Online citations, reference lists, and bibliographies.
← Back to Search

Kinetic Modeling Of Microbially-driven Redox Chemistry Of Subsurface Environments : Coupling Transport, Microbial Metabolism And Geochemistry

K. Hunter, Y. Wang, P. Cappellen
Published 1998 · Geology

Cite This
Download PDF
Analyze on Scholarcy
Share
This paper deals with the treatment of subsurface environments as reactive biogeochemical transport systems. We begin with an overview of the effects of microbial activity on the chemical dynamics in these environments. Then, after a review of earlier modeling efforts, we introduce a one-dimensional, multi-component reactive transport model that accounts for the reaction couplings among the major redox and acid–base elements, O, C, H, N, S, Mn, Fe and Ca. The model incorporates kinetic descriptions for the microbial degradation pathways of organic matter, as well as for the secondary redox reactions and mineral precipitation–dissolution reactions. Local equilibrium only applies to fast homogeneous speciation reactions and sorption processes. The model is used to simulate the distributions of chemical species and reaction rates along flow paths in two subsurface environments. In the first case, waters containing moderate levels of natural soil-derived organics supply a regional groundwater system. In the second case, a pristine aquifer is contaminated by an organic-rich leachate from a landfill. In both environments, the microbial oxidation of organic matter causes the disappearance of dissolved and solid oxidants and the appearance of reduced species, albeit over very different spatial scales. In the second case, a pronounced reaction front develops at the downstream edge of the contaminant plume. The reactivity, or biodegradability, of the organic matter is shown to be a major factor governing the biogeochemical dynamics in the plume. The simulations predict different distributions of the biodegradation pathways, depending on whether the organics of the leachate have uniform or variable reactivity. The secondary reactions also have a significant impact on the concentration profiles of inorganic species and the spatial distributions of the biodegradation pathways. Within the downstream reaction front, large fractions of O2, Mn(IV), Fe(III) and SO2−4 are reduced by secondary reactions, rather than being utilized in the oxidative degradation of leachate organics. Overall, the model simulations emphasize the strong coupling between subsurface heterotrophic activity and an extensive network of secondary reactions.
This paper references
Continuum formulation of multicomponent-multiphase reactive transport
P. Lichtner (1996)
10.1038/349233A0
Microbial production of organic acids in aquitard sediments and its role in aquifer geochemistry
P. B. McMahon (1991)
10.3133/WRI8096
Phreeqe--A Computer Program for Geochemical Calculations
D. L. Parkhurst (1980)
10.3133/WRI914078
An interactive code (NETPATH) for modeling NET geochemical reactions along a flow PATH
N. Plummer (1991)
10.1016/0016-7037(90)90003-4
A new kinetic approach to modeling water-rock interaction: The role of nucleation, precursors, and Ostwald ripening
C. Steefel (1990)
10.1128/AEM.58.4.1164-1174.1992
Microsensor measurements of sulfate reduction and sulfide oxidation in compact microbial communities of aerobic biofilms.
M. Kühl (1992)
10.1515/9781501509650
Chemical weathering rates of silicate minerals
A. White (1995)
The groundwater aquifer microbiota: biomass, community structure, and nutritional status [Florida].
D. White (1983)
10.1029/95WR02567
Simulation of aerobic and anaerobic biodegradation processes at a crude oil spill site
H. Essaid (1995)
10.1016/0016-7037(92)90301-X
THE CYCLING OF IRON IN NATURAL ENVIRONMENTS : CONSIDERATIONS BASED ON LABORATORY STUDIES OF HETEROGENEOUS REDOX PROCESSES
W. Stumm (1992)
10.1111/J.1745-6584.1990.TB01985.X
Production and Carbon Isotopic Composition of Bacterial CO2 in Deep Coastal Plain Sediments of South Carolina
P. B. McMahon (1990)
10.1029/WR024I009P01553
A numerical transport model for oxygen‐ and nitrate‐based respiration linked to substrate and nutrient availability in porous media
M. Widdowson (1988)
10.3133/WRI884227
SOLMINEQ.88; a computer program for geochemical modeling of water-rock interactions
Y. K. Kharaka (1988)
10.1128/AEM.54.6.1472-1480.1988
Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese.
