, Volume 127, Issue 2–3, pp 367–396 | Cite as

Influence of hydrological, biogeochemical and temperature transients on subsurface carbon fluxes in a flood plain environment

  • Bhavna AroraEmail author
  • Nicolas F. Spycher
  • Carl I. Steefel
  • Sergi Molins
  • Markus Bill
  • Mark E. Conrad
  • Wenming Dong
  • Boris Faybishenko
  • Tetsu K. Tokunaga
  • Jiamin Wan
  • Kenneth H. Williams
  • Steven B. Yabusaki


Flood plains play a potentially important role in the global carbon cycle. The accumulation of organic matter in flood plains often induces the formation of chemically reduced groundwater and sediments along riverbanks. In this study, our objective is to evaluate the cumulative impact of such reduced zones, water table fluctuations, and temperature gradients on subsurface carbon fluxes in a flood plain at Rifle, Colorado located along the Colorado River. 2-D coupled variably-saturated, non-isothermal flow and biogeochemical reactive transport modeling was applied to improve our understanding of the abiotic and microbially mediated reactions controlling carbon dynamics at the Rifle site. Model simulations considering only abiotic reactions (thus ignoring microbial reactions) underestimated CO2 partial pressures observed in the unsaturated zone and severely underestimated inorganic (and overestimated organic) carbon fluxes to the river compared to simulations with biotic pathways. Both model simulations and field observations highlighted the need to include microbial contributions from chemolithoautotrophic processes (e.g., Fe+2 and S−2 oxidation) to match locally-observed high CO2 concentrations above reduced zones. Observed seasonal variations in CO2 concentrations in the unsaturated zone could not be reproduced without incorporating temperature gradients in the simulations. Incorporating temperature fluctuations resulted in an increase in the annual groundwater carbon fluxes to the river by 170 % to 3.3 g m−2 d−1, while including water table variations resulted in an overall decrease in the simulated fluxes. We conclude that spatial microbial and redox zonation as well as temporal fluctuations of temperature and water table depth contribute significantly to subsurface carbon fluxes in flood plains and need to be represented appropriately in model simulations.


Flood plain Reduced zones Subsurface carbon dynamics Temporal variability Biogeochemical processes 



This material is based upon work supported as part of the Genomes to Watershed Scientific Focus Area at Lawrence Berkeley National Laboratory funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-AC02-05CH11231. We are grateful to P. E. Long for providing temperature data for this study.


  1. Ahonen L, Tuovinen OH (1990) Kinetics of sulfur oxidation at suboptimal temperatures. Appl Environ Microbiol 56:560–562Google Scholar
  2. Amos RT, Mayer KU, Blowes DW, Ptacek CJ (2004) Reactive transport modeling of column experiments for the remediation of acid mine drainage. Environ Sci Technol 38:3131–3138. doi: 10.1021/es0349608 CrossRefGoogle Scholar
  3. Anderson RT, Vrionis HA, Ortiz-Bernad I et al (2003) Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl Environ Microbiol 69:5884–5891CrossRefGoogle Scholar
  4. Andrews DM, Lin H, Zhu Q et al (2011) Hot spots and hot moments of dissolved organic carbon export and soil organic carbon storage in the Shale Hills Catchment. Vadose Zo J 10:943. doi: 10.2136/vzj2010.0149 CrossRefGoogle Scholar
  5. Arndt S, Jørgensen BB, LaRowe DE et al (2013) Quantifying the degradation of organic matter in marine sediments: a review and synthesis. Earth-Sci Rev 123:53–86. doi: 10.1016/j.earscirev.2013.02.008 CrossRefGoogle Scholar
  6. Arora B, Mohanty BP, McGuire JT, Cozzarelli IM (2013) Temporal dynamics of biogeochemical processes at the Norman Landfill site. Water Resour Res 49:6909–6926. doi: 10.1002/wrcr.20484 CrossRefGoogle Scholar
