1
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Goyal A, Flamholz AI, Petroff AP, Murugan A. Closed ecosystems extract energy through self-organized nutrient cycles. Proc Natl Acad Sci U S A 2023; 120:e2309387120. [PMID: 38127977 PMCID: PMC10756307 DOI: 10.1073/pnas.2309387120] [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: 06/04/2023] [Accepted: 11/18/2023] [Indexed: 12/23/2023] Open
Abstract
Our planet is a self-sustaining ecosystem powered by light energy from the sun, but roughly closed to matter. Many ecosystems on Earth are also approximately closed to matter and recycle nutrients by self-organizing stable nutrient cycles, e.g., microbial mats, lakes, open ocean gyres. However, existing ecological models do not exhibit the self-organization and dynamical stability widely observed in such planetary-scale ecosystems. Here, we advance a conceptual model that explains the self-organization, stability, and emergent features of closed microbial ecosystems. Our model incorporates the bioenergetics of metabolism into an ecological framework. By studying this model, we uncover a crucial thermodynamic feedback loop that enables metabolically diverse communities to almost always stabilize nutrient cycles. Surprisingly, highly diverse communities self-organize to extract [Formula: see text]10[Formula: see text] of the maximum extractable energy, or [Formula: see text]100 fold more than randomized communities. Further, with increasing diversity, distinct ecosystems show strongly correlated fluxes through nutrient cycles. However, as the driving force from light increases, the fluxes of nutrient cycles become more variable and species-dependent. Our results highlight that self-organization promotes the efficiency and stability of complex ecosystems at extracting energy from the environment, even in the absence of any centralized coordination.
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Affiliation(s)
- Akshit Goyal
- Department of Physics, Massachusetts Insitute of Technology, Cambridge, MA02139
| | - Avi I. Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA91125
| | | | - Arvind Murugan
- Department of Physics, University of Chicago, Chicago, IL60637
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2
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Lacroix EM, Aeppli M, Boye K, Brodie E, Fendorf S, Keiluweit M, Naughton HR, Noël V, Sihi D. Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments. ACS EARTH & SPACE CHEMISTRY 2023; 7:1592-1609. [PMID: 37753209 PMCID: PMC10519444 DOI: 10.1021/acsearthspacechem.3c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/07/2023] [Accepted: 07/21/2023] [Indexed: 09/28/2023]
Abstract
Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.
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Affiliation(s)
- Emily M. Lacroix
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Meret Aeppli
- Institut
d’ingénierie de l’environnement (IIE), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Kristin Boye
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Eoin Brodie
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Scott Fendorf
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Marco Keiluweit
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
| | - Hannah R. Naughton
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Vincent Noël
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Debjani Sihi
- Department
of Environmental Sciences, Emory University, Atlanta, Georgia 30322, United States
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3
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George AB, Wang T, Maslov S. Functional convergence in slow-growing microbial communities arises from thermodynamic constraints. THE ISME JOURNAL 2023; 17:1482-1494. [PMID: 37380829 PMCID: PMC10432562 DOI: 10.1038/s41396-023-01455-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 05/15/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The dynamics of microbial communities is complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central element of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network-independent of species composition and biochemical details-providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum free energy dissipation. Our results predict the decrease of functional convergence in faster growing communities, which we validate by analyzing experimental data from anaerobic digesters. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.
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Affiliation(s)
- Ashish B George
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tong Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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4
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Nghiem AA, Prommer H, Mozumder MRH, Siade A, Jamieson J, Ahmed KM, van Geen A, Bostick BC. Sulfate reduction accelerates groundwater arsenic contamination even in aquifers with abundant iron oxides. NATURE WATER 2023; 1:151-165. [PMID: 37034542 PMCID: PMC10074394 DOI: 10.1038/s44221-022-00022-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/19/2022] [Indexed: 02/18/2023]
Abstract
Groundwater contamination by geogenic arsenic is a global problem affecting nearly 200 million people. In South and Southeast Asia, a cost-effective mitigation strategy is to use oxidized low-arsenic aquifers rather than reduced high-arsenic aquifers. Aquifers with abundant oxidized iron minerals are presumably safeguarded against immediate arsenic contamination, due to strong sorption of arsenic onto iron minerals. However, preferential pumping of low-arsenic aquifers can destabilize the boundaries between these aquifers, pulling high-arsenic water into low-arsenic aquifers. We investigate this scenario in a hybrid field-column experiment in Bangladesh where naturally high-arsenic groundwater is pumped through sediment cores from a low-arsenic aquifer, and detailed aqueous and solid-phase measurements are used to constrain reactive transport modelling. Here we show that elevated groundwater arsenic concentrations are induced by sulfate reduction and the predicted formation of highly mobile, poorly sorbing thioarsenic species. This process suggests that contamination of currently pristine aquifers with arsenic can occur up to over 1.5 times faster than previously thought, leading to a deterioration of urgently needed water resources.
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Affiliation(s)
- Athena A. Nghiem
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA
- Present address: Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Present address: Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Henning Prommer
- CSIRO Environment, Wembley, Western Australia, Australia
- School of Earth Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - M. Rajib H. Mozumder
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA
- Ramboll Environment & Health, Westford, MA, USA
| | - Adam Siade
- CSIRO Environment, Wembley, Western Australia, Australia
- School of Earth Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - James Jamieson
- CSIRO Environment, Wembley, Western Australia, Australia
- School of Earth Sciences, University of Western Australia, Perth, Western Australia, Australia
| | | | - Alexander van Geen
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA
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5
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Aeppli M, Thompson A, Dewey C, Fendorf S. Redox Properties of Solid Phase Electron Acceptors Affect Anaerobic Microbial Respiration under Oxygen-Limited Conditions in Floodplain Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17462-17470. [PMID: 36342198 DOI: 10.1021/acs.est.2c05797] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mountain floodplain soils often show spatiotemporal variations in redox conditions that arise due to changing hydrology and resulting biogeochemistry. Under oxygen-depleted conditions, solid phase terminal electron acceptors (TEAs) can be used in anaerobic respiration. However, it remains unclear to what degree the redox properties of solid phases limit respiration rates and hence organic matter degradation. Here, we assess such limitations in soils collected across a gradient in native redox states from the Slate River floodplain (Colorado, U.S.A.). We incubated soils under anoxic conditions and quantified CO2 production and microbial Fe(III) reduction, the main microbial metabolic pathway, as well as the reactivity of whole-soil solid phase TEAs toward mediated electrochemical reduction. Fe(III) reduction occurred together with CO2 production in native oxic soils, while neither Fe(II) nor CO2 production was observed in native anoxic soils. Initial CO2 production rates increased with increasing TEA redox reactivity toward mediated electrochemical reduction across all soil depths. Low TEA redox reactivity appears to be caused by elevated Fe(II) concentrations rather than crystallinity of Fe(III) phases. Our findings illustrate that the buildup of Fe(II) in systems with long residence times limits the thermodynamic viability of dissimilatory Fe(III) reduction and thereby limits the mineralization of organic carbon.
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Affiliation(s)
- Meret Aeppli
- Department of Earth System Science, Stanford University, Stanford, California94305, United States
- School of Architecture, Civil and Environmental Engineering, EPFL, 1015Lausanne, Switzerland
| | - Aaron Thompson
- Department of Crop and Soil Science, University of Georgia, Athens, Georgia30602, United States
| | - Christian Dewey
- Department of Earth System Science, Stanford University, Stanford, California94305, United States
| | - Scott Fendorf
- Department of Earth System Science, Stanford University, Stanford, California94305, United States
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6
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Enouy RW, Walton KM, Malton II, Sra KS, Sihota NN, Daniels EJ, Unger AJA. A mechanistic derivation of the Monod bioreaction equation for a limiting nutrient. J Math Biol 2022; 84:62. [PMID: 35737104 DOI: 10.1007/s00285-022-01760-0] [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: 03/05/2021] [Revised: 04/22/2022] [Accepted: 05/07/2022] [Indexed: 10/17/2022]
Abstract
We present a quasi-steady state mechanistic derivation of the Monod bioreaction equation based upon a conceptual model involving aqueous phase diffusive transport of substrate towards a spherical microbe; transport of the substrate across its surface membrane; and reaction depleting the substrate within the microbe. The resulting Monod coefficients [Formula: see text] and [Formula: see text] are dependent upon substrate-species pairs and the mass transfer properties of the system. Two substrate transport scenarios are investigated: (1) a constant rate model that is a function of a constant flux across the surface of the microbe; and (2) a linear rate model that is the product of a constant transport velocity and the concentration of substrate in contact with the surface of the microbe. The model is verified and parameterized using benzene, toluene, and phenol depletion and biomass growth data obtained from Reardon et al. (Biotechnol Bioeng: 385-400, 2000). Calibration results indicate a normalized surface to bulk concentration ratio of nearly unity in all simulations for benzene, toluene, and phenol when paired with P. putida F1, implying that the process is not aqueous phase diffusion limited.
