Benthic exchange and biogeochemical cycling in permeable sediments

Annual Review of Marine Science

Volumn 6, Issue , 2014, Pages 23-51

  Huettel, Markus ^a   Berg, Peter ^b   Kostka, Joel E ^c  

^a FLORIDA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Benthic primary production; Carbon cycling; Carbonate sands; Denitrification; Shelf sediment; Silicate

Indexed keywords

BENTHIC PRIMARY PRODUCTION; BIOGEOCHEMICAL CYCLING; BIOGEOCHEMICAL REACTIONS; CARBON CYCLING; CARBONATE SAND; SHELF SEDIMENT; SPATIAL AND TEMPORAL PATTERNS; THREE-DIMENSIONAL PATTERNS;

BIOACTIVITY; BIOGEOCHEMISTRY; DENITRIFICATION; SILICATES;

SEDIMENTS;

BENTHIC ENVIRONMENT; BIOACTIVITY; BIOGEOCHEMICAL CYCLE; CARBON CYCLE; CONTINENTAL SHELF; DENITRIFICATION; HYDRODYNAMICS; PERMEABILITY; PRIMARY PRODUCTION; SEDIMENT ANALYSIS; SILICATE; SOLUTE TRANSPORT; THREE-DIMENSIONAL MODELING; WATER COLUMN;

ARTICLE; CHEMISTRY; DIFFUSION; ECOSYSTEM; OCEANOGRAPHY; PERMEABILITY; RECYCLING; SEA; SEDIMENT;

DIFFUSION; ECOSYSTEM; GEOLOGIC SEDIMENTS; OCEANOGRAPHY; OCEANS AND SEAS; PERMEABILITY; RECYCLING;

EID: 84891890089     PISSN: 19411405     EISSN: 19410611     Source Type: Journal    
DOI: 10.1146/annurev-marine-051413-012706     Document Type: Article

References (174)

1. Aller RC. 1978. The effects of animal-sediment interactions on geochemical processes near the sediment-water interface. In Estuarine Interactions, ed. ML Wiley, pp. 157-72. New York: Academic
2. Aller RC. 1994. Bioturbation and remineralization of sedimentary organic-matter: Effects of redox oscillation. Chem. Geol. 114:331-45
3. Amano T, Yoshinaga I, Okada K, Yamagishi T, Ueda S, et al. 2007. Detection of anammox activity and diversity of anammox bacteria-related 16S rRNA genes in coastal marine sediment in Japan. Microbes Environ. 22:232-42
4. Amante C, Eakins BW. 2009. ETOPO1 1 Arc-Minute Global Relief Model: Procedures, data sources and analysis. Tech.Memo.NESDISNGDC-24,Natl.Geophys. DataCent.,Natl. Oceanogr.Atmos.Admin., Boulder, CO
5. Aringhieri R. 2006. Saturated flow properties of different soil-sand systems as related to their particle-And micropore-size distributions: A comparative study. Soil Sci. 171:448-55
6. Arnosti C. 1995. Measurement of depth-related and site-related differences in polysaccharide hydrolysis rates in marine sediments. Geochim. Cosmochim. Acta 59:4247-57
7. Arnosti C, Ziervogel K, Ocampo L, Ghobrial S. 2009. Enzyme activities in the water column and in shallow permeable sediments from the northeastern Gulf of Mexico. Estuar. Coast. Shelf Sci. 84:202-8
8. Bacon MP, Belastock RA, Bothner MH. 1994. 210Pb balance and implications for particle transport on the continental shelf, U.S. Middle Atlantic Bight. Deep-Sea Res. II 41:511-35
9. Ball MM. 1967. Carbonate sand bodies of Florida and the Bahamas. J. Sediment. Petrol. 37:556-91
10. Banta GT, Holmer M, Jensen MH, Kristensen E. 1999. Effects of two polychaete worms, Nereis diversicolor and Arenicola marina, on aerobic and anaerobic decomposition in a sandymarine sediment. Aquat. Microb. Ecol. 19:189-204
11. Bear J. 1972. Dynamics of Fluids in Porous Media. New York: Am. Elsevier
12. Behrens JW, Stahl HJ, Steffensen JF, Glud RN. 2007. Oxygen dynamics around buried lesser sandeels Ammodytes tobianus (Linnaeus 1785): Mode of ventilation and oxygen requirements. J. Exp. Biol. 210:1006-14
13. Bell RJ, Savidge WB, Toler SK, Byrne RH, Short RT. 2012. In situ determination of porewater gases by underwater flow-Through membrane inlet mass spectrometry. Limnol. Oceanogr. Methods 10:117-28
14. Bennett RH, Hulbert MH, Curry C, Johnson HP, Hutnak M, Curry KJ. 2002. In situ permeabilities of selected coastal marine sediments. IEEE J. Ocean. Eng. 27:571-80
15. Berg P, Huettel M. 2008. Monitoring the seafloor using the noninvasive eddy correlation technique: Integrated benthic exchange dynamics. Oceanography 21(4):164-67