D. Lovley (1988)
MINTEQA2/PRODEFA2, a geochemical assessment model for environmental systems: Version 3. 0 user's manual
J. D. Allison (1991)
10.1029/94WR00955
Modeling of multicomponent reactive transport in groundwater: 1. Model development and evaluation
A. Walter (1994)
Ground-Water Microbiology And Geochemistry
F. H. Chapelle (1993)
10.1029/95RG01305
Deep subsurface microbial processes
D. Lovley (1995)
10.1201/9781003069904-1
Adsorption to heterogeneous surfaces.
W. H. Riemsdijk (1993)
10.1016/0016-7037(95)00062-5
Dynamic weathering model: Constraints required by coupled dissolution and pseudomorphic replacement
Y. Wang (1995)
10.1016/0022-1694(83)90226-3
Migration of contaminants in groundwater at a landfill: A case study 6. Hydrogeochemistry
R. Nicholson (1983)
10.1126/science.225.4665.925
Ground Water Redox Reactions: An Analysis of Equilibrium State Applied to Eh Measurements and Geochemical Modeling
R. Lindberg (1984)
10.1016/0043-1354(85)90140-X
Rate of precipitation of ferrous iron and formation of mixed iron-calcium carbonates by naturally occurring carbonate materials
J. E. Wajon (1985)
10.1016/0022-1694(87)90058-8
Geochemical calculations and observations on salt water intrusions, I. A combined geochemical/minxing cell model
C. Appelo (1987)
10.1029/WR026I009P01981
Geochemical Modeling of the Madison Aquifer in Parts of Montana, Wyoming, and South Dakota
L. N. Plummer (1990)
10.1016/0016-7037(91)90302-L
Fluorapatite crystal growth from modified seawater solutions
P. Cappellen (1991)
10.1029/94WR00434
Modeling contaminant transport and biodegradation in a layered porous media system
B. Wood (1994)
10.1080/10643389409388463
Attenuation of landfill leachate pollutants in aquifers
T. Christensen (1994)
10.1016/S0016-7037(05)80015-8
The reactivity of iron oxides in sediments: A kinetic approach
D. Postma (1993)
10.1021/BK-1989-0393.CH018
Thermodynamics and Kinetics of Hydrogen Sulfide in Natural Waters
F. Millero (1989)
10.1029/91WR00474
Numerical Modeling of Natural and Enhanced Denitrification Processes in Aquifers
W. Kinzelbach (1991)
10.1016/0016-7037(86)90043-8
Model for the distribution of sulfate reduction and methanogenesis in freshwater sediments
D. Lovley (1986)
10.1007/978-3-642-76064-8_14
Organic Matter Oxidation in Marine Sediments
D. Canfield (1993)
10.1016/0022-1694(94)90252-6
Modeling of biologically mediated redox processes in the subsurface
H. Lensing (1994)
10.1061/(ASCE)0733-9372(1994)120:5(1327)
Kinetics of Toluene Degradation by Denitrifying Aquifer Microorganisms
P. J. Alvarez (1994)
10.1111/J.1745-6584.1990.TB01988.X
pH and Redox Buffering Mechanisms in a Glacial Drift Aquifer Contaminated by Landfill Leachate
A. E. Kehew (1990)
Brock Biology of Microorganisms
M. Madigan (1996)
10.1021/BK-1989-0393
Biogenic sulfur in the environment
E. Saltzman (1989)
10.22004/AG.ECON.157268
Analytical solutions of the one-dimensional convective-dispersive solute transport equation
M. T. Genuchten (1982)
10.5860/choice.31-4922
Metals in Groundwater
H. Allen (1993)
10.2475/AJS.285.10.963
Steady-state kinetics and dissolution mechanisms of albite
L. Chou (1985)
Approaches to modeling of reactive transport in porous media
C. Steefel (1996)
10.1080/01490457809377721
A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments
Bo Barker J⊘rgensen (1978)
10.1029/WR026I002P00223
Simulation of biodegradable organic contaminants in groundwater: 2. Plume behavior in uniform and random flow fields
K. MacQuarrie (1990)
10.1128/AEM.56.6.1865-1874.1990
Rates of microbial metabolism in deep coastal plain aquifers.
F. H. Chapelle (1990)
10.1098/rsta.1990.0056
Bioturbation and manganese cycling in hemipelagic sediments
R. Aller (1990)
10.1029/WR026I002P00207
Simulation of biodegradable organic contaminants in groundwater. 1. Numerical formulation in principal directions.
