The use of flow-through sediment reactors in biogeochemical kinetics: Methodology and examples of applications

Marine Chemistry

Volumn 106, Issue 1-2 SPEC. ISS., 2007, Pages 256-271

  Pallud, C ^a   Meile, C ^b   Laverman, A M ^a   Abell, J ^a   Van Cappellen, P ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

Biogeochemical kinetics; Estuarine sediment; Flow through reactor; Nitrate reduction; Reactive transport modelling; Sulfate reduction

Indexed keywords

BIOGEOCHEMISTRY; CONCENTRATION (COMPOSITION); ELECTRON; MICROORGANISM; NITRATE; REACTION KINETICS; REDUCTION; SULFATE;

EID: 34547665408     PISSN: 03044203     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.marchem.2006.12.011     Document Type: Article

References (67)

1. Aller R.C., and Mackin J.E. Open-incubation, diffusion methods for measuring solute reaction rates in sediments. J. Mar. Res. 47 (1989) 411-440
2. Altmann D., Stief P., Amann R., de Beer D., and Schramm A. In situ distribution and activity of nitrifying bacteria in freshwater sediment. Environ. Microbiol. 5 (2003) 798-803
3. Bak F., and Pfennig N. Microbial sulfate reduction in littoral sediment of Lake Constance. FEMS Microbiol. Ecol. 85 (1991) 31-42
4. Bear J. Dynamics of Fluids in Porous Media (1972), Elsevier, New York
5. Berg P., Risgaard-Petersen N., and Rysgaard S. Interpretation of measured concentration profiles in sediment pore water. Limnol. Oceanogr. 43 (1998) 1500-1510
6. Berner R.A. Early Diagenesis: A Theoretical Approach (1980), Princeton University Press, Princeton, New Jersey
7. Bonneville S., Van Cappellen P., and Behrends T. Microbial reduction of iron(III) oxyhydroxides: effects of mineral solubility and availability. Chem. Geol. 212 (2004) 255-268
8. Boudreau B.P. Diagenetic Models and their Implementation (1997), Springer, New York
9. Boudreau B.P., and Westrich J.T. The dependence of bacterial sulfate reduction on sulfate concentration in marine sediments. Geochim. Cosmochim. Acta 48 (1984) 2503-2516
10. Brenner H. The diffusion model of longitudinal mixing in beds of finite length. Numerical values. Chem. Eng. Sci. 17 (1962) 229-243
11. Brüchert V., and Arnosti C. Anaerobic carbon transformation: experimental studies with flow-through cells. Mar. Chem. 80 (2003) 171-183
12. Canavan R., Slomp C., Jourabchi P., Van Cappellen P., Laverman A., and van den Berg G. Organic matter mineralization in sediment of a coastal freshwater lake and response to salinization. Geochim. Cosmochim. Acta 70 (2006) 2836-2855
13. Canfield D.E. Factors influencing organic carbon preservation in marine sediments. Chem. Geol. 114 (1994) 315-329
14. Canfield D.E. Isotope fractionation by natural populations of sulfate-reducing bacteria. Geochim. Cosmochim. Acta 65 (2001) 1117-1124
15. Chou L., and Wollast R. Study of the weathering of albite at room temperature and pressure with a fluidized bed reactor. Geochim. Cosmochim. Acta 48 (1984) 2205-2217
16. Christensen P.B., Nielsen L.P., Revsbech N.P., and Sorensen J. Microzonation of denitrification activity in stream sediments as studied with a combined oxygen and nitrous oxide microsensor. Appl. Environ. Microbiol. 55 (1989) 1234-1241
17. Cornish-Bowden A. Fundamentals of Enzyme Kinetics (1995), Portland Press Ltd., London
18. Cornish-Bowden A. Statistical analysis of enzyme kinetic data. In: Eisenthal R., and Danson M.J. (Eds). Enzyme Assays: A Practical Approach. 2nd edition (2002), Oxford University Press
19. Dalsgaard T., and Bak F. Nitrate reduction in a sulfate-bacterium, Desulfovibrio desulfuricans, isolated from a rice paddy soil: sulfide inhibition, kinetics and regulation. Appl. Environ. Microbiol. 60 (1994) 291-297
20. De Smedt F., and Wierenga P.J. Solute transfer through columns of glass beads. Water Resour. Res. 20 (1984) 225-232
21. Dowd J.E., and Riggs D.S. A comparison of estimates of Michaelis-Menten kinetic constants from various linear transformations. J. Biol. Chem. 240 (1965) 863-869