16. Berg P, Long MH, Huettel M, Rheuban JE, McGlathery KJ, et al. 2013. Eddy correlation measurements of oxygen fluxes in permeable sediments exposed to varying current flow and light. Limnol. Oceanogr. 58:1329-43
17. Berg P, Roy H, Janssen F, Meyer V, Jørgensen BB, et al. 2003. Oxygen uptake by aquatic sediments measured with a novel non-invasive eddy-correlation technique. Mar. Ecol. Prog. Ser. 261:75-83
18. Billerbeck M, Roy H, Bosselmann K, Huettel M. 2007. Benthic photosynthesis in submerged Wadden Sea intertidal flats. Estuar. Coast. Shelf Sci. 71:704-16
19. Böer SI, Arnosti C, van Beusekom JEE, Boetius A. 2009. Temporal variations in microbial activities and carbon turnover in subtidal sandy sediments. Biogeosciences 6:1149-65
20. Boucher G, Clavier J, Garrigue C. 1994. Oxygen and carbon-dioxide fluxes at the water-sediment interface of a tropical lagoon. Mar. Ecol. Prog. Ser. 107:185-93
21. Boudreau B. 1997. Diagenetic Models and Their Implementation: Modelling Transport and Reactions in Aquatic Sediments. New York: Springer
22. Bühring SI, Ehrenhauss S, Kamp A, Moodley L, Witte U. 2006. Enhanced benthic activity in sandy sublittoral sediments: Evidence from 13C tracer experiments. Mar. Biol. Res. 2:120-29
23. Burdige D. 2006. Geochemistry of Marine Sediments. Princeton, NJ: Princeton Univ. Press
24. Burnett WC, Bokuniewicz H, Huettel M, Moore WS, Taniguchi M. 2003. Groundwater and pore water inputs to the coastal zone. Biogeochemistry 66:3-33
25. Cahoon LB, Cooke JE. 1992. Benthicmicroalgal production in Onslow Bay, North Carolina, USA. Mar. Ecol. Prog. Ser. 84:185-96
26. Cahoon LB, Nearhoof JE, Tilton CL. 1999. Sediment grain size effect on benthic microalgal biomass in shallow aquatic ecosystems. Estuaries 22:735-41
27. Canfield DE, Des Marais DJ. 1991. Aerobic sulfate reduction in microbial mats. Science 251:1471-73
28. Canfield DE, Jørgensen BB, Fossing H, Glud R, Gundersen J, et al. 1993. Pathways of organic carbon oxidation in three continental margin sediments. Mar. Geol. 113:27-40
29. Canion A, Kostka JE, Gihring TM, Huettel M, van Beusekom JEE, et al. 2013. Temperature response of denitrification and anammox reveals the adaptation of microbial communities to in situ temperatures in permeable marine sediments that span 50 in latitude. Biogeosci. Discuss. 10:14595-626
30. Capone DG, Dunham SE, Horrigan SG, Duguay LE. 1992. Microbial nitrogen transformations in unconsolidated coral-reef sediments. Mar. Ecol. Prog. Ser. 80:75-88
31. Cebrián J, Duarte CM. 1994. The dependence of herbivory on growth-rate in natural plant-communities. Funct. Ecol. 8:518-25
32. Charette MA, Buesseler KO. 2004. Submarine groundwater discharge of nutrients and copper to an urban subestuary of Chesapeake Bay (Elizabeth River). Limnol. Oceanogr. 49:376-85
33. Charette MA, Sholkovitz ER, Hansel CM 2005. Trace element cycling in a subterranean estuary: Part 1 Geochemistry of the permeable sediments. Geochim. Cosmochim. Acta 69:2095-109
34. Chen C-TA. 2010. Cross-boundary exchanges of carbon and nitrogen in continental margins. See Liu et al. 2010b, pp. 561-74
35. Cook PLM, Wenzhöfer F, Glud RN, Janssen F, Huettel M. 2007. Benthic solute exchange and carbon mineralization in two shallow subtidal sandy sediments: Effect of advective pore-water exchange. Limnol. Oceanogr. 52:1943-63
36. Cook PLM, Wenzhöfer F, Rysgaard S, Galaktionov OS, Meysman FJR, et al. 2006. Quantification of denitrification in permeable sediments: Insights from a two-dimensional simulation analysis and experimental data. Limnol. Oceanogr. Methods 4:294-307
37. Darcy H. 1856. Les Fontaines Publiques de la Ville de Dijon. Paris: Dalmont
38. Dauer DM, Ranasinghe JA, Weisberg SB. 2000. Relationships between benthic community condition, water quality, sediment quality, nutrient loads, and land use patterns in Chesapeake Bay. Estuaries 23:80-96