  7. Arora B, Dwivedi D, Hubbard SS et al (2015a) Identifying geochemical hot moments and their controls on a contaminated river floodplain system using wavelet and entropy approaches. Environ Model Softw (in press)Google Scholar
  8. Arora B, Şengör SS, Steefel CI (2015b) A reactive transport benchmark on heavy metal cycling in lake sediments. Comput Geosci 19:613–633. doi: 10.1007/s10596-014-9445-8 CrossRefGoogle Scholar
  9. Atkins ML, Santos IR, Ruiz-Halpern S, Maher DT (2013) Carbon dioxide dynamics driven by groundwater discharge in a coastal floodplain creek. J Hydrol 493:30–42. doi: 10.1016/j.jhydrol.2013.04.008 CrossRefGoogle Scholar
  10. Aufdenkampe AK, Mayorga E, Raymond PA et al (2011) Riverine coupling of biogeochemical cycles between land, oceans, and atmosphere. Front Ecol Environ 9:53–60. doi: 10.1890/100014 CrossRefGoogle Scholar
  11. Bao C, Wu H, Li L et al (2014) Uranium bioreduction rates across scales: biogeochemical “hot moments” and “hot spots” during a biostimulation Experiment at Rifle, Colorado. Environ Sci Technol. doi:  10.1021/es501060d
  12. Bargar JR, Campbell KM, Stubbs JE, et al (2011) Speciation and dynamics of biologically reduced uranium(IV) in the Old Rifle aquifer. Abstr Pap Am Chem Soc 242Google Scholar
  13. Batson J, Noe GB, Hupp CR et al (2015) Soil greenhouse gas emissions and carbon budgeting in a short-hydroperiod floodplain wetland. J Geophys Res Biogeosci 120:77–95. doi: 10.1002/2014JG002817.Received CrossRefGoogle Scholar
  14. Billings SA, Richter DD, Yarie J (1998) Soil carbon dioxide fluxes and profile concentrations in two boreal forests. Can J For Res Can Rech For 28:1773–1783. doi: 10.1139/cjfr-28-12-1773 CrossRefGoogle Scholar
  15. Blazejewski GA, Stolt MH, Gold AJ et al (2009) Spatial distribution of carbon in the subsurface of riparian zones. Soil Sci Soc Am J 73:1733. doi: 10.2136/sssaj2007.0386 CrossRefGoogle Scholar
  16. Bosatta E, Ågren GI (1995) The power and reactive continuum models as particular cases of the q-theory of organic matter dynamics. Geochim Cosmochim Acta 59:3833–3835CrossRefGoogle Scholar
  17. Bourg ACM, Bertin C (1993) Biogeochemical processes during the infiltration of river water into an alluvial aquifer. Environ Sci Technol 27:661–666. doi: 10.1021/es00041a009 CrossRefGoogle Scholar
  18. Brunke M, Gonser T (1997) The ecological significance of exchange processes between rivers and groundwater. Freshw Biol 37:1–33. doi: 10.1046/j.1365-2427.1997.00143.x CrossRefGoogle Scholar
  19. Campbell KM, Kukkadapu RK, Qafoku NP et al (2012) Geochemical, mineralogical and microbiological characteristics of sediment from a naturally reduced zone in a uranium-contaminated aquifer. Appl Geochem 27:1499–1511. doi: 10.1016/j.apgeochem.2012.04.013 CrossRefGoogle Scholar
  20. Cole JJ, Caraco NF (2001) Carbon in catchments : connecting terrestrial carbon losses with aquatic metabolism. Mar Freshw Res 52:101–110CrossRefGoogle Scholar
  21. Cole JJ, Prairie YT, Caraco NF et al (2007) Plumbing the global carbon cycle: integrating inland waters into the terrestrial carbon budget. Ecosystems 10:172–185. doi: 10.1007/s10021-006-9013-8 CrossRefGoogle Scholar
  22. Crow SE, Wieder RK (2005) Sources of CO2 emission from a northern peatland: root respiration, exudation, and decomposition. Ecology 86:1825–1834. doi: 10.1890/04-1575 CrossRefGoogle Scholar
  23. Dai Z, Trettin CC, Li C et al (2012) Effect of assessment scale on spatial and temporal variations in CH4, CO2, and N2O fluxes in a forested wetland. Water Air Soil Pollut 223:253–265. doi: 10.1007/s11270-011-0855-0 CrossRefGoogle Scholar
  24. Davidson EA, Samanta S, Caramori SS, Savage K (2012) The dual arrhenius and michaelis-menten kinetics model for decomposition of soil organic matter at hourly to seasonal time scales. Glob Chang Biol 18:371–384. doi: 10.1111/j.1365-2486.2011.02546.x CrossRefGoogle Scholar