K. MacQuarrie (1990)
10.1130/0091-7613(1994)022<1103:ISROSR>2.3.CO;2
In situ rates of sulfate reduction in an aquifer (Rømø, Denmark) and implications for the reactivity of organic matter
R. Jakobsen (1994)
10.1130/0091-7613(1988)016<0117:BMATCC>2.3.CO;2
Bacterial metabolism and the δ13C composition of ground water, Floridan aquifer system, South Carolina
F. H. Chapelle (1988)
10.1021/ES940722O
In situ and laboratory determined first-order degradation rate constants of specific organic compounds in an aerobic aquifer
P. H. Nielsen (1995)
10.1016/0022-1694(95)02885-4
Attenuation of nitrate in aquitard sediments of southern Ontario
W. D. Robertson (1996)
10.1029/91WR02678
The Influence of Microbial Activity and Sedimentary Organic Carbon on the Isotope Geochemistry of the Middendorf Aquifer
E. M. Murphy (1992)
10.1201/9780203747643
Metal Contaminated Aquatic Sediments
H. E. Allen (1996)
10.1515/9781501509650-004
Chapter 2. FUNDAMENTAL APPROACHES IN DESCRIBING MINERAL DISSOLUTION AND PRECIPITATION RATES
A. Lasaga (1995)
10.2172/6451946
Calculation of chemical equilibrium between aqueous solution and minerals: the EQ3/6 software package. [In FORTRAN extended 4. 6 for CDC6600 and 7600]
T. Wolery (1979)
Microbiological processes in reactive modeling
B. Rittmann (1996)
10.1029/94WR01305
Modeling reactive transport of organic compounds in groundwater using a partial redox disequilibrium approach
W. Mcnab (1994)
Reactive transport in porous media
P. Lichtner (1996)
10.1029/WR022I013P01973
Transport of dissolved hydrocarbons influenced by oxygen‐limited biodegradation: 1. Theoretical development
R. Borden (1986)
10.1016/0016-7037(69)90127-6
Evaluation of irreversible reactions in geochemical processes involving minerals and aqueous solutions—II. Applications
H. C. Helgeson (1969)
10.1029/93WR01394
An analytical solution to the solute transport equation with rate-limited desorption and decay
V. A. Fry (1993)
10.1021/ES960249+
Comparison of Eh and H2 Measurements for Delineating Redox Processes in a Contaminated Aquifer
F. H. Chapelle (1996)
10.2475/AJS.296.3.197
Cycling of iron and manganese in surface sediments; a general theory for the coupled transport and reaction of carbon, oxygen, nitrogen, sulfur, iron, and manganese
P. Cappellen (1996)
10.3133/WRI954227
USER'S GUIDE TO PHREEQC A COMPUTER PROGRAM FOR SPECIATION, REACTION-PATH, ADVECTIVE-TRANSPORT, AND INVERSE GEOCHEMICAL CALCULATIONS
D. Parkhurst (1995)
10.1021/es00005a035
Distribution of redox-sensitive groundwater quality parameters downgradient of a landfill (Grindsted, Denmark).
P. L. Bjerg (1995)
10.1016/0016-7037(93)90333-R
Simultaneous precipitation kinetics of kaolinite and gibbsite at 80°C and pH 3
K. L. Nagy (1993)
10.1016/0016-7037(93)90107-8
Redox chemistry of iron and manganese minerals in river-recharged aquifers: A model interpretation of a column experiment
T. Matsunaga (1993)
10.1080/01490457809377722
A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments
Jørgensen BoBarker (1978)
10.1007/978-3-642-76064-8
Interactions of C, N, P and S Biogeochemical Cycles and Global Change: NATO ASI Series I: Global Environmental Change, Vol. 4, 521p.
R. Wollast (1993)
10.1016/0016-7037(96)00156-1
Redox zonation: Equilibrium constraints on the Fe(III)/SO4-reduction interface
D. Postma (1996)
10.1007/978-3-642-76064-8_17
Biogeochemical Transformations in Sediments: Kinetic Models of Early Diagenesis
P. Cappellen (1993)
10.1029/92WR00667
Modeling transport and biodegradation of benzene and toluene in sandy aquifer material: Comparisons With experimental measurements
Y. Chen (1992)
10.1029/94WR00067
Temporal and spatial changes of terminal electron‐accepting processes in a petroleum hydrocarbon‐contaminated aquifer and the significance for contaminant biodegradation
D. A. Vroblesky (1994)
10.1128/AEM.50.3.580-588.1985
Characterization of subsurface bacteria associated with two shallow aquifers in oklahoma.