22. Ewing R.E., and Wang H. A summary of numerical methods for time-dependent advection-dominated partial differential equations. J. Comput. Appl. Math. 128 (2001) 423-445
23. Fiadeiro M.E., and Veronis G. On weighted-mean schemes for the finite-difference approximation to the advection-diffusion equation. Tellus 29 (1977) 512-522
24. Garcia-Ruiz R., Pattinson S.N., and Whitton B.A. Kinetic parameters of denitrification in a river continuum. Appl. Environ. Microbiol. 64 (1998) 2533-2538
25. Gribsholt B., and Kristensen E. Benthic metabolism and sulfur cycling along an inundation gradient in a tidal Spartina anglica salt marsh. Limnol. Oceanogr. 48 (2003) 2151-2162
26. Harnett H.E., Keil R.G., Hedges J.I., and Devol A.H. Influence of oxygen exposure time on organic carbon preservation in continental margin sediments. Nature 391 (1998) 572-574
27. Henderson J.F. Statistical analysis of enzyme kinetic data. In: Eisenthal R., and Danson M.J. (Eds). Enzyme Assays: A Practical Approach (1993), Oxford University Press
28. 2S in iron sulfide transformations: examples from Effingham Inlet, Orca Basin, and the Black Sea. Am. J. Sci. 299 (1999) 556-588
29. Hyacinthe C., and Van Cappellen P. An authigenic phosphate phase in estuarine sediments: composition, formation and chemical reactivity. Mar. Chem. 91 (2004) 227-251
30. Ingvorsen K., and Jørgensen B.B. Kinetics of sulfate uptake by freshwater and marine species of Desulfovibrio. Arch. Microbiol. 139 (1984) 61-66
31. Ingvorsen K., Zehnder A., and Jørgensen B.B. Kinetics of sulfate and actetate uptake by Desulfovibrio postgatei. Appl. Environ. Microbiol. 47 (1984) 403-408
32. Jørgensen B.B. The sulfur cycle of a coastal marine sediment (Limfjorden, Denmark). Limnol. Oceanogr. 22 (1977) 814-932
33. Jørgensen B.B. A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments I. Measurement with radiotracer techniques. Geomicrobiol. J. 1 (1978) 11-27
34. Joye S.B., Smith S.V., Hollibaugh J.T., and Paerl H.W. Estimating denitrification rates in estuarine sediments: a comparison of stoichiometric and acetylene based methods. Biogeochemistry 33 (1996) 197-215
35. Koretsky C., Moore C., Lowe K., Meile C., DiChristina T., and Van Cappellen P. Seasonal oscillation of microbial iron and sulfate reduction in saltmarsh sediments. Biogeochemistry 64 (2003) 179-203
36. Kristensen E., Ahmed S.I., and Devol A.H. Aerobic and anaerobic decomposition of organic matter in marine sediment: which is fastest?. Limnol. Oceanogr. 40 (1995) 1430-1437
37. Laverman A.M., van Rotterdam-Los D., Pallud C., Abell J., and Van Cappellen P. Potential rates and pathways of microbial nitrate reduction in coastal sediments. FEMS Microbiol. Ecol. 58 (2006) 179-192
38. Leij F.J., and Dane J.H. Solute transport in a two-layer medium investigated with time moments. Soil Sci. Soc. Am. J. 55 (1991) 1529-1535
39. Leij F.J., and Dane J.H. Comments on "A moment method for analyzing breakthrough curves of step inputs" by C. Yu et al. Water Resour. Res. 37 (2001) 1535-1537
40. Li J.-H., Takii S., Kotakemori R., and Hayashi H. Sulfate reduction in profundal sediments in Lake Kizaki, Japan. Hydrobiologia 333 (1996) 201-208
41. Maher K., Steefel C.I., DePaolo D.J., and Viani B.E. The mineral dissolution rate conundrum: Insights from reactive transport modeling of U isotopes and pore fluid chemistry n marine sediments. Geochim. Cosmochim. Acta 70 (2006) 337-363
42. Marxsen J., and Fiebig D.M. Use of perfused cores for evaluating extracellular enzyme activity in stream-bed sediments. FEMS Microbiol. Ecol. 13 (1993) 1-12
43. Meile C., and Tuncay K. Scale dependence of reaction rates in porous media. Adv. Water Resour. 29 (2005) 62-71
44. 2 exposure times: timescales in bioturbated sediments. Glob. Biogeochem. Cycles 19 (2005) 3013 10.1029/2004GB002371
