation(s)
- Tânia Sousa
- Environment and Energy Section, DEM, Instituto Superior Técnico, Avenida Rovisco Pais, 1. 1049-001 Lisbon, Portugal.
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von Stockar U, Maskow T, Liu J, Marison IW, Patiño R. Thermodynamics of microbial growth and metabolism: An analysis of the current situation. J Biotechnol 2006; 121:517-33. [PMID: 16185782 DOI: 10.1016/j.jbiotec.2005.08.012] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Revised: 07/29/2005] [Accepted: 08/04/2005] [Indexed: 11/29/2022]
Abstract
This paper attempts to review in how far thermodynamic analysis can be used to understand and predict the performance of microorganisms with respect to growth and bio-product synthesis. In the first part, a simple thermodynamic model of microbial growth is developed which explains the relationship between the driving force for growth in terms of Gibbs energy dissipation and biomass yield. From the currently available literature, it appears that the Gibbs energy dissipation per C-mol of biomass grown, which represents the driving force for chemotrophic growth, may have been adapted by evolutionary processes to strike a reasonable compromise between metabolic rate and growth efficiency. Based on empirical correlations of the C-molar Gibbs energy dissipation, the wide variety of biomass yields observed in nature can be explained and roughly predicted. This type of analysis may be highly useful in environmental applications, where such wide variations occur. It is however not able to predict biomass yields in very complex systems such as mammalian cells nor is it able to predict or to assess bio-product or recombinant protein yields. For this purpose, a much more sophisticated treatment that accounts for individual metabolic pathways separately is required. Based on glycolysis as a test example, it is shown in the last part that simple thermodynamic analysis leads to erroneous conclusions even in well-known, simple cases. Potential sources for errors have been analyzed and can be used to identify the most important needs for future research.
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Affiliation(s)
- Urs von Stockar
- Laboratory of Chemical and Biochemical Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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Barros N, Feijóo S. A combined mass and energy balance to provide bioindicators of soil microbiological quality. Biophys Chem 2003; 104:561-72. [PMID: 12914903 DOI: 10.1016/s0301-4622(03)00059-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this work, a method is proposed to quantify the efficiency of carbon utilization by soil microbes. Microcalorimetry was used to compute the heat yield (Y(Q/X)) of six soil samples collected in the Amazon. A combined mass and energy balance is developed to quantify the enthalpy of the glucose oxidation reaction (Delta(r)H(s)) and the biomass yield (Y(X/S)) from the experimental values of Y(Q/X). Results were compared by graphical analysis to establish the kinetics of the glucose oxidation and the microbial growth reactions in terms of energy dissipation. The correlations found suggest that the measured values for Y(Q/X) and Delta(r)H(s) are biomass yield dependent. The main environmental factors affecting the kinetics of the glucose oxidation and the microbial growth reactions in soils are the initial microbial population and the percentage of nitrogen of the samples. The comparative study among the samples showed that the deforestation of the Primary forests in the Amazon to establish arable lands, affected the efficiency of the carbon utilization by soil microorganisms.
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Affiliation(s)
- Nieves Barros
- Faculty of Physics, Department of Applied Physics, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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von Stockar U, van der Wielen LAM. Back to basics: thermodynamics in biochemical engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2003; 80:1-17. [PMID: 12747540 DOI: 10.1007/3-540-36782-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Rational and efficient process development in chemical technology always makes heavy use of process analysis in terms of balances, kinetics, and thermodynamics. While the first two of these concepts have been extensively used in biotechnology, it appears that thermodynamics has received relatively little attention from biotechnologists. This state of affairs is one among several reasons why development and design of biotechnological processes is today mostly carried out in an essentially empirical fashion and why bioprocesses are often not as thoroughly optimized as many chemical processes. Since quite a large body of knowledge in the area of bio thermodynamics already existed in the early nineties, the Steering Committee of a European Science Foundation program on Process Integration in Biochemical Engineering identified a need to stimulate a more systematic use of thermodynamics in the area. To this effect, a bianual course for advanced graduate students and researchers was developed. The present contribution uses the course structure to provide an outline of the area and to characterize very briefly the achievements, the challenges, and the research needs in the various sub-topics.
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Affiliation(s)
- U von Stockar
- Institut de Génie Chimique, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland.
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Daverio E, Spanjers H, Bassani C, Ligthart J, Nieman H. Calorimetric investigation of anaerobic digestion: Biomass adaptation and temperature effect. Biotechnol Bioeng 2003; 82:499-505. [PMID: 12652473 DOI: 10.1002/bit.10595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A high-resolution bench-scale calorimeter (Bio-RC1), specially suited for microbiological studies, has been used to investigate the response of an anaerobic granular sludge to repetitive glucose additions at various temperatures. Through the analysis of heat-evolution profiles resulting from substrate degradation, significant biological events have been identified: the feeble net heat uptake related to aceticlastic methanogenesis has been evaluated, and the detrimental effect of a nutrient deficiency, which led up to 75% decrease in heat production rate, has been detected. After several glucose pulses under non-limiting nutrient conditions, a reliable and reproducible reference thermal response, which is an important condition for the application of calorimetric measurements to detect inhibitory effects, was finally obtained. Afterward, glucose additions were repeated at various temperatures, and 57% biomass activity reduction, with respect to the reference value at 35 degrees C, was observed when temperature was fixed at 20 degrees C. Additionally, a preliminary toxicity test was also performed by exposing the biomass to increasing formaldehyde concentrations.
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Affiliation(s)
- E Daverio
- European Commission, JRC, IES, Inland and Marine Waters Unit, TP 300, 21020 Ispra, Varese, Italy
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