  25. Dermody O, Weltzin JF, Engel EC et al (2007) How do elevated [CO2], warming, and reduced precipitation interact to affect soil moisture and LAI in an old field ecosystem? Plant Soil 301:255–266. doi: 10.1007/s11104-007-9443-x CrossRefGoogle Scholar
  26. Dick JJ, Tetzlaff D, Birkel C, Soulsby C (2014) Modelling landscape controls on dissolved organic carbon sources and fluxes to streams. Biogeochemistry 122:361–374. doi: 10.1007/s10533-014-0046-3 CrossRefGoogle Scholar
  27. Doussan C, Poitevin G, Ledoux E, Delay M (1997) River bank filtration: modelling of the changes in water chemistry with emphasis on nitrogen species. J Contam Hydrol 25:129–156. doi: 10.1016/S0169-7722(96)00024-1 CrossRefGoogle Scholar
  28. Druhan JL, Bill M, Lim H et al (2014a) A large column analog experiment of stable isotope variations during reactive transport: II. Carbon mass balance, microbial community structure and predation. Geochim Cosmochim Acta 124:394–409. doi: 10.1016/j.gca.2013.08.036 CrossRefGoogle Scholar
  29. Druhan JL, Steefel CI, Conrad ME, DePaolo DJ (2014b) A large column analog experiment of stable isotope variations during reactive transport: i. A comprehensive model of sulfur cycling and δ34S fractionation. Geochim Cosmochim Acta 124:366–393. doi: 10.1016/j.gca.2013.08.037 CrossRefGoogle Scholar
  30. Duckworth OW, Martin ST (2004) Role of molecular oxygen in the dissolution of siderite and rhodochrosite. Geochim Cosmochim Acta 68:607–621. doi: 10.1016/S0016-7037(00)00464-2 CrossRefGoogle Scholar
  31. Eliasson PE, McMurtrie RE, Pepper DA et al (2005) The response of heterotrophic CO2 flux to soil warming. Glob Chang Biol 11:167–181. doi: 10.1111/j.1365-2486.2004.00878.x CrossRefGoogle Scholar
  32. Etiope G (1999) Subsoil CO 2 and CH 4 and their advective transfer from faulted grassland to the atmosphere. J Geophys Res 104:16889. doi: 10.1029/1999JD900299 CrossRefGoogle Scholar
  33. Fan Z, Neff JC, Waldrop MP et al (2014) Transport of oxygen in soil pore-water systems: implications for modeling emissions of carbon dioxide and methane from peatlands. Biogeochemistry 121:455–470. doi: 10.1007/s10533-014-0012-0 CrossRefGoogle Scholar
  34. Fang Y, Yabusaki SB, Morrison SJ et al (2009) Multicomponent reactive transport modeling of uranium bioremediation field experiments. Geochim Cosmochim Acta 73:6029–6051. doi: 10.1016/j.gca.2009.07.019 CrossRefGoogle Scholar
  35. Farouki OT (1982) Thermal properties of soils. Hanover, New HampshireGoogle Scholar
  36. Flores Orozco A, Williams KH, Long PE et al (2011) Using complex resistivity imaging to infer biogeochemical processes associated with bioremediation of an uranium-contaminated aquifer. J Geophys Res 116:G03001. doi: 10.1029/2010JG001591 Google Scholar
  37. Fox PM, Davis JA, Hay MB et al (2012) Rate-limited U(VI) desorption during a small-scale tracer test in a heterogeneous uranium-contaminated aquifer. Water Resour Res 48:n/a–n/a. doi:  10.1029/2011WR011472
  38. Frey SD, Drijber R, Smith H, Melillo J (2008) Microbial biomass, functional capacity, and community structure after 12 years of soil warming. Soil Biol Biochem 40:2904–2907. doi: 10.1016/j.soilbio.2008.07.020 CrossRefGoogle Scholar
  39. Gandy CJ, Smith JWN, Jarvis AP (2007) Attenuation of mining-derived pollutants in the hyporheic zone: a review. Sci Total Environ 373:435–446. doi: 10.1016/j.scitotenv.2006.11.004 CrossRefGoogle Scholar
  40. Handley KM, VerBerkmoes NC, Steefel CI et al (2013) Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J 7:800–816. doi: 10.1038/ismej.2012.148 CrossRefGoogle Scholar
  41. Hanson PJ, Edwards NT, Garten CT, Andrews JA (2000) Separating root and soil microbial contributions to soil respiration: a review of methods and observations. Biogeochemistry 48:115–146. doi: 10.1023/A:1006244819642 CrossRefGoogle Scholar
  42. Harshman EN (1972) Geology and uranium deposits, Shirley Basin area. Wyoming, WashingtonGoogle Scholar