D. Balkwill (1985)
Étude thermodynamique et simulation des réactions entre minéraux et solutions : application à la géochimie des altérations et des eaux continentales
B. Fritz (1975)
10.1029/96WR00678
Application of a model accounting for kinetic sorption and degradation to in situ microcosm observations on the fate of aromatic hydrocarbons in an aerobic aquifer
P. L. Bjerg (1996)
10.1029/97WR00014
Intrinsic biodegradation of MTBE and BTEX in a gasoline‐contaminated aquifer
R. Borden (1997)
10.1016/0022-1694(79)90183-5
Modern marine sediments as a natural analog to the chemically stressed environment of a landfill
M. J. Baedecker (1979)
10.1016/0016-7037(93)90340-3
The anaerobic degradation of organic matter in Danish coastal sediments: iron reduction, manganese reduction, and sulfate reduction.
D. Canfield (1993)
10.1128/AEM.53.7.1536-1540.1987
Rapid assay for microbially reducible ferric iron in aquatic sediments.
D. Lovley (1987)
10.2475/AJS.294.5.529
A coupled model for transport of multiple chemical species and kinetic precipitation/dissolution rea
C. Steefel (1994)
10.1007/BF00662027
Comparison between geochemical and biological estimates of subsurface microbial activities
T. Phelps (2004)
Geochemistry, groundwater and pollution
C. Appelo (1993)
10.1306/212F7C7F-2B24-11D7-8648000102C1865D
A New Geochemical Classification of Sedimentary Environments
R. Berner (1981)
10.1038/296643A0
Mineralization of organic matter in the sea bed—the role of sulphate reduction
B. Jørgensen (1982)
10.1016/0016-7037(94)90152-X
Diffusion and reaction in rock matrix bordering a hyperalkaline fluid-filled fracture
C. Steefel (1994)
10.5860/choice.33-6312
Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters
W. Stumm (1970)
10.1021/es00058a023
Speciation of Fe(II) and Fe(III) in Contaminated Aquifer Sediments Using Chemical Extraction Techniques.
G. Heron (1994)
10.1016/0016-7037(96)00140-8
A multicomponent reactive transport model of early diagenesis: Application to redox cycling in coastal marine sediments
Y. Wang (1996)
Biogeochemical dynamics in aquatic sediments
P. Cappellen (1996)
10.1080/01490459209377902
Effects of manganese oxide mineralogy on microbial and chemical manganese reduction
David J. Burdige (1992)
10.1016/0883-2927(93)90014-8
Crude oil in a shallow sand and gravel aquifer-III
M. J. Baedecker (1993)
10.1029/WR026I004P00637
Comparison of biodegradation kinetics with an instantaneous reaction model for groundwater
H. S. Rifai (1990)
10.1111/J.1745-6584.1992.TB00808.X
Competitive Exclusion of Sulfate Reduction by Fe(lll)‐Reducing Bacteria: A Mechanism for Producing Discrete Zones of High‐Iron Ground Water
F. H. Chapelle (1992)
10.1201/9780203747643-2
Metal cycling in surface sediments; modeling the interplay of transport and reaction
Van Cappellen Philippe (1995)



This paper is referenced by
10.1016/J.ECOLENG.2016.06.098
Assessment of the denitrification process in alluvial wetlands at floodplain scale using the SWAT model
Xiaoling Sun (2017)
Modelling Bioremediation of Uranium Contaminated Aquifers
B. Rotter (2008)
Development of a Protocol and a Screening Tool for Selection of DNAPL Source Area Remediation
D. W. Major (2012)
10.1007/S00254-008-1258-4
Modeling of solute transport and biological sulfate reduction using low cost electron donor
O. Eljamal (2009)
10.4172/2252-5211.1000169
Kinetic Study for Compost Production by Isolated Fungal Strains
N. Kabbashi (2014)
10.1144/1470-9236/08-109
Finite-element model simulation of nitrate transport behaviour in saturated fractured porous media