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Affiliation(s)
- Robert W Enouy
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON, Canada
| | - Kenneth M Walton
- Morwick G360 Groundwater Research Institute, University of Guelph, Guelph, ON, Canada
| | - Ioanna I Malton
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON, Canada
| | - Kanwartej S Sra
- Chevron Technical Center (a Chevron U.S.A. Inc. Division), 1400 Smith Street, Houston, TX, 77002, USA
| | - Natasha N Sihota
- Chevron Technical Center (a Chevron U.S.A. Inc. Division), 6001 Bollinger Canyon Road, San Ramon, CA, 94583, USA
| | - Eric J Daniels
- Chevron Technical Center (a Chevron U.S.A. Inc. Division), 6001 Bollinger Canyon Road, San Ramon, CA, 94583, USA
| | - Andre J A Unger
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, ON, Canada.
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7
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Wu Q, Guthrie MJ, Jin Q. Physiological Acclimation Extrapolates the Kinetics and Thermodynamics of Methanogenesis From Laboratory Experiments to Natural Environments. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.838487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chemotrophic microorganisms face the steep challenge of limited energy resources in natural environments. This observation has important implications for interpreting and modeling the kinetics and thermodynamics of microbial reactions. Current modeling frameworks treat microbes as autocatalysts, and simulate microbial energy conservation and growth with fixed kinetic and thermodynamic parameters. However, microbes are capable of acclimating to the environment and modulating their parameters in order to gain competitive fitness. Here we constructed an optimization model and described microbes as self-adapting catalysts by linking microbial parameters to intracellular metabolic resources. From the optimization results, we related microbial parameters to the substrate concentration and the energy available in the environment, and simplified the relationship between the kinetics and the thermodynamics of microbial reactions. We took as examples Methanosarcina and Methanosaeta – the methanogens that produce methane from acetate – and showed how the acclimation model extrapolated laboratory observations to natural environments and improved the simulation of methanogenesis and the dominance of Methanosaeta over Methanosarcina in lake sediments. These results highlight the importance of physiological acclimation in shaping the kinetics and thermodynamics of microbial reactions and in determining the outcome of microbial interactions.
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8
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Reactive Transport: A Review of Basic Concepts with Emphasis on Biochemical Processes. ENERGIES 2022. [DOI: 10.3390/en15030925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reactive transport (RT) couples bio-geo-chemical reactions and transport. RT is important to understand numerous scientific questions and solve some engineering problems. RT is highly multidisciplinary, which hinders the development of a body of knowledge shared by RT modelers and developers. The goal of this paper is to review the basic conceptual issues shared by all RT problems, so as to facilitate advancement along the current frontier: biochemical reactions. To this end, we review the basic equations to indicate that chemical systems are controlled by the set of equilibrium reactions, which are easy to model, but whose rate is controlled by mixing. Since mixing is not properly represented by the standard advection-dispersion equation (ADE), we conclude that this equation is poor for RT. This leads us to review alternative transport formulations, and the methods to solve RT problems using both the ADE and alternative equations. Since equilibrium is easy, difficulties arise for kinetic reactions, which is especially true for biochemistry, where numerous challenges are open (how to represent microbial communities, impact of genomics, effect of biofilms on flow and transport, etc.). We conclude with the basic eleven conceptual issues that we consider fundamental for any conceptually sound RT effort.
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9
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Dopffel N, Jamieson J, Bryce C, Joshi P, Mansor M, Siade A, Prommer H, Kappler A. Temperature dependence of nitrate-reducing Fe(II) oxidation by Acidovorax strain BoFeN1 - evaluating the role of enzymatic vs. abiotic Fe(II) oxidation by nitrite. FEMS Microbiol Ecol 2021; 97:6442174. [PMID: 34849752 DOI: 10.1093/femsec/fiab155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/24/2021] [Indexed: 11/14/2022] Open
Abstract
Fe(II) oxidation coupled to nitrate reduction is a widely observed metabolism. However, to what extent the observed Fe(II) oxidation is driven enzymatically or abiotically by metabolically produced nitrite remains puzzling. To distinguish between biotic and abiotic reactions, we cultivated the mixotrophic nitrate-reducing Fe(II)-oxidizing Acidovorax strain BoFeN1 over a wide range of temperatures and compared it to abiotic Fe(II) oxidation by nitrite at temperatures up to 60°C. The collected experimental data were subsequently analyzed through biogeochemical modeling. At 5°C, BoFeN1 cultures consumed acetate and reduced nitrate but did not significantly oxidize Fe(II). Abiotic Fe(II) oxidation by nitrite at different temperatures showed an Arrhenius-type behavior with an activation energy of 80±7 kJ/mol. Above 40°C, the kinetics of Fe(II) oxidation were abiotically driven, whereas at 30°C, where BoFeN1 can actively metabolize, the model-based interpretation strongly suggested that an enzymatic pathway was responsible for a large fraction (ca. 62%) of the oxidation. This result was reproduced even when no additional carbon source was present. Our results show that at below 30°C, i.e., at temperatures representing most natural environments, biological Fe(II) oxidation was largely responsible for overall Fe(II) oxidation, while abiotic Fe(II) oxidation by nitrite played a less important role.
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Affiliation(s)
- Nicole Dopffel
- Norwegian Research Center - NORCE, 22 Nygårdstangen, 5838 Bergen, Norway
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - James Jamieson
- School of Earth Sciences, University of Western Australia, 35 Stirling Highway, 6009 Crawley, Australia
- CSIRO Land and Water, 147 Underwood Avenue, 6014 Floreat, Australia
| | - Casey Bryce
- School of Earth Sciences, University of Bristol, Queens Road, Bristol BS8 1RJ, United Kingdom
| | - Prachi Joshi
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Muammar Mansor
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
| | - Adam Siade
- School of Earth Sciences, University of Western Australia, 35 Stirling Highway, 6009 Crawley, Australia
- CSIRO Land and Water, 147 Underwood Avenue, 6014 Floreat, Australia
| | - Henning Prommer
- School of Earth Sciences, University of Western Australia, 35 Stirling Highway, 6009 Crawley, Australia
- CSIRO Land and Water, 147 Underwood Avenue, 6014 Floreat, Australia
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, 72074 Tübingen, Germany
- Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infection, University of Tubingen, 72074 Tübingen, Germany
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10
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Veshareh MJ, Dolfing J, Nick HM. Importance of thermodynamics dependent kinetic parameters in nitrate-based souring mitigation studies. WATER RESEARCH 2021; 206:117673. [PMID: 34624655 DOI: 10.1016/j.watres.2021.117673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/30/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Souring is the unwanted formation of hydrogen sulfide (H2S) by sulfate-reducing microorganisms (SRM) in sewer systems and seawater flooded oil reservoirs. Nitrate treatment (NT) is one of the major methods to alleviate souring: The mechanism of souring remediation by NT is stimulation of nitrate reducing microorganisms (NRM) that depending on the nitrate reduction pathway can outcompete SRM for common electron donors, or oxidize sulfide to sulfate. However, some nitrate reduction pathways may challenge the efficacy of NT. Therefore, a precise understanding of souring rate, nitrate reduction rate and pathways is crucial for efficient souring management. Here, we investigate the necessity of incorporating two thermodynamic dependent kinetic parameters, namely, the growth yield (Y), and FT, a parameter related to the minimum catabolic energy production required by cells to utilize a given catabolic reaction. We first show that depending on physiochemical conditions, Y and FT for SRM change significantly in the range of [0-0.4] mole biomass per mole electron donor and [0.0006-0.5], respectively, suggesting that these parameters should not be considered constant and that it is important to couple souring models with thermodynamic models. Then, we highlight this further by showing an experimental dataset that can be modeled very well by considering variable FT. Next, we show that nitrate based lithotrophic sulfide oxidation to sulfate (lNRM3) is the dominant nitrate reduction pathway. Then, arguing that thermodynamics would suggest that S° consumption should proceed faster than S0 production, we infer that the reason for frequently observed S0 accumulation is its low solubility. Last, we suggest that nitrate based souring treatment will suffer less from S0 accumulation if we (i) act early, (ii) increase temperature and (iii) supplement stoichiometrically sufficient nitrate.
