1
|
Dawi MA, Sanchez-Vila X. Simulating degradation of organic compounds accounting for the growth of microorganisms (Monod kinetics) in a fully Lagrangian framework. JOURNAL OF CONTAMINANT HYDROLOGY 2022; 251:104074. [PMID: 36126368 DOI: 10.1016/j.jconhyd.2022.104074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/24/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Biologically mediated degradation of organic compounds in porous media is a complex mathematical problem, described by a non-linear differential equation. The organic compound gets in contact with the biomass, and an enzyme-catalysed reaction takes place. The net result is that part of the parent compound degrades into some daughter product, while some of the organic carbon is used for microbial growth. The rate of biomass growth in the presence of a limiting nutrient supply is usually modelled with the experimentally derived Monod equation, i.e., it is proportional to the actual existing biomass multiplied by a factor that is non-linear in terms of available organic matter. This non-linearity in the degradation equation implies a strong difficulty in directly implementing a numerical solution within a fully Lagrangian framework, and thus, numerical solutions have traditionally been sought in either an Eulerian, or else an Eulerian-Lagrangian framework. Here we pursue a fully Lagrangian solution to the problem. First, the Monod empirical equation is formulated as the outcome of a two-step reaction; while the approach is less general than other derivations existing in the literature based on a full understanding of the thermodynamics of the process, it allows two things: 1) providing some physical meaning to the actual parameters in the Monod equation, and more interestingly, 2) formulating a methodology for the solution of the degradation equation incorporating Monod kinetics by means of a particle tracking formulation. For the latter purpose, both reactants and biomass are represented by particles, and their location at any given time is represented by a kernel that accounts for the uncertainty in the actual physical location. By solving the reaction equation in a kernel framework, we can reproduce the Monod kinetics and, as a particular result in the case no biomass growth is allowed, the Michaelis-Menten kinetics. The methodology proposed is then successfully applied to reproduce two studies of microbially induced degradation of organic compounds in porous media, first, the observed kinetics of Pseudomonas putida F1 in batch reactors while growing on benzene, toluene and phenol, and second, the column study of carbon tetrachloride biodegradation by the denitrifying bacterium Pseudomonas Stutzeri KC.
Collapse
Affiliation(s)
- Malik A Dawi
- International Centre for Numerical Methods in Engineering (CIMNE), Barcelona, Spain.
| | - Xavier Sanchez-Vila
- Hydrogeology Group, Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya, Barcelona, Spain
| |
Collapse
|
2
|
Jung H, Meile C. Upscaling of microbially driven first-order reactions in heterogeneous porous media. JOURNAL OF CONTAMINANT HYDROLOGY 2019; 224:103483. [PMID: 31029464 DOI: 10.1016/j.jconhyd.2019.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 06/09/2023]
Abstract
Reactions mediated by microorganisms determine the fate of many chemicals in natural porous media. At the pore scale, the distribution of chemicals and microorganisms is not homogeneous, leading to heterogeneous distribution of microbial activities at the pore scale. We conducted pore scale reactive transport simulations to investigate the scaling of microbially mediated consumption reaction rates under a range of flow and reaction conditions. The results reveal that the scaling effects largely depended on Péclet and Damköhler numbers. Consumption rate estimates based on volume-averaged concentrations and reaction kinetics overestimated the true volumetric reaction rates, and large-sized biomass aggregates intensified these scaling errors. In contrast, the macroscopic rates estimated via flux-weighted concentrations underestimated the true volumetric reaction rates, with large microbial aggregates reducing scaling errors. This study also demonstrated that macroscopic rate estimates can be improved by combining information on the reaction kinetics with the flux-weighted concentrations.
Collapse
Affiliation(s)
- Heewon Jung
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Christof Meile
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| |
Collapse
|
3
|
König S, Worrich A, Banitz T, Harms H, Kästner M, Miltner A, Wick LY, Frank K, Thullner M, Centler F. Functional Resistance to Recurrent Spatially Heterogeneous Disturbances Is Facilitated by Increased Activity of Surviving Bacteria in a Virtual Ecosystem. Front Microbiol 2018; 9:734. [PMID: 29696013 PMCID: PMC5904252 DOI: 10.3389/fmicb.2018.00734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial degradation of organic compounds is an important ecosystem function with relevance to, e.g., the cycling of elements or the degradation of organic contaminants. It remains an open question, however, to which extent ecosystems are able to maintain such biodegradation function under recurrent disturbances (functional resistance) and how this is related to the bacterial biomass abundance. In this paper, we use a numerical simulation approach to systematically analyze the dynamic response of a microbial population to recurrent disturbances of different spatial distribution. The spatially explicit model considers microbial degradation, growth, dispersal, and spatial networks that facilitate bacterial dispersal mimicking effects of mycelial networks in nature. We find: (i) There is a certain capacity for high resistance of biodegradation performance to recurrent disturbances. (ii) If this resistance capacity is exceeded, spatial zones of different biodegradation performance develop, ranging from no or reduced to even increased performance. (iii) Bacterial biomass and biodegradation dynamics respond inversely to the spatial fragmentation of disturbances: overall biodegradation performance improves with increasing fragmentation, but bacterial biomass declines. (iv) Bacterial dispersal networks can enhance functional resistance against recurrent disturbances, mainly by reactivating zones in the core of disturbed areas, even though this leads to an overall reduction of bacterial biomass.
Collapse
Affiliation(s)
- Sara König
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Environmental Systems Research, University of Osnabrück, Osnabrück, Germany
| | - Anja Worrich
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Thomas Banitz
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Anja Miltner
- Department of Environmental Biotechnology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Lukas Y. Wick
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Karin Frank
- Department of Ecological Modelling, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
- Institute of Environmental Systems Research, University of Osnabrück, Osnabrück, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Martin Thullner
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, The UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
| |
Collapse
|