39. Deflaun MF, Mayer LM. 1983. Relationships between bacteria and grain surfaces in intertidal sediments. Limnol. Oceanogr. 28:873-81
40. Duarte CM. 1991. Seagrass depth limits. Aquat. Bot. 40:363-77
41. Duarte CM, Cebrián J. 1996. The fate of marine autotrophic production. Limnol. Oceanogr. 41:1758-66
42. Duarte CM, Chiscano CL. 1999. Seagrass biomass and production: A reassessment. Aquat. Bot. 65:159-74
43. Duarte CM, Middelburg JJ, Caraco N. 2005. Major role of marine vegetation on the oceanic carbon cycle. Biogeosciences 2:1-8
44. Ducklow HW, McCallister SL. 2005. The biogeochemistry of carbon dioxide in the coastal ocean. In The Global Coastal Ocean, ed. KHB Allan, R Robinson, pp. 269-316. Cambridge, MA: Harvard Univ. Press
45. Emery KO. 1968. Relict sediments on continental shelves of the world. Am. Assoc. Pet. Geol. 52:445-64
46. Eyre BD, Ferguson AJP. 2009. Denitrification efficiency for defining critical loads of carbon in shallow coastal ecosystems. Hydrobiologia 629:137-46
47. Eyre BD, Glud RN, Patten N. 2008. Mass coral spawning: A natural large-scale nutrient addition experiment. Limnol. Oceanogr. 53:997-1013
48. Fenchel T. 1970. Studies on the decomposition of organic detritus derived from the turtle grass Thalassia testudinum. Limnol. Oceanogr. 15:14-20
49. Fogaren KE, Sansone FJ, De Carlo EH. 2013. Porewater temporal variability in a wave-impacted permeable nearshore sediment. Mar. Chem. 149:74-84
50. Fourqurean JW, Duarte CM, Kennedy H, Marba N, Holmer M, et al. 2012. Seagrass ecosystems as a globally significant carbon stock. Nat. Geosci. 5:505-9
51. Gao H, Schreiber F, Collins G, Jensen MM, Kostka JE, et al. 2010. Aerobic denitrification in permeable Wadden Sea sediments. ISME J. 4:417-26
52. Gattuso JP, Frankignoulle M, Wollast R. 1998. Carbon and carbonate metabolism in coastal aquatic ecosystems. Annu. Rev. Ecol. Syst. 29:405-34
53. Gattuso JP, Gentili B, Duarte CM, Kleypas JA, Middelburg JJ, Antoine D. 2006. Light availability in the coastal ocean: Impact on the distribution of benthic photosynthetic organisms and their contribution to primary production. Biogeosciences 3:489-513
54. George DA, Hill PS. 2008. Wave climate, sediment supply and the depth of the sand-mud transition: A global survey. Mar. Geol. 254:121-28
55. Giere O. 1993. Meiobenthology: The Microscopic Fauna in Aquatic Sediments. Berlin: Springer-Verlag
56. Gihring TM, Canion A, Riggs A, Huettel M, Kostka JE. 2010. Denitrification in shallow, sublittoral Gulf of Mexico permeable sediments. Limnol. Oceanogr. 55:43-54
57. Gihring TM, Humphrys M, Mills HJ, Huettel M, Kostka JE. 2009. Identification of phytodetritus-degrading microbial communities in sublittoral Gulf of Mexico sands. Limnol. Oceanogr. 54:1073-83
58. Glud RN. 2008. Oxygen dynamics of marine sediments. Mar. Biol. Res. 4:243-89
59. Glud RN, Eyre BD, Patten N. 2008. Biogeochemical responses to mass coral spawning at the Great Barrier Reef: Effects on respiration and primary production. Limnol. Oceanogr. 53:1014-24
60. Gobet A, Böer SI, Huse SM, van Beusekom JEE, Quince C, et al. 2012. Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J. 6:542-53
61. Goharzadeh A, Saidi A, Wang D, Merzkirc W, Khalil A. 2005. An experimental investigation of the Brinkman layer thickness at a fluid-porous interface. In IUTAM Symposium on One Hundred Years of Boundary Layer Research: Proceedings of the IUTAM Symposium Held at DLR-Göttingen, Germany, August 12-14, 2004, ed. GEA Meier, KR Sreenivasan, HJ Heinemann, pp. 445-54. Solid Mech. Its Appl. 129. Dordrecht: Springer
62. Grenz C, Denis L, Boucher G, Chauvaud L, Clavier J, et al. 2003. Spatial variability in sediment oxygen consumption under winter conditions in a lagoonal system in New Caledonia (South Pacific). J. Exp. Mar. Biol. Ecol. 285:33-47
63. Gruber N, Galloway JN. 2008. An Earth-system perspective of the global nitrogen cycle. Nature 451:293-96