T. Iqbal (2011)
10.1051/AGRO:2001001
Interactions between microbial processes and geochemical transformations under anaerobic conditions: a review
F. Dassonville (2002)
10.1557/PROC-807-811
Model for the Microbiological Corrosion of Copper Containers in a Deep Geologic Repository
F. King (2003)
10.1007/S10040-006-0053-0
Chemical characterization of the Neogene Aquifer, Belgium
M. Coetsiers (2006)
Natural Gradient Tracer Tests to Investigate the Fate and Migration of Oil Sands Process-Affected Water in the Wood Creek Sand Channel
Trevor Tompkins (2009)
10.1016/J.JHYDROL.2004.02.018
Nutrient inputs to the coastal ocean through submarine groundwater discharge: controls and potential impact
C. Slomp (2004)
10.1021/BK-2011-1071.CH026
Evolution of redox processes in groundwater
P. McMahon (2011)
10.1016/J.CHEMGEO.2011.06.004
A reaction-transport model of periodic precipitation of pyrite in anoxic marine sediments
R. Bektursunova (2011)
An Update of the State-of-the-art Report on the Corrosion of Copper Under Expected Conditions in a Deep Geologic Repository
F. King (2012)
REDUCTION OF A COMPLEX BIOGEOCHEMICAL MODEL WITH NEURAL NETWORK AND CLUSTERING TECHNIQUES
M. Baurmann (2003)
10.1016/j.jconhyd.2010.07.003
A combined PHREEQC-2/parallel fracture model for the simulation of laminar/non-laminar flow and contaminant transport with reactions.
C. Masciopinto (2010)
10.1016/J.ADVWATRES.2012.11.016
Role of water flow in modeling methane emissions from flooded paddy soils
A. Rizzo (2013)
10.1002/2017JG003822
Modeling hydrologic controls on sulfur processes in sulfate‐impacted wetland and stream sediments
G. C. Ng (2017)
10.1186/s40168-018-0556-7
Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake
Keith Arora-Williams (2018)
MICROBIAL AND TRANSPORT MECHANISM IN THE SEDIMENTS : INTERPLAY AND RELATIVE IMPORTANCE FOR SIMULATED CAND N-CYCLES
K. Wirtz (2004)
10.1016/J.JHYDROL.2011.02.029
Modeling the effectiveness of U(VI) biomineralization in dual-porosity porous media
B. Rotter (2011)
Modelling ofnitrogen transport and turnover during soil and groundwater passagein a small lowland catchment of Northern Germany
Gunter Wriedt (2004)
10.1016/J.CHEMGEO.2003.12.013
Migration of the sulphate–methane reaction zone in marine sediments of the Sea of Marmara—can this mechanism be tectonically induced?
P. Halbach (2004)
10.1007/978-3-540-72937-2_9
Ordinary Differential Equations–Dynamical Systems
E. Holzbecher (2007)
10.1016/J.ADVWATRES.2007.08.005
Calibration of subsurface batch and reactive-transport models involving complex biogeochemical processes
L. S. Matott (2008)
10.1042/BST0390243
A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus 'Methylomirabilis oxyfera'.
M. Wu (2011)
Coupled Biogeochemical Modeling of Ground Water Contamination at the Bemidji Minnesota Crude Oil Spill Site
G. Curtis (1999)
10.1029/2019wr026528
Flexible and Modular Simultaneous Modeling of Flow and Reactive Transport in Rivers and Hyporheic Zones
Bing Li (2020)
10.1002/2017WR021388
Spatial and Temporal Dynamics of Dissolved Oxygen Concentrations and Bioactivity in the Hyporheic Zone
W. Reeder (2018)
THE CARBON BUDGET OF A SHALLOW, TROPICAL AQUIFER: SOURCES, SINKS, AND PROCESSES
N. Richmond (2003)
10.5539/JAS.V2N2P17
Agricultural Contamination of Subterranean Water with Nitrates and Nitrites: An Environmental and Public Health Problem
Itzel Galaviz-Villa (2010)
10.1111/j.1745-6584.2008.00536.x
Distinguishing iron-reducing from sulfate-reducing conditions.
F. H. Chapelle (2009)
See more
Semantic Scholar Logo Some data provided by SemanticScholar