  43. Helgeson HC, Delany JM, Nesbitt HW, Bird DK (1978) Summary and critique of the thermodynamic properties of rock-forming minerals. Am J Sci 278:229Google Scholar
  44. Helz GR, Adelson JM (2013) Trace element profiles in sediments as proxies of dead zone history; rhenium compared to molybdenum. Environ Sci Technol 47:1257–1264. doi: 10.1021/es303138d CrossRefGoogle Scholar
  45. Hinton MJ, Schiff SL, English MC (1997) The significance of storms for the concentration and export of dissolved organic carbon from two Precambrian Shield catchments. Biogeochemistry 36:67–88. doi: 10.1023/A:1005779711821 CrossRefGoogle Scholar
  46. Hiscock KM, Grischek T (2002) Attenuation of groundwater pollution by bank filtration. J Hydrol 266:139–144. doi: 10.1016/S0022-1694(02)00158-0 CrossRefGoogle Scholar
  47. Hope D, Billett MF, Cresser MS (1994) A review of the export of carbon in river water: fluxes and processes. Environ Pollut 84:301–324. doi: 10.1016/0269-7491(94)90142-2 CrossRefGoogle Scholar
  48. Hunter KS, Wang Y, Van Cappellen P (1998) Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry. J Hydrol 209:53–80. doi: 10.1016/S0022-1694(98)00157-7 CrossRefGoogle Scholar
  49. Jansen B, Kalbitz K, McDowell WH (2014) Dissolved organic matter: linking soils and aquatic systems. Vadose Zo J. doi: 10.2136/vzj2014.05.0051 Google Scholar
  50. Kalbitz K, Solinger S, Park JH et al (2000) Controls on the dynamics of dissolved organic matter in soils: a review. Soil Sci 165:277–304. doi: 10.1097/00010694-200004000-00001 CrossRefGoogle Scholar
  51. Kang S, Running SW, Kimball JS et al (2014) Effects of spatial and temporal climatic variability on terrestrial carbon and water fluxes in the Pacific Northwest, USA. Environ Model Softw 51:228–239. doi: 10.1016/j.envsoft.2013.09.020 CrossRefGoogle Scholar
  52. Keller CK, Bacon DH (1998) Soil respiration and georespiration distinguished by transport analyses of vadose CO2, 13CO2, and 14CO2. Global Biogeochem Cycles 12:361–372CrossRefGoogle Scholar
  53. Kim JH, Guo X, Park HS (2008) Comparison study of the effects of temperature and free ammonia concentration on nitrification and nitrite accumulation. Process Biochem 43:154–160. doi: 10.1016/j.procbio.2007.11.005 CrossRefGoogle Scholar
  54. Kim DG, Vargas R, Bond-Lamberty B, Turetsky MR (2012) Effects of soil rewetting and thawing on soil gas fluxes: a review of current literature and suggestions for future research. Biogeosciences 9:2459–2483. doi: 10.5194/bg-9-2459-2012 CrossRefGoogle Scholar
  55. Kukkadapu RK, Qafoku NP, Arey BW et al (2010) Effect of extent of natural subsurface bioreduction on Fe-mineralogy of subsurface sediments. J Phys 217:012047. doi: 10.1088/1742-6596/217/1/012047 Google Scholar
  56. Lasaga AC (1998) Kinetic theory in the earth sciences. Princeton University Press, PrincetonCrossRefGoogle Scholar
  57. Leirós M, Trasar-Cepeda C, Seoane S, Gil-Sotres F (1999) Dependence of mineralization of soil organic matter on temperature and moisture. Soil Biol Biochem 31:327–335. doi: 10.1016/S0038-0717(98)00129-1 CrossRefGoogle Scholar
  58. Li L, Steefel CI, Williams KH et al (2009) Mineral transformation and biomass accumulation associated with uranium bioremediation at Rifle, Colorado. Environ Sci Technol 43:5429–5435. doi: 10.1021/es900016v CrossRefGoogle Scholar
  59. Li L, Steefel CI, Kowalsky MB et al (2010) Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during biostimulation experiments at Rifle, Colorado. J Contam Hydrol 112:45–63. doi: 10.1016/j.jconhyd.2009.10.006 CrossRefGoogle Scholar
  60. Long P (2009) Rifle integrated field research challenge site, quarterly report, fiscal year 2009, 2nd and 3rd QuartersGoogle Scholar
  61. Long PE, Williams KH, Davis JA et al (2015) Bicarbonate impact on U(VI) bioreduction in a shallow alluvial aquifer. Geochim Cosmochim Acta 150:106–124. doi: 10.1016/j.gca.2014.11.013 CrossRefGoogle Scholar