64. Hall SJ. 2002. The continental shelf benthic ecosystem: Current status, agents for change and future prospects. Environ. Conserv. 29:350-74
65. Hargrave BT. 1972. Aerobic decomposition of sediment and detritus as a function of particle surface area and organic content. Limnol. Oceanogr. 17:583-96
66. Hartwig EO. 1978. Factors affecting respiration and photosynthesis by benthic community of a subtidal siliceous sediment. Mar. Biol. 46:283-93
67. Harvey RW, Kinner NE, Bunn A, Macdonald D, Metge D. 1995. Transport behavior of groundwater protozoa and protozoan-sized microspheres in sandy aquifer sediments. Appl. Environ. Microbiol. 61:209-17
68. Hayes MO. 1967. Relationship between coastal climate and bottom sediment type on the inner continental shelf. Mar. Geol. 5:111-32
69. Hedges JI, Baldock JA, Gelinas Y, Lee C, Peterson ML, Wakeham SG. 2002. The biochemical and elemental compositions of marine plankton: A NMR perspective. Mar. Chem. 78:47-63
70. Hedges JI, Keil RG, Benner R. 1997. What happens to terrestrial organic matter in the oceanörg. Geochem. 27:195-212
71. Hellebust JA, Lewin J. 1977. Heterotrophic nutrition. In The Biology of Diatoms, ed. D Werner, pp. 169-97 Berkeley: Univ. Calif. Press
72. Holtappels M, Glud RN, Donis D, Liu B, Hume A, et al. 2013. Effects of transient bottom water currents and oxygen concentrations on benthic exchange rates as assessed by eddy correlation measurements. J. Geophys. Res. 118:1157-69
73. Hudson JH. 1984. Seasonal growth rates and carbonate production in Halimeda opuntia at Marquesas Keys, Florida. AAPG Bull. 68:489-89
74. Huettel M. 1990. Influence of the lugworm Arenicola marina on porewater nutrient profiles of sand flat sediments. Mar. Ecol. Prog. Ser. 62:241-48
75. Huettel M, Cook P, Janssen F, Lavik G, Middelburg JJ. 2007. Transport and degradation of a dinoflagellate bloom in permeable sublittoral sediment. Mar. Ecol. Prog. Ser. 340:139-53
76. Huettel M, Gust G. 1992. Impact of bioroughness on interfacial solute exchange in permeable sediments. Mar. Ecol. Prog. Ser. 89:253-67
77. Huettel M, Røy H, Precht E, Ehrenhauss S. 2003. Hydrodynamical impact on biogeochemical processes in aquatic sediments. Hydrobiologia 494:231-36
78. Huettel M, Rusch A. 2000. Transport and degradation of phytoplankton in permeable sediment. Limnol. Oceanogr. 45:534-49
79. Huettel M, Webster IT. 2000. Porewater flow in permeable sediment. In The Benthic Boundary Layer: Transport Processes and Biogeochemistry, ed.BPBoudreau, BBJørgensen, pp. 144-79. Oxford, UK: Oxford Univ.Press
80. Huettel M, Ziebis W, Forster S. 1996. Flow-induced uptake of particulate matter in permeable sediments. Limnol. Oceanogr. 41:309-22
81. Huettel M, Ziebis W, Forster S, Luther GW. 1998. Advective transport affecting metal and nutrient distributions and interfacial fluxes in permeable sediments. Geochim. Cosmochim. Acta 62:613-31
82. Hume AC, Berg P, McGlathery KJ. 2011. Dissolved oxygen fluxes and ecosystem metabolism in an eelgrass (Zostera marina) meadow measured with the eddy correlation technique. Limnol. Oceanogr. 56:86-96
83. Hunter EM, Mills HJ, Kostka JE. 2006. Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments. Appl. Environ. Microbiol. 72:5689-701
84. Inman DL, Jenkins SA. 2005. Energy and sediment budgets of the global coastal zone. In Encyclopedia of Coastal Science, ed. M Schwartz, pp. 408-15. Dordrecht: Springer
85. Inman DL, Nordstrom CE. 1971. Tectonic and morphologic classification of coasts. J. Geol. 79:1-21
86. Jago CF, Jones SE, Latter RJ, McCandliss RR, Hearn MR, Howarth MJ. 2002. Resuspension of benthic fluff by tidal currents in deep stratified waters, northern North Sea. J. Sea Res. 48:259-69
87. Jahnke RA. 2010. Global synthesis. See Liu et al. 2010b, pp. 597-615