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Affiliation(s)
- Moein Jahanbani Veshareh
- Danish Hydrocarbon Research and Technology Centre, Technical University of Denmark, Lyngby, Denmark.
| | - Jan Dolfing
- Faculty of Engineering and Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Hamidreza M Nick
- Danish Hydrocarbon Research and Technology Centre, Technical University of Denmark, Lyngby, Denmark
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11
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Predicting degradation of organic molecules in cementitious media. PROGRESS IN NUCLEAR ENERGY 2021. [DOI: 10.1016/j.pnucene.2021.103888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Multiscale Modeling of Uranium Bioreduction in Porous Media by One-Dimensional Biofilms. Bull Math Biol 2021; 83:105. [PMID: 34477982 DOI: 10.1007/s11538-021-00938-9] [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: 03/15/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
We formulate a multiscale mathematical model that describes the bioreduction of uranium in porous media. On the mesoscale we describe the bioreduction of uranium [VI] to uranium [IV] using a multispecies one-dimensional biofilm model with suspended bacteria and thermodynamic growth inhibition. We upscale the mesoscopic (colony scale) model to the macroscale (reactor scale) and investigate the behavior of substrate utilization and production, attachment and detachment processes, and thermodynamic effects not usually considered in biofilm growth models. Simulation results of the reactor model indicate that thermodynamic inhibition quantitatively alters the dynamics of the model and neglecting thermodynamic effects may over- or underestimate chemical concentrations in the system. Furthermore, we numerically investigate uncertainties related to the specific choice of attachment and detachment rate coefficients and find that while increasing the attachment rate coefficient or decreasing the detachment rate coefficient leads to thicker biofilms, performance of the reactor remains largely unaffected.
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13
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The view of microbes as energy converters illustrates the trade-off between growth rate and yield. Biochem Soc Trans 2021; 49:1663-1674. [PMID: 34282835 DOI: 10.1042/bst20200977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 12/11/2022]
Abstract
The application of thermodynamics to microbial growth has a long tradition that originated in the middle of the 20th century. This approach reflects the view that self-replication is a thermodynamic process that is not fundamentally different from mechanical thermodynamics. The key distinction is that a free energy gradient is not converted into mechanical (or any other form of) energy but rather into new biomass. As such, microbes can be viewed as energy converters that convert a part of the energy contained in environmental nutrients into chemical energy that drives self-replication. Before the advent of high-throughput sequencing technologies, only the most central metabolic pathways were known. However, precise measurement techniques allowed for the quantification of exchanged extracellular nutrients and heat of growing microbes with their environment. These data, together with the absence of knowledge of metabolic details, drove the development of so-called black-box models, which only consider the observable interactions of a cell with its environment and neglect all details of how exactly inputs are converted into outputs. Now, genome sequencing and genome-scale metabolic models (GEMs) provide us with unprecedented detail about metabolic processes inside the cell. However, mostly due to computational complexity issues, the derived modelling approaches make surprisingly little use of thermodynamic concepts. Here, we review classical black-box models and modern approaches that integrate thermodynamics into GEMs. We also illustrate how the description of microbial growth as an energy converter can help to understand and quantify the trade-off between microbial growth rate and yield.
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14
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LaRowe DE, Carlson HK, Amend JP. The Energetic Potential for Undiscovered Manganese Metabolisms in Nature. Front Microbiol 2021; 12:636145. [PMID: 34177823 PMCID: PMC8220133 DOI: 10.3389/fmicb.2021.636145] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/03/2021] [Indexed: 11/13/2022] Open
Abstract
Microorganisms are found in nearly every surface and near-surface environment, where they gain energy by catalyzing reactions among a wide variety of chemical compounds. The discovery of new catabolic strategies and microbial habitats can therefore be guided by determining which redox reactions can supply energy under environmentally-relevant conditions. In this study, we have explored the thermodynamic potential of redox reactions involving manganese, one of the most abundant transition metals in the Earth's crust. In particular, we have assessed the Gibbs energies of comproportionation and disproportionation reactions involving Mn2+ and several Mn-bearing oxide and oxyhydroxide minerals containing Mn in the +II, +III, and +IV oxidation states as a function of temperature (0-100°C) and pH (1-13). In addition, we also calculated the energetic potential of Mn2+ oxidation coupled to O2, NO2 -, NO3 -, and FeOOH. Results show that these reactions-none of which, except O2 + Mn2+, are known catabolisms-can provide energy to microorganisms, particularly at higher pH values and temperatures. Comproportionation between Mn2+ and pyrolusite, for example, can yield 10 s of kJ (mol Mn)-1. Disproportionation of Mn3+ can yield more than 100 kJ (mol Mn)-1 at conditions relevant to natural settings such as sediments, ferromanganese nodules and crusts, bioreactors and suboxic portions of the water column. Of the Mn2+ oxidation reactions, the one with nitrite as the electron acceptor is most energy yielding under most combinations of pH and temperature. We posit that several Mn redox reactions represent heretofore unknown microbial metabolisms.
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Affiliation(s)
- Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Harold K Carlson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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15
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Controls on Interspecies Electron Transport and Size Limitation of Anaerobically Methane-Oxidizing Microbial Consortia. mBio 2021; 12:mBio.03620-20. [PMID: 33975943 PMCID: PMC8263020 DOI: 10.1128/mbio.03620-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
About 382 Tg yr−1 of methane rising through the seafloor is oxidized anaerobically (W. S. Reeburgh, Chem Rev 107:486–513, 2007, https://doi.org/10.1021/cr050362v), preventing it from reaching the atmosphere, where it acts as a strong greenhouse gas. Microbial consortia composed of anaerobic methanotrophic archaea and sulfate-reducing bacteria couple the oxidation of methane to the reduction of sulfate under anaerobic conditions via a syntrophic process. Recent experimental studies and modeling efforts indicate that direct interspecies electron transfer (DIET) is involved in this syntrophy. Here, we explore a fluorescent in situ hybridization-nanoscale secondary ion mass spectrometry data set of large, segregated anaerobic oxidation of methane (AOM) consortia that reveal a decline in metabolic activity away from the archaeal-bacterial interface and use a process-based model to identify the physiological controls on rates of AOM. Simulations reproducing the observational data reveal that ohmic resistance and activation loss are the two main factors causing the declining metabolic activity, where activation loss dominated at a distance of <8 μm. These voltage losses limit the maximum spatial distance between syntrophic partners with model simulations, indicating that sulfate-reducing bacterial cells can remain metabolically active up to ∼30 μm away from the archaeal-bacterial interface. Model simulations further predict that a hybrid metabolism that combines DIET with a small contribution of diffusive exchange of electron donors can offer energetic advantages for syntrophic consortia.