  62. Lovley DR, Phillips EJP (1986) Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl Environ Microbiol 51:683–689Google Scholar
  63. Luther GW, Findlay AJ, MacDonald DJ et al (2011) Thermodynamics and kinetics of sulfide oxidation by oxygen: a look at inorganically controlled reactions and biologically mediated processes in the environment. Front Microbiol 2:1–9. doi: 10.3389/fmicb.2011.00062 CrossRefGoogle Scholar
  64. Lynch S, Batty L, Byrne P (2014) Environmental risk of metal mining contaminated river bank sediment at redox-transitional zones. Minerals 4:52–73. doi: 10.3390/min4010052 CrossRefGoogle Scholar
  65. Macpherson GL (2009) CO2 distribution in groundwater and the impact of groundwater extraction on the global C cycle. Chem Geol 264:328–336. doi: 10.1016/j.chemgeo.2009.03.018 CrossRefGoogle Scholar
  66. Maggi F, Gu C, Riley WJ et al (2008) A mechanistic treatment of the dominant soil nitrogen cycling processes: model development, testing, and application. J Geophys Res Biogeosci 113:1–13. doi: 10.1029/2007JG000578 CrossRefGoogle Scholar
  67. Majzlan J, Navrotsky A, Schwertmann U (2004) Thermodynamics of iron oxides: part III, Enthalpies of formation and stability of ferrihydrite (~ Fe(OH)3/4(S04)1/8), and ε-Fe2O3. Geochmica Cosmochim Acta 68:1049–1059CrossRefGoogle Scholar
  68. Mayer KU, Frind EO, Blowes DW (2002) Multicomponent reactive transport modeling in variably saturated porous media using a generalized formulation for kinetically controlled reactions. Water Resour Res 38:13–1–13–21. doi:  10.1029/2001WR000862
  69. McClain ME, Boyer EW, Dent CL et al (2003) Biogeochemical hot spots and hot moments at the interface of terrestrial and aquatic ecosystems. Ecosystems 6:301–312CrossRefGoogle Scholar
  70. McKenney DJ, Johnson GP, Findlay WI (1984) Effect of temperature on consecutive denitrification reactions in brookston clay and fox sandy loam. Appl Environ Microbiol 47:919–926Google Scholar
  71. Miall AD (2001) Sedimentary basins: evolution, facies, and sediment budget. Sediment Geol 143:185–186CrossRefGoogle Scholar
  72. Millington RJ, Quirk JP (1961) Permeability of porous solids. Trans Faraday Soc 57:1200–1207CrossRefGoogle Scholar
  73. Morel FMM, Hering JG (1993) Principles and applications of aquatic chemistry. Wiley, New YorkGoogle Scholar
  74. Oba Y, Poulson SR (2009) Oxygen isotope fractionation of dissolved oxygen during abiological reduction by aqueous sulfide. Chem Geol 268:226–232. doi: 10.1016/j.chemgeo.2009.09.002 CrossRefGoogle Scholar
  75. Palandri JL, Kharaka YK (2004) A compilation of rate parameters of water-mineral interaction kinetics for application to geochemical modeling. U.S. geological survey open file report 2004–1068, Menlo ParkGoogle Scholar
  76. Palmer K, Drake HL, Horn MA (2010) Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen. Appl Environ Microbiol 76:1125–1134. doi: 10.1128/AEM.02256-09 CrossRefGoogle Scholar
  77. Parkhurst DL, Appelo CAJ (1999) User’s guide to PHREEQC (version 2)—a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations. Denver, COGoogle Scholar
  78. Parton WJ, Schimel DS, Cole CV, Ojima DS (1987) Analysis of factors controlling soil organic matter levels in Great Plains grasslands. Soil Sci Soc Am J 51:1173–1179. doi: 10.2136/sssaj1987.03615995005100050015x CrossRefGoogle Scholar
  79. Pruess K, Oldenburg CM, Moridis GJ (1999) TOUGH2 user’s guide version 2. Lawrence Berkeley National Laboratory, BerkeleyCrossRefGoogle Scholar
  80. Pulliam WM (1992) Carbon dioxide and methane exportsfrom a southeastern floodplain swamp. Ecol Monogr 63:29–53CrossRefGoogle Scholar
  81. Qafoku NP, Kukkadapu RK, McKinley JP et al (2009) Uranium in framboidal pyrite from a naturally bioreduced alluvial sediment. Environ Sci Technol 43:8528–8534. doi: 10.1021/es9017333 CrossRefGoogle Scholar