88. Jahnke RA, Nelson JR, Marinelli RL, Eckman JE. 2000. Benthic flux of biogenic elements on the southeastern US continental shelf: Influence of pore water advective transport and benthic microalgae. Cont. Shelf Res. 20:109-27
89. Jahnke RA, Nelson JR, Richards ME, Robertson CY, Rao AMF, Jahnke DB. 2008. Benthic primary productivity on the Georgia midcontinental shelf: Benthic flux measurements and high-resolution, continuous in situ PAR records. J. Geophys. Res. 113:C08022
90. Jahnke RA, Richards M, Nelson J, Robertson C, Rao A, Jahnke D. 2005. Organic matter remineralization and porewater exchange rates in permeable South Atlantic Bight continental shelf sediments. Cont. Shelf Res. 25:1433-52
91. Janssen F, Faerber P, Huettel M, Meyer V, Witte U. 2005a. Pore-water advection and solute fluxes in permeable marine sediments (I): Calibration and performance of the novel benthic chamber system Sandy. Limnol. Oceanogr. 50:768-78
92. Janssen F, Huettel M, Witte U. 2005b. Pore-water advection and solute fluxes in permeable marine sediments (II): Benthic respiration at three sandy sites with different permeabilities (German Bight, North Sea Limnol. Oceanogr. 50:779-92
93. Jonsson BF, Salisbury JE, Mahadevan A. 2011. Large variability in continental shelf production of phytoplankton carbon revealed by satellite. Biogeosciences 8:1213-23
94. Jørgensen BB. 1983. Processes at the sediment water interface. In The Major Biogeochemical Cycles and Their Interactions, ed. B Bolin, RB Cook, pp. 477-515. New York: Wiley
95. Joye SB, Hollibaugh JT. 1995. Influence of sulfide inhibition of nitrification on nitrogen regeneration in sediments. Science 270:623-25
96. Keil RG, Hedges JI. 1993. Sorption of organic matter to mineral surfaces and the preservation of organic matter in coastal marine sediments. Chem. Geol. 107:385-88
97. Kessler AJ, Glud RN, Cardenas MB, Larsen M, Bourke MF, Cook PLM. 2012. Quantifying denitrification in rippled permeable sands through combined flume experiments and modeling. Limnol. Oceanogr. 57:1217-32
98. Kingston MB. 2002. Effect of subsurface nutrient supplies on the vertical migration of Euglena proxima (Euglenophyta). J. Phycol. 38:872-80
99. Köster M, Meyer-Reil L-A. 2001. Characterization of carbon and microbial biomass pools in shallow water coastal sediments of the southern Baltic Sea (Nordrügensche Bodden). Mar. Ecol. Prog. Ser. 214:25-41
100. Kostka JE, Gihring T, Mills H, Lavik G, Gao H, et al. 2008. Nitrogen loss and temperature regulation of microbial communities that mediate denitrification and anammox in permeable marine sediments across a 50 latitudinal gradient. Abstr. Gen. Meet. Am. Soc. Microbiol. 108:400-1 (Abstr
101. Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, et al. 2011. Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the deepwater horizon oil spill. Appl. Environ. Microbiol. 77:7962-74
102. Kristensen E, Ahmed SI, Devol AH. 1995. Aerobic and anaerobic decomposition of organic matter in marine sediment:Which is fastest? Limnol. Oceanogr. 40:1430-37
103. Kristensen E, Jensen MH, Jensen KM. 1997. Temporal variations in microbenthic metabolism and inorganic nitrogen fluxes in sandy and muddy sediments of a tidally dominated bay in the northern Wadden Sea. Helgol. Meeresunters. 51:295-320
104. Kühl M, Jørgensen BB. 1994. The light field of microbenthic communities: Radiance distribution and microscale optics of sandy coastal sediments. Limnol. Oceanogr. 39:1368-98
105. Laursen AE, Seitzinger SP. 2002. The role of denitrification in nitrogen removal and carbon mineralization in Mid-Atlantic Bight sediments. Cont. Shelf Res. 22:1397-416
106. Liu K-K, Atkinson L, Quïnones R, Talaue-McManus L. 2010a. Biogeochemistry of continental margins in a global context. See Liu et al. 2010b, pp. 3-24
107. Liu K-K, Atkinson L, Quïnones R, Talaue-McManus L, eds. 2010b. Carbon and Nutrient Fluxes in Continental Margins: A Global Synthesis. Berlin: Springer