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16
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Wegener G, Gropp J, Taubner H, Halevy I, Elvert M. Sulfate-dependent reversibility of intracellular reactions explains the opposing isotope effects in the anaerobic oxidation of methane. SCIENCE ADVANCES 2021; 7:7/19/eabe4939. [PMID: 33952515 PMCID: PMC8099194 DOI: 10.1126/sciadv.abe4939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/17/2021] [Indexed: 06/01/2023]
Abstract
The anaerobic oxidation of methane (AOM) is performed by methanotrophic archaea (ANME) in distinct sulfate-methane interfaces of marine sediments. In these interfaces, AOM often appears to deplete methane in the heavy isotopes toward isotopic compositions similar to methanogenesis. Here, we shed light on this effect and its physiological underpinnings using a thermophilic ANME-1-dominated culture. At high sulfate concentrations, residual methane is enriched in both 13C and 2H (13α = 1.016 and 2α = 1.155), as observed previously. In contrast, at low sulfate concentrations, the residual methane is substantially depleted in 13C (13α = 0.977) and, to a lesser extent, in 2H. Using a biochemical-isotopic model, we explain the sulfate dependence of the net isotopic fractionation through the thermodynamic drive of the involved intracellular reactions. Our findings relate these isotopic patterns to the physiology and environment of the ANME, thereby explaining a commonly observed isotopic enigma.
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Affiliation(s)
- Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Jonathan Gropp
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Heidi Taubner
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Itay Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359 Bremen, Germany
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17
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Rotiroti M, Bonomi T, Sacchi E, McArthur JM, Jakobsen R, Sciarra A, Etiope G, Zanotti C, Nava V, Fumagalli L, Leoni B. Overlapping redox zones control arsenic pollution in Pleistocene multi-layer aquifers, the Po Plain (Italy). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143646. [PMID: 33257069 DOI: 10.1016/j.scitotenv.2020.143646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Understanding the factors that control As concentrations in groundwater is vital for supplying safe groundwater in regions with As-polluted aquifers. Despite much research, mainly addressing Holocene aquifers hosting young (<100 yrs) groundwater, the source, transport, and fate of As in Pleistocene aquifers with fossil (>12,000 yrs) groundwaters are not yet fully understood and so are assessed here through an evaluation of the redox properties of the system in a type locality, the Po Plain (Italy). Analyses of redox-sensitive species and major ions on 22 groundwater samples from the Pleistocene arsenic-affected aquifer in the Po Plain shows that groundwater concentrations of As are controlled by the simultaneous operation of several terminal electron accepters. Organic matter, present as peat, is abundant in the aquifer, allowing groundwater to reach a quasi-steady-state of highly reducing conditions close to thermodynamic equilibrium. In this system, simultaneous reduction of Fe-oxide and sulfate results in low concentrations of As (median 7 μg/L) whereas As reaches higher concentrations (median of 82 μg/L) during simultaneous methanogenesis and Fe-reduction. The position of well-screens is an additional controlling factor on groundwater As: short screens that overlap confining aquitards generate higher As concentrations than long screens placed away from them. A conceptual model for groundwater As, applicable worldwide in other Pleistocene aquifers with reducible Fe-oxides and abundant organic matter is proposed: As may have two concentration peaks, the first after prolonged Fe-oxide reduction and until sulfate reduction takes place, the second during simultaneous Fe-reduction and methanogenesis.
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Affiliation(s)
- Marco Rotiroti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Tullia Bonomi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Elisa Sacchi
- Department of Earth and Environmental Sciences, University of Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - John M McArthur
- Department of Earth Sciences, University College London, Gower Street, WC1E 6BT London, United Kingdom
| | - Rasmus Jakobsen
- Geological Survey of Denmark and Greenland, Øster Voldgade 10, 1350 Copenhagen, Denmark
| | - Alessandra Sciarra
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Roma 1, Via di Vigna Murata 605, 00143 Rome, Italy
| | - Giuseppe Etiope
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Roma 2, Via di Vigna Murata 605, 00143 Rome, Italy
| | - Chiara Zanotti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Veronica Nava
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Letizia Fumagalli
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Barbara Leoni
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
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18
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Gaebler HJ, Hughes JM, Eberl HJ. Thermodynamic Inhibition in a Biofilm Reactor with Suspended Bacteria. Bull Math Biol 2021; 83:10. [PMID: 33415496 DOI: 10.1007/s11538-020-00840-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023]
Abstract
We formulate a biofilm reactor model with suspended bacteria that accounts for thermodynamic growth inhibition. The reactor model is a chemostat style model consisting of a single replenished growth promoting substrate, a single reaction product, suspended bacteria, and wall attached bacteria in the form of a bacterial biofilm. We present stability conditions for the washout equilibrium using standard techniques, demonstrating that analytical results are attainable even with the added complexity from thermodynamic inhibition. Furthermore, we numerically investigate the longterm behaviour. In the computational study, we investigate model behaviour for select parameters and two commonly used detachment functions. We investigate the effects of thermodynamic inhibition on the model and find that thermodynamic inhibition limits substrate utilization/production both inside the biofilm and inside the aqueous phase, resulting in less suspended bacteria and a thinner biofilm.
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Affiliation(s)
- Harry J Gaebler
- University of Guelph, 50 Stone Road East, Guelph, ON, Canada.
| | - Jack M Hughes
- University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Hermann J Eberl
- University of Guelph, 50 Stone Road East, Guelph, ON, Canada
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19
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Vallino JJ, Tsakalakis I. Phytoplankton Temporal Strategies Increase Entropy Production in a Marine Food Web Model. ENTROPY 2020; 22:e22111249. [PMID: 33287017 PMCID: PMC7712749 DOI: 10.3390/e22111249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/11/2020] [Accepted: 10/30/2020] [Indexed: 01/01/2023]
Abstract
We develop a trait-based model founded on the hypothesis that biological systems evolve and organize to maximize entropy production by dissipating chemical and electromagnetic free energy over longer time scales than abiotic processes by implementing temporal strategies. A marine food web consisting of phytoplankton, bacteria, and consumer functional groups is used to explore how temporal strategies, or the lack thereof, change entropy production in a shallow pond that receives a continuous flow of reduced organic carbon plus inorganic nitrogen and illumination from solar radiation with diel and seasonal dynamics. Results show that a temporal strategy that employs an explicit circadian clock produces more entropy than a passive strategy that uses internal carbon storage or a balanced growth strategy that requires phytoplankton to grow with fixed stoichiometry. When the community is forced to operate at high specific growth rates near 2 d−1, the optimization-guided model selects for phytoplankton ecotypes that exhibit complementary for winter versus summer environmental conditions to increase entropy production. We also present a new type of trait-based modeling where trait values are determined by maximizing entropy production rather than by random selection.
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Affiliation(s)
- Joseph J. Vallino
- Marine Biological Laboratory, Woods Hole, MA 02543, USA;
- Correspondence:
| | - Ioannis Tsakalakis
- Marine Biological Laboratory, Woods Hole, MA 02543, USA;
- Department of Earth, Atmosphere and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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20
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Not Just Numbers: Mathematical Modelling and Its Contribution to Anaerobic Digestion Processes. Processes (Basel) 2020. [DOI: 10.3390/pr8080888] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mathematical modelling of bioprocesses has a long and notable history, with eminent contributions from fields including microbiology, ecology, biophysics, chemistry, statistics, control theory and mathematical theory. This richness of ideas and breadth of concepts provide great motivation for inquisitive engineers and intrepid scientists to try their hand at modelling, and this collaboration of disciplines has also delivered significant milestones in the quality and application of models for both theoretical and practical interrogation of engineered biological systems. The focus of this review is the anaerobic digestion process, which, as a technology that has come in and out of fashion, remains a fundamental process for addressing the global climate emergency. Whether with conventional anaerobic digestion systems, biorefineries, or other anaerobic technologies, mathematical models are important tools that are used to design, monitor, control and optimise the process. Both highly structured, mechanistic models and data-driven approaches have been used extensively over half a decade, but recent advances in computational capacity, scientific understanding and diversity and quality of process data, presents an opportunity for the development of new modelling paradigms, augmentation of existing methods, or even incorporation of tools from other disciplines, to ensure that anaerobic digestion research can remain resilient and relevant in the face of emerging and future challenges.