45. Meile C., Koretsky C.M., and Van Cappellen P. Quantifying bioirrigation in aquatic sediments: an inverse modeling approach. Limnol. Oceanogr. 46 (2001) 164-177
46. Michaelis L., and Menten M.L. Die Kinetic der Invertinwirkung. Biochem. Z. 49 (1913) 333-369
47. Oremland R.S., Umberger C., Culbertsen C.W., and Smith R.L. Denitrification in San Francisco Bay intertidal sediments. Appl. Environ. Microbiol. 47 (1984) 1106-1112
48. Pallud C., and Van Cappellen P. Kinetics of microbial sulfate reduction in estuarine sediments. Geochim. Cosmochim. Acta 70 (2006) 1148-1162
49. Peters G.P., and Smith D.W. Numerical study of boundary conditions for solute transport through a porous medium. Int. J. Numer. Anal. Methods Geomech. 25 (2001) 629-650
50. Pfannkuch H.O. Contribution à l'étude des déplacements de fluides miscibles dans un milieu poreux. Rev. Inst. Fr. Pet. 18 (1963) 215-270
51. Regnier P., Dale A., Pallud C., van Lith Y., Bonneville S., Hyacinthe C., Thullner M., Laverman A.M., and Van Cappellen P. Incorporating geomicrobial processes in reactive transport models of subsurface environments. In: Nuetzmann G., Viotti P., and Aagaard P. (Eds). Reactive Transport in Soil and Groundwater: Processes and Models (2005), Springer Verlag, Berlin 107-126
52. Roychoudhury A.N. Dispersion in unconsolidated aquatic sediments. Estuar. Coast. Shelf Sci. 53 (2001) 745-757
53. Roychoudhury A.N. Sulfate respiration in extreme environments: a kinetic study. Geomicrobiol. J. 21 (2004) 33-43
54. Roychoudhury A.N., Viollier E., and Van Cappellen P. A flow-through reactor for studying biogeochemical reactions in undisturbed aquatic sediments. Appl. Geochem. 13 (1998) 269-280
55. Roychoudhury A.N., Van Cappellen P., Kostka J., and Viollier E. Kinetics of microbially mediated reactions: Dissimilatory sulfate reduction in saltmarsh sediments (Sapelo Island, Georgia, USA). Estuar. Coast. Shelf Sci. 56 (2003) 1001-1010
56. Schwartz R.C., McInnes K.J., Juo A.S.R., Wilding L.P., and Reddell D.L. Boundary effects on solute transport in finite soil columns. Water Resour. Res. 35 (1999) 671-681
57. Smith R.L., and Klug M.J. Reduction of sulfur compounds in the sediments of a eutrophic lake basin. Appl. Environ. Microbiol. 41 (1981) 1230-1237
58. Sonne-Hansen J., Westermann P., and Ahring B.K. Kinetics of sulfate and hydrogen uptake by the thermophilic sulfate-reducing bacteria Thermodesulfobacterium sp. strain JSP and Thermodesulfovibrio sp. strain R1Ha3. Appl. Environ. Microbiol. 65 (1999) 1304-1307
59. Stief P., Schramm A., Altmann D., and de Beer D. Temporal variation of nitrification rates in experimental freshwater sediments enriched with ammonia or nitrite. FEMS Microbiol. Ecol. 46 (2003) 63-71
60. 2, and S in coastal marine sediments. Limnol. Oceanogr. 34 (1989) 793-806
61. Van Cappellen P., and Gaillard J.-F. Biogeochemical dynamics in aquatic sediments. In: Lichtner P.C., Steefel C.I., and Oelkers E.H. (Eds). Reactive Transport in Porous Media vol. 34 (1996), Mineral. Soc. of Am., Washington, D.C. 335-376
62. van Genuchten M.Th., and Alves W.J. Analytical solutions of the one-dimensional convective-dispersive solute transport equation. USDA Tech. Bull. (1984) 1661
63. van Genuchten M.Th., and Parker J.C. Boundary conditions for displacement experiments through short laboratory soil columns. Soil Sci. Soc. Am. J. 48 (1984) 703-708
64. Vanwesenbeeck V. Geomorphology and sedimentology in the study area "Lillo" in the maritime part of the Scheldt Estuary. Hydrogr. J. 95 (2000) 1-10
65. Weston N.B., and Joye S.B. Temperature driven decoupling of key phases of organic matter degradation in marine sediments. Proc. Natl. Acad. Sci. 102 (2005) 17036-17040
66. Westrich J.T., and Berner R.A. The role of sedimentary organic matter in bacterial sulfate reduction: the G model tested. Limnol. Oceanogr. 29 (1984) 236-249
67. Yu C., Warrick A.W., and Conklin M.H. A moment method for analyzing breakthrough curves of step inputs. Water Resour. Res. 35 (1999) 3567-3572