108. Macintyre HL, Geider RJ, Miller DC. 1996. Microphytobenthos: The ecological role of the secret garden of unvegetated, shallow-watermarine habitats. 1. Distribution, abundance and primary production. Estuaries 19:186-201
109. Malan DE, McLachlan A. 1985. Vertical gradients ofmeiofauna and bacteria in subtidal sandy sediments from two high-energy surf zones in Algoa Bay, South Africa. S. Afr. J. Mar. Sci. 3:43-54
110. Marinelli RL, Jahnke RA, Craven DB, Nelson JR, Eckman JE. 1998. Sediment nutrient dynamics on the South Atlantic Bight continental shelf. Limnol. Oceanogr. 43:1305-20
111. McCave IN. 2003. Sedimentary settings on continental margins-An overview. In OceanMargin Systems, ed.G Wefer, D Billett, D Hebbeln, BB Jørgensen, MSchlüter, TCE vanWeering, pp. 1-14. Berlin: Springer
112. McDowell-Boyer LM, Hunt JR, Sitar N. 1986. Particle transport through porous media. Water Resour. Res. 22:1901-21
113. McGee D, Laws RA, Cahoon LB. 2008. Live benthic diatoms from the upper continental slope: Extending the limits of marine primary production. Mar. Ecol. Prog. Ser. 356:103-12
114. McLachlan A, Eliot IG, Clarke DJ. 1985. Water filtration through reflective microtidal beaches and shallow sublittoral sands and its implications for an inshore ecosystem inWestern Australia. Estuar. Coast. Shelf. Sci. 21:91-104
115. Meadows PS, Anderson JG. 1966. Micro-organisms attached to marine and freshwater sand grains. Nature 212:1059-60
116. Meadows PS, Anderson JG. 1968. Micro-organisms attached to marine sand grains. J. Mar. Biol. Assoc. UK 48:161-75
117. Middelburg JJ, Barranguet C, Boschker HTS, Herman PMJ, Moens T, Heip CHR. 2000. The fate of intertidal microphytobenthos carbon: An in situ 13C-labeling study. Limnol. Oceanogr. 45:1224-34
118. Middelburg JJ, Duarte CM, Gattuso JP. 2004. Respiration in coastal benthic communities. In Respiration in Aquatic Ecosystems, ed. PJLB Williams, PA del Giorgio, pp. 206-25. Oxford, UK: Oxford Univ. Press
119. Middelburg JJ, Levin LA. 2009. Coastal hypoxia and sediment biogeochemistry. Biogeosciences 6:1273-93
120. Middelburg JJ, Soetaert K. 2004. The role of sediments in shelf ecosystem dynamics. Geochim. Cosmochim. Acta 68:A343
121. Middelburg JJ, Soetaert K. 2005. The role of sediments in shelf ecosystem dynamics. In The Global Coastal Ocean, ed. KHB Allan, R Robinson, pp. 353-75. Cambridge, MA: Harvard Univ. Press
122. Miller DC. 1989. Abrasion effects on microbes in sandy sediments. Mar. Ecol. Prog. Ser. 55:73-82
123. Mills HJ, Hunter E, Humphrys M, Kerkhof L, McGuinness L, et al. 2008. Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico. Appl. Environ. Microbiol. 74:4440-53
124. Miyajima T, Suzumura M, Umezawa Y, Koike I. 2001. Microbiological nitrogen transformation in carbonate sediments of a coral-reef lagoon and associated seagrass beds. Mar. Ecol. Prog. Ser. 217:273-86
125. Moore WS. 1999. The subterranean estuary: A reaction zone of ground water and sea water. Mar. Chem. 65:111-25
126. Mudryk ZJ, Podgorska B. 2005. Spatial variability in the activity of hydrolytic enzymes in a marine beach (Southern Baltic Sea). Pol. J. Ecol. 53:255-60
127. Nelson JR, Eckman JE, Robertson CY, Marinelli RL, Jahnke RA. 1999. Benthic microalgal biomass and irradiance at the sea floor on the continental shelf of the South Atlantic Bight: Spatial and temporal variability and storm effects. Cont. Shelf Res. 19:477-505
128. Nittrouer CA, ed. 1981. Sedimentary Dynamics of Continental Shelves. Amsterdam: Elsevier
129. Nixon SW, Pilson M. 1983. Nitrogen in estuarine and coastal marine ecosystems. In Nitrogen in the Marine Environment, ed. EJ Carpenter, DG Capone, pp. 565-648. New York: Academic
130. Packman AI, Brooks NH. 2001. Hyporheic exchange of solutes and colloids with moving bed forms. Water Resour. Res. 37:2591-605
131. Pilditch CA, Miller DC. 2006. Phytoplankton deposition to permeable sediments under oscillatory flow: Effects of ripple geometry and resuspension. Cont. Shelf Res. 26:1806-25