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21
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Gaebler HJ, Eberl HJ. Thermodynamic Inhibition in Chemostat Models : With an Application to Bioreduction of Uranium. Bull Math Biol 2020; 82:76. [PMID: 32535693 DOI: 10.1007/s11538-020-00758-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/30/2020] [Indexed: 10/24/2022]
Abstract
We formulate a mathematical model of bacterial populations in a chemostat setting that also accounts for thermodynamic growth inhibition as a consequence of chemical reactions. Using only elementary mathematical and chemical arguments, we carry this out for two systems: a simple toy model with a single species, a single substrate, and a single reaction product, and a more involved model that describes bioreduction of uranium[VI] into uranium[IV]. We find that in contrast to most traditional chemostat models, as a consequence of thermodynamic inhibition the equilibria concentrations of nutrient substrates might depend on their inflow concentration and not only on reaction parameters and the reactor's dilution rate. Simulation results of the uranium degradation model indicate that thermodynamic growth inhibition quantitatively alters the solution of the model. This suggests that neglecting thermodynamic inhibition effects in systems where they play a role might lead to wrong model predictions and under- or over-estimate the efficacy of the process under investigation.
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22
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Delattre H, Chen J, Wade MJ, Soyer OS. Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis. J R Soc Interface 2020; 17:20200053. [PMID: 32370691 PMCID: PMC7276542 DOI: 10.1098/rsif.2020.0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol−1) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol−1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.
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Affiliation(s)
| | - Jing Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Matthew J Wade
- School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry, UK
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23
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Alvarez-Ramirez J, Meraz M, Jaime Vernon-Carter E. A theoretical derivation of the monod equation with a kinetics sense. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Population dynamics of chemotrophs in anaerobic conditions where the metabolic energy acquisition per redox reaction is limited. J Theor Biol 2019; 467:164-173. [DOI: 10.1016/j.jtbi.2019.01.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 11/17/2022]
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25
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He X, Chadwick G, Kempes C, Shi Y, McGlynn S, Orphan V, Meile C. Microbial interactions in the anaerobic oxidation of methane: model simulations constrained by process rates and activity patterns. Environ Microbiol 2019; 21:631-647. [DOI: 10.1111/1462-2920.14507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 12/01/2022]
Affiliation(s)
- Xiaojia He
- Department of Marine Sciences University of Georgia Athens GA USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | | | - Yimeng Shi
- Department of Marine Sciences University of Georgia Athens GA USA
| | - Shawn McGlynn
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
- Earth‐Life Science Institute Tokyo Institute of Technology Ookayama, Meguro‐ku Tokyo Japan
| | - Victoria Orphan
- Division of Geological and Planetary Sciences California Institute of Technology Pasadena CA USA
| | - Christof Meile
- Department of Marine Sciences University of Georgia Athens GA USA
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26
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Delattre H, Desmond-Le Quéméner E, Duquennoi C, Filali A, Bouchez T. Consistent microbial dynamics and functional community patterns derived from first principles. ISME JOURNAL 2018; 13:263-276. [PMID: 30194430 DOI: 10.1038/s41396-018-0272-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 06/14/2018] [Accepted: 06/20/2018] [Indexed: 01/26/2023]
Abstract
Microbial communities are key engines that drive earth's biogeochemical cycles. However, existing ecosystem models have only limited ability to predict microbial dynamics and require the calibration of multiple population-specific empirical equations. In contrast, we build on a new kinetic "Microbial Transition State" (MTS) theory of growth derived from first principles. We show how the theory coupled to simple mass and energy balance calculations provides a framework with intrinsically important qualitative properties to model microbial community dynamics. We first show how the theory can simultaneously account for the influence of all the resources needed for growth (electron donor, acceptor, and nutrients) while still producing consistent dynamics that fulfill the Liebig rule of a single limiting substrate. We also show consistent patterns of energy-dependent microbial successions in mixed culture without the need for calibration of population-specific parameters. We then show how this approach can be used to model a simplified activated sludge community. To this end, we compare MTS-derived dynamics with those of a widely used activated sludge model and show that similar growth yields and overall dynamics can be obtained using two parameters instead of twelve. This new kinetic theory of growth grounded by a set of generic physical principles parsimoniously gives rise to consistent microbial population and community dynamics, thereby paving the way for the development of a new class of more predictive microbial ecosystem models.
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Affiliation(s)
| | - Elie Desmond-Le Quéméner
- Irstea, UR HBAN, F-92761, Antony, France.,LBE, University of Montpellier, INRA, Narbonne, France
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27
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Jamieson J, Prommer H, Kaksonen AH, Sun J, Siade AJ, Yusov A, Bostick B. Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5771-5781. [PMID: 29676145 PMCID: PMC6427828 DOI: 10.1021/acs.est.8b01122] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.
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Affiliation(s)
- James Jamieson
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Henning Prommer
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- National Centre for Groundwater Research and Training, Adelaide, South Australia 5001, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- Corresponding Author: .
| | - Anna H. Kaksonen
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jing Sun
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Adam J. Siade
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- National Centre for Groundwater Research and Training, Adelaide, South Australia 5001, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Anna Yusov
- Department of Chemistry, Barnard College, 3009 Broadway, New York, New York 10027, United States
| | - Benjamin Bostick
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, New York 10964, United States
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28
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Considering a Threshold Energy in Reactive Transport Modeling of Microbially Mediated Redox Reactions in an Arsenic-Affected Aquifer. WATER 2018. [DOI: 10.3390/w10010090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Ebrahimi A, Or D. Dynamics of soil biogeochemical gas emissions shaped by remolded aggregate sizes and carbon configurations under hydration cycles. GLOBAL CHANGE BIOLOGY 2018; 24:e378-e392. [PMID: 29028292 DOI: 10.1111/gcb.13938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
Changes in soil hydration status affect microbial community dynamics and shape key biogeochemical processes. Evidence suggests that local anoxic conditions may persist and support anaerobic microbial activity in soil aggregates (or in similar hot spots) long after the bulk soil becomes aerated. To facilitate systematic studies of interactions among environmental factors with biogeochemical emissions of CO2 , N2 O and CH4 from soil aggregates, we remolded silt soil aggregates to different sizes and incorporated carbon at different configurations (core, mixed, no addition). Assemblies of remolded soil aggregates of three sizes (18, 12, and 6 mm) and equal volumetric proportions were embedded in sand columns at four distinct layers. The water table level in each column varied periodically while obtaining measurements of soil GHG emissions for the different aggregate carbon configurations. Experimental results illustrate that methane production required prolonged inundation and highly anoxic conditions for inducing measurable fluxes. The onset of unsaturated conditions (lowering water table) resulted in a decrease in CH4 emissions while temporarily increasing N2 O fluxes. Interestingly, N2 O fluxes were about 80% higher form aggregates with carbon placement in center (anoxic) core compared to mixed carbon within aggregates. The fluxes of CO2 were comparable for both scenarios of carbon sources. These experimental results highlight the importance of hydration dynamics in activating different GHG production and affecting various transport mechanisms about 80% of total methane emissions during lowering water table level are attributed to physical storage (rather than production), whereas CO2 emissions (~80%) are attributed to biological activity. A biophysical model for microbial activity within soil aggregates and profiles provides a means for results interpretation and prediction of trends within natural soils under a wide range of conditions.