  82. Qafoku NP, Gartman BN, Kukkadapu RK et al (2014) Geochemical and mineralogical investigation of uranium in multi-element contaminated, organic-rich subsurface sediment. Appl Geochemistry 42:77–85. doi: 10.1016/j.apgeochem.2013.12.001 CrossRefGoogle Scholar
  83. Raich JW, Potter CS (1995) Global patterns of carbon-dioxide emissions from soils. Global Biogeochem Cycles 9:23–36. doi: 10.1029/94gb02723 CrossRefGoogle Scholar
  84. Raymond PA, Bauer JE, Cole JJ (2000) Atmospheric CO2 evasion, dissolved inorganic carbon production, and net heterotrophy in the York River estuary. Limnol Oceanogr 45:1707–1717. doi: 10.4319/lo.2000.45.8.1707 CrossRefGoogle Scholar
  85. Reed MH, Palandri JL (2006) SOLTHERM.H06, a database of equilibrium constants for minerals and aqueous species. University of Oregon, EugeneGoogle Scholar
  86. Richards LA (1931) Capillary conduction of liquids through porous mediums. Physics (College Park Md) 1:318. doi: 10.1063/1.1745010 Google Scholar
  87. Richey JE, Melack JM, Aufdenkampe AK et al (2002) Outgassing from Amazonian rivers and wetlands as a large tropical source of atmospheric CO2. Nature 416:617–620. doi: 10.1038/416617a CrossRefGoogle Scholar
  88. Rickard D (2006) The solubility of FeS. Geochim Cosmochim Acta 70:5779–5789. doi: 10.1016/j.gca.2006.02.029 CrossRefGoogle Scholar
  89. Riley WJ, Maggi F, Kleber M et al (2014) Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically resolved model (BAMS1) to soil carbon dynamics. Geosci Model Dev 7:1335–1355. doi: 10.5194/gmd-7-1335-2014 CrossRefGoogle Scholar
  90. Robertson AI, Bunn SE, Boon PI, Walker KF (1999) Sources, sinks and transformations of organic carbon in Australian floodplain rivers. Mar Freshw Res 50:813. doi: 10.1071/MF99112 CrossRefGoogle Scholar
  91. Russell EW (1973) Soil conditions and plant growth, 10th edn. Longmans Publishing, LondonGoogle Scholar
  92. Schlesinger WH, Andrews JA (2000) Soil respiration and the global carbon cycle. Biogeochemistry 48:7–20CrossRefGoogle Scholar
  93. Schmidt MWI, Torn MS, Abiven S et al (2011) Persistence of soil organic matter as an ecosystem property. Nature 478:49–56CrossRefGoogle Scholar
  94. Shock EL, Koretsky CM (1993) Metal-organic complexes in geochemical processes: calculation of standard partial molal thermodynamic properties of aqueous acetate complexes at high pressures and temperatures. Geochim Cosmochim Acta 57:4899–4922. doi: 10.1016/0016-7037(93)90128-J CrossRefGoogle Scholar
  95. Shock EL, Sassani DC, Willis M, Sverjensky DA (1997) Inorganic species in geologic fluids: correlations among standard molal thermodynamic properties of aqueous ions and hydroxide complexes. Geochim Cosmochim Acta 61:907–950. doi: 10.1016/S0016-7037(96)00339-0 CrossRefGoogle Scholar
  96. Simunek J, Suarez D (1993) Modeling of carbon dioxide transport and production in soil. Water Resour Res 29:487–497CrossRefGoogle Scholar
  97. Smith KA, Ball T, Conen F et al (2003) Exchange of greenhouse gases between soil and atmosphere: interactions of soil physical factors and biological processes. Eur J Soil Sci 54:779–791. doi: 10.1046/j.1365-2389.2003.00567.x CrossRefGoogle Scholar
  98. SNL (2007) Qualification of thermodynamic data for geochemical modeling of mineral-water interactions in dilute systems. Las Vegas, NevadaGoogle Scholar
  99. Sonnenthal E, Spycher N, Xu T et al (2014) TOUGHREACT V3.0-OMP reference manual: a parallel simulation program for non-isothermal multiphase geochemical reactive transport. Lawrence Berkeley National Laboratory, BerkeleyGoogle Scholar
  100. Southwell M, Thoms M (2011) Patterns of nutrient concentrations across multiple floodplain surfaces in a large Dryland River system. Geogr Res 49:431–443. doi: 10.1111/j.1745-5871.2011.00699.x CrossRefGoogle Scholar
  101. Spirakis CS (1996) The roles of organic matter in the formation of uranium deposits in sedimentary rocks. Ore Geol Rev 11:53–69. doi: 10.1016/0169-1368(95)00015-1 CrossRefGoogle Scholar