132. Precht E, Franke U, Polerecky L, Huettel M. 2004. Oxygen dynamics in permeable sediments with wavedriven pore water exchange. Limnol. Oceanogr. 49:693-705
133. Precht E, Huettel M. 2004. Rapid wave-driven advective pore water exchange in a permeable coastal sediment. J. Sea Res. 51:93-107
134. Rao AMF, McCarthy MJ, Gardner WS, Jahnke RA. 2007. Respiration and denitrification in permeable continental shelf deposits on the South Atlantic Bight: Rates of carbon and nitrogen cycling from sediment column experiments. Cont. Shelf Res. 27:1801-19
135. Rao AMF, McCarthy MJ, Gardner WS, Jahnke RA. 2008. Respiration and denitrification in permeable continental shelf deposits on the South Atlantic Bight: N2:Ar and isotope pairing measurements in sediment column experiments. Cont. Shelf Res. 28:602-13
136. Rasheed M, Wild C, Franke U, Huettel M. 2004. Benthic photosynthesis and oxygen consumption in permeable carbonate sediments at Heron Island, Great Barrier Reef, Australia. Estuar. Coast. Shelf Sci. 59:139-50
137. Reimers CE, Stecher HA III, Taghon GL, Fuller CM, Huettel M, et al. 2004. In situ measurements of advective solute transport in permeable shelf sands. Cont. Shelf Res. 24:183-201
138. Rhoads DC, Aller RC, Goldhaber MB. 1977. The influence of colonizing benthos on physical properties and chemical diagenesis of the estuarine seafloor. In Ecology of Marine Benthos, ed. BC Coull, pp. 113-38 Columbia: Univ. NC Press
139. Riedl R, Huang N, Machan R. 1972. The subtidal pump: A mechanism of intertidal water exchange by wave action. Mar. Biol. 13:210-21
140. Riisgård HU, Banta GT. 1998. Irrigation and deposit feeding by the lugworm Arenicola marina, characteristics and secondary effects on the environment: A review of current knowledge. Vie Milieu 48:243-57
141. Rocha C. 2000. Density-driven convection during flooding of warm, permeable intertidal sediments: The ecological importance of the convective turnover pump. J. Sea Res. 43:1-14
142. Rusch A, Forster S, Huettel M. 2001. Bacteria, diatoms and detritus in an intertidal sandflat subject to advective transport across the water-sediment interface. Biogeochemistry 55:1-27
143. Rusch A, Huettel M, Reimers CE, Taghon GL, Fuller CM. 2003. Activity and distribution of bacterial populations in Middle Atlantic Bight shelf sands. FEMS Microbiol. Ecol. 44:89-100
144. Rusch A, Huettel M, Wild C, Reimers CE. 2006. Benthic oxygen consumption and organic matter turnover in organic-poor, permeable shelf sands. Aquat. Geochem. 12:1-19
145. Sansone FJ, Pawlak G, Stanton TP, McManus MA, Glazer BT, et al. 2008. Kilo Nalu: Physical/biogeochemical dynamics above and within permeable sediments. Oceanography 21(4):173-78
146. Santos IR, Eyre BD, Glud RN. 2012a. Influence of porewater advection on denitrification in carbonate sands: Evidence from repacked sediment column experiments. Geochim. Cosmochim. Acta 96:247-58
147. Santos IR, Eyre BD, Huettel M. 2012b. The driving forces of porewater and groundwater flow in permeable coastal sediments: A review. Estuar. Coast. Shelf Sci. 98:1-15
148. Santos IR, Glud RN, Maher D, Erler D, Eyre BD. 2011. Diel coral reef acidification driven by porewater advection in permeable carbonate sands, Heron Island, Great Barrier Reef. Geophys. Res. Lett. 38:L03604
149. Schöttner S, Pfitzner B, Grünke S, Rasheed M, Wild C, Ramette A. 2011. Drivers of bacterial diversity dynamics in permeable carbonate and silicate coral reef sands from the Red Sea. Environ. Microbiol. 13:1815-26
150. Seitzinger SP, Giblin AE. 1996. Estimating denitrification in North Atlantic continental shelf sediments. Biogeochemistry 35:235-60
151. Seitzinger SP, Harrison JA, Bohlke JK, Bouwman AF, Lowrance R, et al. 2006. Denitrification across landscapes and waterscapes: A synthesis. Ecol. Appl. 16:2064-90