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Affiliation(s)
- Ali Ebrahimi
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Dani Or
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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30
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Anaerobic microsites have an unaccounted role in soil carbon stabilization. Nat Commun 2017; 8:1771. [PMID: 29176641 PMCID: PMC5701132 DOI: 10.1038/s41467-017-01406-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/14/2017] [Indexed: 12/03/2022] Open
Abstract
Soils represent the largest carbon reservoir within terrestrial ecosystems. The mechanisms controlling the amount of carbon stored and its feedback to the climate system, however, remain poorly resolved. Global carbon models assume that carbon cycling in upland soils is entirely driven by aerobic respiration; the impact of anaerobic microsites prevalent even within well-drained soils is missed within this conception. Here, we show that anaerobic microsites are important regulators of soil carbon persistence, shifting microbial metabolism to less efficient anaerobic respiration, and selectively protecting otherwise bioavailable, reduced organic compounds such as lipids and waxes from decomposition. Further, shifting from anaerobic to aerobic conditions leads to a 10-fold increase in volume-specific mineralization rate, illustrating the sensitivity of anaerobically protected carbon to disturbance. The vulnerability of anaerobically protected carbon to future climate or land use change thus constitutes a yet unrecognized soil carbon–climate feedback that should be incorporated into terrestrial ecosystem models. Mechanisms controlling soil carbon storage and feedbacks to the climate system remain poorly constrained. Here, the authors show that anaerobic microsites stabilize soil carbon by shifting microbial metabolism to less efficient anaerobic respiration and protecting reduced organic compounds from decomposition.
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31
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Tarpgaard IH, Jørgensen BB, Kjeldsen KU, Røy H. The marine sulfate reducer Desulfobacterium autotrophicum HRM2 can switch between low and high apparent half-saturation constants for dissimilatory sulfate reduction. FEMS Microbiol Ecol 2017; 93:2966865. [DOI: 10.1093/femsec/fix012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
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32
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Stackhouse B, Lau MCY, Vishnivetskaya T, Burton N, Wang R, Southworth A, Whyte L, Onstott TC. Atmospheric CH 4 oxidation by Arctic permafrost and mineral cryosols as a function of water saturation and temperature. GEOBIOLOGY 2017; 15:94-111. [PMID: 27474434 DOI: 10.1111/gbi.12193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 05/09/2016] [Indexed: 06/06/2023]
Abstract
The response of methanotrophic bacteria capable of oxidizing atmospheric CH4 to climate warming is poorly understood, especially for those present in Arctic mineral cryosols. The atmospheric CH4 oxidation rates were measured in microcosms incubated at 4 °C and 10 °C along a 1-m depth profile and over a range of water saturation conditions for mineral cryosols containing type I and type II methanotrophs from Axel Heiberg Island (AHI), Nunavut, Canada. The cryosols exhibited net consumption of ~2 ppmv CH4 under all conditions, including during anaerobic incubations. Methane oxidation rates increased with temperature and decreased with increasing water saturation and depth, exhibiting the highest rates at 10 °C and 33% saturation at 5 cm depth (260 ± 60 pmol CH4 gdw-1 d-1 ). Extrapolation of the CH4 oxidation rates to the field yields net CH4 uptake fluxes ranging from 11 to 73 μmol CH4 m-2 d-1 , which are comparable to field measurements. Stable isotope mass balance indicates ~50% of the oxidized CH4 is incorporated into the biomass regardless of temperature or saturation. Future atmospheric CH4 uptake rates at AHI with increasing temperatures will be determined by the interplay of increasing CH4 oxidation rates vs. water saturation and the depth to the water table during summer thaw.
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Affiliation(s)
- B Stackhouse
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - T Vishnivetskaya
- The Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
| | - N Burton
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - R Wang
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - A Southworth
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - L Whyte
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada
| | - T C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, USA
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An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers. Proc Natl Acad Sci U S A 2016; 113:E7927-E7936. [PMID: 27872277 DOI: 10.1073/pnas.1612244113] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2 Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4 to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H2 oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface.
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Jin Q, Kirk MF. Thermodynamic and Kinetic Response of Microbial Reactions to High CO 2. Front Microbiol 2016; 7:1696. [PMID: 27909425 PMCID: PMC5112241 DOI: 10.3389/fmicb.2016.01696] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 10/12/2016] [Indexed: 11/13/2022] Open
Abstract
Geological carbon sequestration captures CO2 from industrial sources and stores the CO2 in subsurface reservoirs, a viable strategy for mitigating global climate change. In assessing the environmental impact of the strategy, a key question is how microbial reactions respond to the elevated CO2 concentration. This study uses biogeochemical modeling to explore the influence of CO2 on the thermodynamics and kinetics of common microbial reactions in subsurface environments, including syntrophic oxidation, iron reduction, sulfate reduction, and methanogenesis. The results show that increasing CO2 levels decreases groundwater pH and modulates chemical speciation of weak acids in groundwater, which in turn affect microbial reactions in different ways and to different extents. Specifically, a thermodynamic analysis shows that increasing CO2 partial pressure lowers the energy available from syntrophic oxidation and acetoclastic methanogenesis, but raises the available energy of microbial iron reduction, hydrogenotrophic sulfate reduction and methanogenesis. Kinetic modeling suggests that high CO2 has the potential of inhibiting microbial sulfate reduction while promoting iron reduction. These results are consistent with the observations of previous laboratory and field studies, and highlight the complexity in microbiological responses to elevated CO2 abundance, and the potential power of biogeochemical modeling in evaluating and quantifying these responses.
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Affiliation(s)
- Qusheng Jin
- Department of Earth Sciences, University of Oregon Eugene, OR, USA
| | - Matthew F Kirk
- Department of Geology, Kansas State University Manhattan, KS, USA
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Faußer AC, Dušek J, Čížková H, Kazda M. Diurnal dynamics of oxygen and carbon dioxide concentrations in shoots and rhizomes of a perennial in a constructed wetland indicate down-regulation of below ground oxygen consumption. AOB PLANTS 2016; 8:plw025. [PMID: 27207278 PMCID: PMC4940480 DOI: 10.1093/aobpla/plw025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 03/19/2016] [Indexed: 06/02/2023]
Abstract
Wetland plants actively provide oxygen for aerobic processes in submerged tissues and the rhizosphere. The novel concomitant assessment of diurnal dynamics of oxygen and carbon dioxide concentrations under field conditions tests the whole-system interactions in plant-internal gas exchange and regulation. Oxygen concentrations ([O2]) were monitored in-situ in central culm and rhizome pith cavities of common reed (Phragmites australis) using optical oxygen sensors. The corresponding carbon dioxide concentrations ([CO2]) were assessed via gas samples from the culms. Highly dynamic diurnal courses of [O2] were recorded, which started at 6.5-13 % in the morning, increased rapidly up to 22 % during midday and declined exponentially during the night. Internal [CO2] were high in the morning (1.55-17.5 %) and decreased (0.04-0.94 %) during the rapid increase of [O2] in the culms. The observed negative correlations between [O2] and [CO2] particularly describe the below ground relationship between plant-mediated oxygen supply and oxygen use by respiration and biogeochemical processes in the rhizosphere. Furthermore, the nocturnal declining slopes of [O2] in culms and rhizomes indicated a down-regulation of the demand for oxygen in the complete below ground plant-associated system. These findings emphasize the need for measurements of plant-internal gas exchange processes under field conditions because it considers the complex interactions in the oxic-anoxic interface.
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Affiliation(s)
- Anna C Faußer
- Ulm University, Institute of Systematic Botany and Ecology, Ulm, Germany
| | - Jiří Dušek
- CzechGlobe - Global Change Research Centre AS CR, Department of Matters and Energy Fluxes, v.v.i. České Budějovice, Czech Republic
| | - Hana Čížková
- CzechGlobe - Global Change Research Centre AS CR, Department of Matters and Energy Fluxes, v.v.i. České Budějovice, Czech Republic University of South Bohemia, Faculty of Agriculture, Department of Biology, České Budějovice, Czech Republic
| | - Marian Kazda
- Ulm University, Institute of Systematic Botany and Ecology, Ulm, Germany
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Microbial diversity arising from thermodynamic constraints. ISME JOURNAL 2016; 10:2725-2733. [PMID: 27035705 PMCID: PMC5042319 DOI: 10.1038/ismej.2016.49] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 01/15/2023]
Abstract
The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.