  102. Steefel CI (2000) New directions in hydrogeochemical transport modeling: Incorporating multiple kinetic and equilibrium reaction pathways. Comput Methods Water Resour Vols 1 2 Comput Methods Subsurf Flow Transp—Comput Methods, Surf Water Syst Hydrol 331–338Google Scholar
  103. Steefel CI, Brodie EL, Bouskill N et al (2014) The GEWaSC framework: multiscale modeling of coupled biogeochemical, microbiological, and. Goldschmidt Abstracts. Sacramento, CA, p 2373Google Scholar
  104. Stielstra CM, Lohse KA, Chorover J et al (2015) Climatic and landscape influences on soil moisture are primary determinants of soil carbon fluxes in seasonally snow-covered forest ecosystems. Biogeochemistry. doi: 10.1007/s10533-015-0078-3 Google Scholar
  105. Stumm W, Morgan JJ (eds) (1993) Aquatic chemistry: chemical equilibria and rates in natural waters. Wiley, New YorkGoogle Scholar
  106. Suchomel KH, Kreamer DK, Long A (1990) Production and transport of carbon dioxide in a contaminated vadose zone: a stable and radioactive carbon isotope study. Environ Sci Technol 24:1824–1831. doi: 10.1021/es00082a006 CrossRefGoogle Scholar
  107. Thamdrup B, Hansen JW, Jorgensen BB (1998) Temperature dependence of aerobic respiration in a coastal sediment. FEMS Microbiol Ecol 25:189–200. doi: 10.1111/j.1574-6941.1998.tb00472.x CrossRefGoogle Scholar
  108. Thornton SF, McManus J (1994) Application of organic carbon and nitrogen stable isotope and C/N ratios as source indicators of organic matter provenance in estuarine systems: evidence from the Tay Estuary, Scotland. Estuar Coast Shelf Sci 38:219–233CrossRefGoogle Scholar
  109. Tockner K, Pennetzdorfer D, Reiner N et al (1999) Hydrological connectivity, and the exchange of organic matter and nutrients in a dynamic river-floodplain system (Danube, Austria). Freshw Biol 41:521–535. doi: 10.1046/j.1365-2427.1999.00399.x CrossRefGoogle Scholar
  110. Tokunaga T, Kim Y, Williams KH et al (2015) Vadose zone borehole instrumentation for monitoring water, solute, and gas fluxes: installations in a cobbly floodplain and initial results. Vadose Zo J 8:1–16Google Scholar
  111. Tufenkji N, Ryan JN, Elimelech M (2002) Peer reviewed: the promise of bank filtration. Environ Sci Technol 36:422A–428A. doi: 10.1021/es022441j CrossRefGoogle Scholar
  112. U.S. Department of Energy (1999) Final Site Observational Work Plan for the UMTRA Project Old Rifle Site. Grand Junction, COGoogle Scholar
  113. U.S. Department of Energy (2012) groundwater compliance action plan for the Old Rifle, Colorado, UMTRCA Title I Processing SiteGoogle Scholar
  114. Van Breukelen BM, Griffioen J, Röling WFM, Van Verseveld HW (2004) Reactive transport modelling of biogeochemical processes and carbon isotope geochemistry inside a landfill leachate plume. J Contam Hydrol 70:249–269. doi: 10.1016/j.jconhyd.2003.09.003 CrossRefGoogle Scholar
  115. Van Cappellen P, Gaillard J-F (1996) Biogeochemical dynamics in aquatic sediments. In: Lichtner PC, Steefel CI, Oelkers EH (eds) Reactive transport in porous media, vol 34. Mineralogical Society of America, Washington, pp 335–376Google Scholar
  116. van Griethuysen C, Luitwieler M, Joziasse J, Koelmans AA (2005) Temporal variation of trace metal geochemistry in floodplain lake sediment subject to dynamic hydrological conditions. Environ Pollut 137:281–294. doi: 10.1016/j.envpol.2005.01.023 CrossRefGoogle Scholar
  117. Vrionis HA, Anderson RT, Ortiz-Bernad I et al (2005) Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl Environ Microbiol 71:6308–6318. doi: 10.1128/AEM.71.10.6308-6318.2005 CrossRefGoogle Scholar
  118. Wainwright HM, Orozco AF, Bücker M et al (2015) Hierarchical Bayesian method for mapping biogeochemical hot spots using induced polarization imaging. Water Resour Res n/a–n/a. doi: 10.1002/2015WR017763 Google Scholar