152. Stolzenbach KD, Newman KA, Wong CS. 1992. Aggregation of fine particles at the sediment-water interface. J. Geophys. Res. 97:17889-98
153. Sundbäck K, Miles A, Goransson E. 2000. Nitrogen fluxes, denitrification and the role of microphytobenthos in microtidal shallow-water sediments: An annual study. Mar. Ecol. Prog. Ser. 200:59-76
154. Sundbäck K, Miles A, Linares F. 2006. Nitrogen dynamics in nontidal littoral sediments: Role of microphytobenthos and denitrification. Estuaries Coasts 29:1196-211
155. Thibodeaux LJ, Boyle JD. 1987. Bedform-generated convective transport in bottom sediment. Nature 325:341-43
156. Tribble GW, Sansone FJ, Buddemeier RW, Li Y-H. 1992. Hydraulic exchange between a coral reef and surface sea water. Geol. Soc. Am. Bull. 104:1280-91
157. Underwood GJC, Kromkamp J. 1999. Primary production by phytoplankton and microphytobenthos in estuaries. Adv. Ecol. Res. 29:93-153
158. Vance-Harris C, Ingall E. 2005. Denitrification pathways and rates in the sandy sediments of the Georgia continental shelf, USA. Geochem. Trans. 6:12-18
159. Vandevivere P, Baveye P. 1992. Effect of bacterial extracellular polymers on the saturated hydraulic conductivity of sand columns. Appl. Environ. Microbiol. 58:1690-98
160. Van Raaphorst W, Kloosterhuis HT, Berghuis EM, Gieles AJM, Malschaert JFP, Van Noort GJ. 1992. Nitrogen cycling in two types of sediments of the southern North Sea (Frisian Front, Broad Fourteens) field data and mesocosm results. Neth. J. Sea Res. 28:293-316
161. Viana AR, Faugeres JC, Stow DAV. 1998. Bottom-current-controlled sand deposits: A review of modern shallow-To deep-water environments. Sediment. Geol. 115:53-80
162. Volkenborn N, Hedtkamp SIC, van Beusekom JEE, Reise K. 2007. Effects of bioturbation and bioirrigation by lugworms (Arenicola marina) on physical and chemical sediment properties and implications for intertidal habitat succession. Estuar. Coast. Shelf Sci. 74:331-43
163. Volkenborn N, Polerecky L, Wethey DS, Woodin SA. 2010. Oscillatory porewater bioadvection in marine sediments induced by hydraulic activities of Arenicola marina. Limnol. Oceanogr. 55:1231-47
164. Webb JE, Theodor J. 1968. Irrigation of submerged marine sands through wave action. Nature 220:682-85
165. Webster IT, Norquay SJ, Ross FC, Wooding RA. 1996. Solute exchange by convection within estuarine sediments. Estuar. Coast. Shelf Sci. 42:171-83
166. Webster IT, Taylor JH. 1992. Rotational dispersion in porous media due to fluctuating flow. Water Resour. Res. 28:109-19
167. Wiberg PL, Smith JD. 1987. Calculations of the critical shear-stress for motion of uniform and heterogeneous sediments. Water Resour. Res. 23:1471-80
168. Wild C, Huettel M, Klueter A, Kremb SG, Rasheed MYM, Jørgensen BB. 2004a. Coral mucus functions as an energy carrier and particle trap in the reef ecosystem. Nature 428:66-70
169. Wild C, Rasheed M, Werner U, Franke U, Johnstone R, Huettel M. 2004b. Degradation and mineralization of coral mucus in reef environments. Mar. Ecol. Prog. Ser. 267:159-71
170. Wild C, Laforsch C, Huettel M. 2006. Detection and enumeration of microbial cells within highly porous calcareous reef sands. Mar. Freshw. Res. 57:415-20
171. Wilson AM. 2005. Fresh and saline groundwater discharge to the ocean: A regional perspective. Water Resour. Res. 41:W02016
172. Wollast R. 1998. Evaluation and comparison of the global carbon cycle in the coastal zone and in the open ocean. In The Global Coastal Ocean: Processes and Methods, ed. KH Brink, AR Robinson, pp. 213-52. New York:Wiley and Sons
173. Ziebis W, Forster S, Huettel M, Jørgensen BB. 1996a.Complex burrows of themud shrimp Callianassa truncata and their geochemical impact in the sea bed. Nature 383:457-57
174. Ziebis W, Huettel M, Forster S. 1996b. Impact of biogenic sediment topography on oxygen fluxes in permeable seabeds. Mar. Ecol. Prog. Ser. 140:227-37