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Vallino JJ, Algar CK. The Thermodynamics of Marine Biogeochemical Cycles: Lotka Revisited. ANNUAL REVIEW OF MARINE SCIENCE 2015; 8:333-356. [PMID: 26515809 DOI: 10.1146/annurev-marine-010814-015843] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nearly 100 years ago, Alfred Lotka published two short but insightful papers describing how ecosystems may organize. Principally, Lotka argued that ecosystems will grow in size and that their cycles will spin faster via predation and nutrient recycling so as to capture all available energy, and that evolution and natural selection are the mechanisms by which this occurs and progresses. Lotka's ideas have often been associated with the maximum power principle, but they are more consistent with recent developments in nonequilibrium thermodynamics, which assert that complex systems will organize toward maximum entropy production (MEP). In this review, we explore Lotka's hypothesis within the context of the MEP principle, as well as how this principle can be used to improve marine biogeochemistry models. We need to develop the equivalent of a climate model, as opposed to a weather model, to understand marine biogeochemistry on longer timescales, and adoption of the MEP principle can help create such models.
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Affiliation(s)
- Joseph J Vallino
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543;
| | - Christopher K Algar
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia B2H 4R2, Canada;
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Abstract
To better understand the origin, evolution, and extent of life, we seek to determine the minimum flux of energy needed for organisms to remain viable. Despite the difficulties associated with direct measurement of the power limits for life, it is possible to use existing data and models to constrain the minimum flux of energy required to sustain microorganisms. Here, a we apply a bioenergetic model to a well characterized marine sedimentary environment in order to quantify the amount of power organisms use in an ultralow-energy setting. In particular, we show a direct link between power consumption in this environment and the amount of biomass (cells cm-3) found in it. The power supply resulting from the aerobic degradation of particular organic carbon (POC) at IODP Site U1370 in the South Pacific Gyre is between ∼10-12 and 10-16 W cm-3. The rates of POC degradation are calculated using a continuum model while Gibbs energies have been computed using geochemical data describing the sediment as a function of depth. Although laboratory-determined values of maintenance power do a poor job of representing the amount of biomass in U1370 sediments, the number of cells per cm-3 can be well-captured using a maintenance power, 190 zW cell-1, two orders of magnitude lower than the lowest value reported in the literature. In addition, we have combined cell counts and calculated power supplies to determine that, on average, the microorganisms at Site U1370 require 50–3500 zW cell-1, with most values under ∼300 zW cell-1. Furthermore, we carried out an analysis of the absolute minimum power requirement for a single cell to remain viable to be on the order of 1 zW cell-1.
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Affiliation(s)
- Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles CA, USA
| | - Jan P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles CA, USA ; Department of Biological Sciences, University of Southern California, Los Angeles CA, USA
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Ling YC, Bush R, Grice K, Tulipani S, Berwick L, Moreau JW. Distribution of iron- and sulfate-reducing bacteria across a coastal acid sulfate soil (CASS) environment: implications for passive bioremediation by tidal inundation. Front Microbiol 2015; 6:624. [PMID: 26191042 PMCID: PMC4490247 DOI: 10.3389/fmicb.2015.00624] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 06/08/2015] [Indexed: 11/13/2022] Open
Abstract
Coastal acid sulfate soils (CASS) constitute a serious and global environmental problem. Oxidation of iron sulfide minerals exposed to air generates sulfuric acid with consequently negative impacts on coastal and estuarine ecosystems. Tidal inundation represents one current treatment strategy for CASS, with the aim of neutralizing acidity by triggering microbial iron- and sulfate-reduction and inducing the precipitation of iron-sulfides. Although well-known functional guilds of bacteria drive these processes, their distributions within CASS environments, as well as their relationships to tidal cycling and the availability of nutrients and electron acceptors, are poorly understood. These factors will determine the long-term efficacy of "passive" CASS remediation strategies. Here we studied microbial community structure and functional guild distribution in sediment cores obtained from 10 depths ranging from 0 to 20 cm in three sites located in the supra-, inter- and sub-tidal segments, respectively, of a CASS-affected salt marsh (East Trinity, Cairns, Australia). Whole community 16S rRNA gene diversity within each site was assessed by 454 pyrotag sequencing and bioinformatic analyses in the context of local hydrological, geochemical, and lithological factors. The results illustrate spatial overlap, or close association, of iron-, and sulfate-reducing bacteria (SRB) in an environment rich in organic matter and controlled by parameters such as acidity, redox potential, degree of water saturation, and mineralization. The observed spatial distribution implies the need for empirical understanding of the timing, relative to tidal cycling, of various terminal electron-accepting processes that control acid generation and biogeochemical iron and sulfur cycling.
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Affiliation(s)
- Yu-Chen Ling
- School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
| | - Richard Bush
- Southern Cross GeoScience, Southern Cross UniversityLismore, NSW, Australia
| | - Kliti Grice
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - Svenja Tulipani
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - Lyndon Berwick
- Department of Chemistry, Western Australia Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, Curtin UniversityPerth, WA, Australia
| | - John W. Moreau
- School of Earth Sciences, University of MelbourneMelbourne, VIC, Australia
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40
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Effects of temperature and glucose concentration on the growth and respiration of fungal species isolated from a highly productive coastal upwelling ecosystem. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2014.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Payn R, Helton A, Poole G, Izurieta C, Burgin A, Bernhardt E. A generalized optimization model of microbially driven aquatic biogeochemistry based on thermodynamic, kinetic, and stoichiometric ecological theory. Ecol Modell 2014. [DOI: 10.1016/j.ecolmodel.2014.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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42
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Larson LN, Sánchez-España J, Kaley B, Sheng Y, Bibby K, Burgos WD. Thermodynamic controls on the kinetics of microbial low-pH Fe(II) oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9246-54. [PMID: 25072394 DOI: 10.1021/es501322d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Acid mine drainage (AMD) is a major worldwide environmental threat to surface and groundwater quality. Microbial low-pH Fe(II) oxidation could be exploited for cost-effective AMD treatment; however, its use is limited because of uncertainties associated with its rate and ability to remove Fe from solution. We developed a thermodynamic-based framework to evaluate the kinetics of low-pH Fe(II) oxidation. We measured the kinetics of low-pH Fe(II) oxidation at five sites in the Appalachian Coal Basin in the US and three sites in the Iberian Pyrite Belt in Spain and found that the fastest rates of Fe(II) oxidation occurred at the sites with the lowest pH values. Thermodynamic calculations showed that the Gibbs free energy of Fe(II) oxidation (ΔG(oxidation)) was also most negative at the sites with the lowest pH values. We then conducted two series of microbial Fe(II) oxidation experiments in laboratory-scale chemostatic bioreactors operated through a series of pH values (2.1-4.2) and found the same relationships between Fe(II) oxidation kinetics, ΔG(oxidation), and pH. Conditions that favored the fastest rates of Fe(II) oxidation coincided with higher Fe(III) solubility. The solubility of Fe(III) minerals, thus plays an important role on Fe(II) oxidation kinetics. Methods to incorporate microbial low-pH Fe(II) oxidation into active and passive AMD treatment systems are discussed in the context of these findings. This study presents a simplified model that describes the relationship between free energy and microbial kinetics and should be broadly applicable to many biogeochemical systems.
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Affiliation(s)
- Lance N Larson
- Department of Civil and Environmental Engineering, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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43
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Marlow JJ, Larowe DE, Ehlmann BL, Amend JP, Orphan VJ. The potential for biologically catalyzed anaerobic methane oxidation on ancient Mars. ASTROBIOLOGY 2014; 14:292-307. [PMID: 24684241 DOI: 10.1089/ast.2013.1078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
This study examines the potential for the biologically mediated anaerobic oxidation of methane (AOM) coupled to sulfate reduction on ancient Mars. Seven distinct fluids representative of putative martian groundwater were used to calculate Gibbs energy values in the presence of dissolved methane under a range of atmospheric CO2 partial pressures. In all scenarios, AOM is exergonic, ranging from -31 to -135 kJ/mol CH4. A reaction transport model was constructed to examine how environmentally relevant parameters such as advection velocity, reactant concentrations, and biomass production rate affect the spatial and temporal dependences of AOM reaction rates. Two geologically supported models for ancient martian AOM are presented: a sulfate-rich groundwater with methane produced from serpentinization by-products, and acid-sulfate fluids with methane from basalt alteration. The simulations presented in this study indicate that AOM could have been a feasible metabolism on ancient Mars, and fossil or isotopic evidence of this metabolic pathway may persist beneath the surface and in surface exposures of eroded ancient terrains.