  119. Waldrop M, Balser T, Firestone M (2000) Linking microbial community composition to function in a tropical soil. Soil Biol Biochem 32:1837–1846. doi: 10.1016/S0038-0717(00)00157-7 CrossRefGoogle Scholar
  120. Walvoord MA., Striegl RG, Prudic DE, Stonestrom DA (2005) CO 2 dynamics in the Amargosa Desert: fluxes and isotopic speciation in a deep unsaturated zone. Water Resour Res 41:n/a–n/a. doi:  10.1029/2004WR003599
  121. Wang JH, Baltzis BC, Lewandowski GA (1995) Fundamental denitrification kinetic studies with Pseudomonas denitrificans. Biotechnol Bioeng 47:26–41. doi: 10.1002/bit.260470105 CrossRefGoogle Scholar
  122. Westerhoff P (2003) Reduction of nitrate, bromate, and chlorate by zero valent iron. J Environ Eng 129:10–16. doi: 10.1061/(ASCE)0733-9372(2003)129:1(10) CrossRefGoogle Scholar
  123. Widdowson MA, Molz FJ, Benefield LD (1988) A numerical transport model for oxygen- and nitrate-based respiration linked to substrate and nutrient availability in porous media. Water Resour Res 24:1553–1565. doi: 10.1029/WR024i009p01553 CrossRefGoogle Scholar
  124. Wilhelm SW, LeCleir GR, Bullerjahn GS et al (2014) Seasonal changes in microbial community structure and activity imply winter production is linked to summer hypoxia in a large lake. FEMS Microbiol Ecol 87:475–485. doi: 10.1111/1574-6941.12238 CrossRefGoogle Scholar
  125. Williams KH, Long PE, Davis JA et al (2011) Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater. Geomicrobiol J 28:519–539. doi: 10.1080/01490451.2010.520074 CrossRefGoogle Scholar
  126. Williamson MA, Rimstidt JD (1994) The kinetics and electrochemical rate-determining step of aqueous pyrite oxidation. Geochim Cosmochim Acta 58:5443–5454CrossRefGoogle Scholar
  127. Wójcicki KJ (2012) Stratigraphy of organic-rich deposits in floodplain environments: examples from the upper Odra River basin. Quaest Geogr 31:107–117Google Scholar
  128. Wójcicki KJ, Marynowski L (2012) The organic and mineral matter contents in deposits infilling floodplain basins: holocene alluviation record from the Kłodnica and Osobłoga river valleys, southern Poland. Geomorphology 159–160:15–29. doi: 10.1016/j.geomorph.2012.02.020 CrossRefGoogle Scholar
  129. Wood WW, Petraitis MJ (1984) Origin and distribution of carbon dioxide in the unsaturated zone of the southern high plains of texas. Water Resour Res 20:1193–1208. doi: 10.1029/WR020i009p01193 CrossRefGoogle Scholar
  130. Wu Y, Ajo-Franklin JB, Spycher N et al (2011) Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation. Geochem Trans 12:7. doi: 10.1186/1467-4866-12-7 CrossRefGoogle Scholar
  131. Xu T, Spycher N, Sonnenthal E et al (2011) TOUGHREACT Version 2.0: a simulator for subsurface reactive transport under non-isothermal multiphase flow conditions. Comput Geosci 37:763–774. doi: 10.1016/j.cageo.2010.10.007 CrossRefGoogle Scholar
  132. Yabusaki SB, Fang Y, Williams KH et al (2011) Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment. J Contam Hydrol 126:271–290. doi: 10.1016/j.jconhyd.2011.09.002 CrossRefGoogle Scholar
  133. Zogg GP, Zak DR, Ringelberg DB et al (1997) Compositional and functional shifts in microbial communities due to soil warming. Soil Sci Soc Am J 61:475. doi: 10.2136/sssaj1997.03615995006100020015x CrossRefGoogle Scholar

Copyright information

© US Government 2016

Authors and Affiliations

  • Bhavna Arora
    • 1
    Email author
  • Nicolas F. Spycher
    • 1
  • Carl I. Steefel
    • 1
  • Sergi Molins
    • 1
  • Markus Bill
    • 1
  • Mark E. Conrad
    • 1
  • Wenming Dong
    • 1
  • Boris Faybishenko
    • 1
  • Tetsu K. Tokunaga
    • 1
  • Jiamin Wan
    • 1
  • Kenneth H. Williams
    • 1
  • Steven B. Yabusaki
    • 2
  1. 1.Energy Geosciences DivisionLawrence Berkeley National LaboratoryBerkeleyUSA
  2. 2.Pacific Northwest National LaboratoryRichlandUSA

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