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Affiliation(s)
- Jeffrey J Marlow
- 1 Division of Geological and Planetary Sciences, California Institute of Technology , Pasadena, California
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44
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Anaerobic microbial growth near thermodynamic equilibrium as a function of ATP/ADP cycle: The effect of maintenance energy requirements. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Orcutt BN, Larowe DE, Biddle JF, Colwell FS, Glazer BT, Reese BK, Kirkpatrick JB, Lapham LL, Mills HJ, Sylvan JB, Wankel SD, Wheat CG. Microbial activity in the marine deep biosphere: progress and prospects. Front Microbiol 2013; 4:189. [PMID: 23874326 PMCID: PMC3708129 DOI: 10.3389/fmicb.2013.00189] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/20/2013] [Indexed: 11/17/2022] Open
Abstract
The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
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Affiliation(s)
- Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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46
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Wang G, Post WM, Mayes MA. Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2013; 23:255-272. [PMID: 23495650 DOI: 10.1890/12-0681.1] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We developed a microbial-enzyme-mediated decomposition (MEND) model, based on the Michaelis-Menten kinetics, that describes the dynamics of physically defined pools of soil organic matter (SOC). These include particulate, mineral-associated, dissolved organic matter (POC, MOC, and DOC, respectively), microbial biomass, and associated exoenzymes. The ranges and/or distributions of parameters were determined by both analytical steady-state and dynamic analyses with SOC data from the literature. We used an improved multi-objective parameter sensitivity analysis (MOPSA) to identify the most important parameters for the full model: maintenance of microbial biomass, turnover and synthesis of enzymes, and carbon use efficiency (CUE). The model predicted that an increase of 2 degrees C (baseline temperature 12 degrees C) caused the pools of POC-cellulose, MOC, and total SOC to increase with dynamic CUE and decrease with constant CUE, as indicated by the 50% confidence intervals. Regardless of dynamic or constant CUE, the changes in pool size of POC, MOC, and total SOC varied from -8% to 8% under +2 degrees C. The scenario analysis using a single parameter set indicates that higher temperature with dynamic CUE might result in greater net increases in both POC-cellulose and MOC pools. Different dynamics of various SOC pools reflected the catalytic functions of specific enzymes targeting specific substrates and the interactions between microbes, enzymes, and SOC. With the feasible parameter values estimated in this study, models incorporating fundamental principles of microbial-enzyme dynamics can lead to simulation results qualitatively different from traditional models with fast/slow/passive pools.
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Affiliation(s)
- Gangsheng Wang
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6301, USA.
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47
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Wang G, Post WM. A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling. FEMS Microbiol Ecol 2012; 81:610-7. [PMID: 22500928 DOI: 10.1111/j.1574-6941.2012.01389.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/15/2012] [Accepted: 04/09/2012] [Indexed: 11/28/2022] Open
Abstract
We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.
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Affiliation(s)
- Gangsheng Wang
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6301, USA.
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48
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Lande ADL, Babcock NS, Řezáč J, Lévy B, Sanders BC, Salahub DR. Quantum effects in biological electron transfer. Phys Chem Chem Phys 2012; 14:5902-18. [DOI: 10.1039/c2cp21823b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Chang I, Heiske M, Letellier T, Wallace D, Baldi P. Modeling of mitochondria bioenergetics using a composable chemiosmotic energy transduction rate law: theory and experimental validation. PLoS One 2011; 6:e14820. [PMID: 21931590 PMCID: PMC3169640 DOI: 10.1371/journal.pone.0014820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 05/12/2011] [Indexed: 12/28/2022] Open
Abstract
Mitochondrial bioenergetic processes are central to the production of cellular energy, and a decrease in the expression or activity of enzyme complexes responsible for these processes can result in energetic deficit that correlates with many metabolic diseases and aging. Unfortunately, existing computational models of mitochondrial bioenergetics either lack relevant kinetic descriptions of the enzyme complexes, or incorporate mechanisms too specific to a particular mitochondrial system and are thus incapable of capturing the heterogeneity associated with these complexes across different systems and system states. Here we introduce a new composable rate equation, the chemiosmotic rate law, that expresses the flux of a prototypical energy transduction complex as a function of: the saturation kinetics of the electron donor and acceptor substrates; the redox transfer potential between the complex and the substrates; and the steady-state thermodynamic force-to-flux relationship of the overall electro-chemical reaction. Modeling of bioenergetics with this rate law has several advantages: (1) it minimizes the use of arbitrary free parameters while featuring biochemically relevant parameters that can be obtained through progress curves of common enzyme kinetics protocols; (2) it is modular and can adapt to various enzyme complex arrangements for both in vivo and in vitro systems via transformation of its rate and equilibrium constants; (3) it provides a clear association between the sensitivity of the parameters of the individual complexes and the sensitivity of the system's steady-state. To validate our approach, we conduct in vitro measurements of ETC complex I, III, and IV activities using rat heart homogenates, and construct an estimation procedure for the parameter values directly from these measurements. In addition, we show the theoretical connections of our approach to the existing models, and compare the predictive accuracy of the rate law with our experimentally fitted parameters to those of existing models. Finally, we present a complete perturbation study of these parameters to reveal how they can significantly and differentially influence global flux and operational thresholds, suggesting that this modeling approach could help enable the comparative analysis of mitochondria from different systems and pathological states. The procedures and results are available in Mathematica notebooks at http://www.igb.uci.edu/tools/sb/mitochondria-modeling.html.
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Affiliation(s)
- Ivan Chang
- Department of Biomedical Engineering, University of California Irvine, Irvine, California, United States of America
- Institute of Genomic Biology, University of California Irvine, Irvine, California, United States of America
| | - Margit Heiske
- INSERM U688, University of Bordeaux-2, Bordeaux, France
| | | | - Douglas Wallace
- Department of Biochemistry, University of California Irvine, Irvine, California, United States of America
- Center for Mitochondrial and Molecular Medicine and Genetics (MAMMAG), University of California Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California Irvine, Irvine, California, United States of America
| | - Pierre Baldi
- Institute of Genomic Biology, University of California Irvine, Irvine, California, United States of America
- Department of Computer Science, University of California Irvine, Irvine, California, United States of America
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Kirk MF. Variation in energy available to populations of subsurface anaerobes in response to geological carbon storage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:6676-82. [PMID: 21740040 DOI: 10.1021/es201279e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Microorganisms can strongly influence the chemical and physical properties of the subsurface. Changes in microbial activity caused by geological CO(2) storage, therefore, have the potential to influence the capacity, injectivity, and integrity of CO(2) storage reservoirs and ultimately the environmental impact of CO(2) injection. This analysis uses free energy calculations to examine variation in energy available to Fe(III) and SO(4)(2-) reducers and methanogens because of changes in the bulk composition of brine and shallow groundwater following subsurface CO(2) injection. Calculations were performed using data from two field experiments, the Frio Formation experiment and an experiment at the Zero Emission Research and Technology test site. Energy available for Fe(III) reduction increased significantly during CO(2) injection in both experiments, largely because of a decrease in pH from near-neutral levels to just below 6. Energy available to SO(4)(2-) reducers and methanogens varied little. These changes can lead to a greater rate of microbial Fe(III) reduction following subsurface CO(2) injection in reservoirs where Fe(III) oxides or oxyhydroxides are available and the rate of Fe(III) reduction is limited by energy available prior to injection.
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Affiliation(s)
- Matthew F Kirk
- Geochemistry Department, Sandia National Laboratories, Albuquerque, New Mexico 87185-0754, United States.
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