Alkhatib M, Lehmann MF, Del Giorgio PA (2012) The nitrogen isotope effect of benthic remineralization-nitrification- denitrification coupling in an estuarine environment. Biogeosciences 9:1633–1646. https://doi.org/10.5194/bg-9-1633-2012
Article
Google Scholar
Aller RC (1977) Influence of macrobenthos on chemical diagenesis of marine sediments. Yale University, New Haven
Book
Google Scholar
Aller RC (1980a) Diagenetic processes near the sediment-water interface of Long Island Sound. II. Fe and Mn. Adv Geophys 22:351–415. https://doi.org/10.1016/S0065-2687(08)60068-0
Article
Google Scholar
Aller RC (1980b) Diagenetic processes near the sediment-water interface of Long Island Sound. I.: decomposition and nutrient element geochemistry (S, N, P). Adv Geophys 22:237–350. https://doi.org/10.1016/S0065-2687(08)60067-9
Article
Google Scholar
An S, Gardner WS (2002) Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas). Mar Ecol Prog Ser 237:41–50. https://doi.org/10.3354/meps237041
Article
Google Scholar
An S, Joye SB (2001) Enhancement of coupled nitrification-denitrification by benthic photosynthesis in shallow estuarine sediments. Limnol Oceanogr 46:62–74. https://doi.org/10.4319/lo.2001.46.1.0062
Article
Google Scholar
Anderson TH, Taylor GT (2001) Nutrient pulses, plankton blooms, and seasonal hypoxia in Western Long Island Sound. Estuaries 24:228–243. https://doi.org/10.2307/1352947
Article
Google Scholar
Angell JH, Peng X, Ji Q et al (2018) Community composition of nitrous oxide-related genes in salt marsh sediments exposed to nitrogen enrichment. Front Microbiol 9:170. https://doi.org/10.3389/fmicb.2018.00170
Article
Google Scholar
Antler G, Turchyn AV, Herut B et al (2014) Sulfur and oxygen isotope tracing of sulfate driven anaerobic methane oxidation in estuarine sediments. Estuar Coast Shelf Sci 142:4–11. https://doi.org/10.1016/j.ecss.2014.03.001
Article
Google Scholar
Arar EJ, Collins GB (1997) Method 445.0: in vitro determination of chlorophyll a and pheophytin a in marine and freshwater algae by fluorescence. Washington, DC
Arndt S, Jørgensen BB, LaRowe DE et al (2013) Quantifying the degradation of organic matter in marine sediments: a review and synthesis. Earth 123:53–86. https://doi.org/10.1016/j.earscirev.2013.02.008
Article
Google Scholar
Aromokeye DA, Kulkarni AC, Elvert M et al (2020) Rates and microbial players of iron-driven anaerobic oxidation of methane in methanic marine sediments. Front Microbiol 10:3041. https://doi.org/10.3389/fmicb.2019.03041
Article
Google Scholar
Aurin DA, Dierssen HM, Twardowski MS, Roesler CS (2010) Optical complexity in Long Island Sound and implications for coastal ocean color remote sensing. J Geophys Res 115:005837. https://doi.org/10.1029/2009jc005837
Article
Google Scholar
Babbin AR, Jayakumar A, Ward BB (2016) Organic matter loading modifies the microbial community responsible for nitrogen loss in estuarine sediments. Microb Ecol 71:555–565. https://doi.org/10.1007/s00248-015-0693-5
Article
Google Scholar
Balcom PH, Godfrey JM, Bennett DC et al (2007) Deploying benthic chambers to measure sediment oxygen demand in Long Island Sound. Diving Sci 8:135–141
Google Scholar
Banta GT, Giblin AE, Hobbie JE, Tucker J (1995) Benthic respiration and nitrogen release in Buzzards Bay, Massachusetts. J Mar Res 53:107–135. https://doi.org/10.1357/0022240953213287
Article
Google Scholar
Barnes J, Upstill-Goddard RC (2018) The denitrification paradox: the role of O2 in sediment N2O production. Estuar Coast Shelf Sci 200:270–276. https://doi.org/10.1016/j.ecss.2017.11.018
Article
Google Scholar
Bates D, Mächler M, Bolker BM, Walker SC (2015) Fitting linear mixed-effects models using lme4. J Stat Softw 67:1–51. https://doi.org/10.18637/jss.v067.i01
Article
Google Scholar
Bernard RJ, Mortazavi B, Wang L et al (2014) Benthic nutrient fluxes and limited denitrification in a sub-tropical groundwater-influenced coastal lagoon. Mar Ecol Prog Ser 504:13–26. https://doi.org/10.3354/meps10783
Article
Google Scholar
Bertics VJ, Ziebis W (2009) Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches. ISME J 3:1269–1285. https://doi.org/10.1038/ismej.2009.62
Article
Google Scholar
Bolker BM, Brooks ME, Clark CJ et al (2009) Generalized linear mixed models: a practical guide for ecology and evolution. Trends Ecol Evol 24:127–135
Article
Google Scholar
Bonaglia S, Deutsch B, Bartoli M et al (2014) Seasonal oxygen, nitrogen and phosphorus benthic cycling along an impacted Baltic Sea estuary: regulation and spatial patterns. Biogeochemistry 119:139–160. https://doi.org/10.1007/s10533-014-9953-6
Article
Google Scholar
Borges AV, Speeckaert G, Champenois W et al (2018) Productivity and temperature as drivers of seasonal and spatial variations of dissolved methane in the Southern Bight of the North Sea. Ecosystems 21:583–599. https://doi.org/10.1007/s10021-017-0171-7
Article
Google Scholar
Bowman MJ (1977) Nutrient distributions and transport in Long Island Sound. Estuar Coast Mar Sci 5:531–548. https://doi.org/10.1016/0302-3524(77)90100-1
Article
Google Scholar
Boynton W, Kemp W (1985) Nutrient regeneration and oxygen consumption by sediments along an estuarine salinity gradient. Mar Ecol Prog Ser 23:45–55. https://doi.org/10.3354/meps023045
Article
Google Scholar
Bratek A, Van Beusekom JEE, Neumann A et al (2020) Spatial variations in sedimentary N-transformation rates in the North Sea (German Bight). Biogeosciences 17:2839–2851. https://doi.org/10.5194/bg-17-2839-2020
Article
Google Scholar
Bravo F, Grant J (2020) Benthic habitat mapping and sediment nutrient fluxes in a shallow coastal environment in Nova Scotia, Canada. Estuar Coast Shelf Sci 242:106816. https://doi.org/10.1016/j.ecss.2020.106816
Article
Google Scholar
Burgin AJ, Hamilton SK (2007) Have we overemphasized the role of denitrification in aquatic ecosystems? A review of nitrate removal pathways. Front Ecol Environ 5:89–96. https://doi.org/10.1890/1540-9295(2007)5[89:HWOTRO]2.0.CO;2
Article
Google Scholar
Callender E (1982) Benthic phosphorus regeneration in the Potomac River Estuary. Sediment/Freshw Interact. https://doi.org/10.1007/978-94-009-8009-9_42
Article
Google Scholar
Carini SA, Orcutt BN, Joye SB (2003) Interactions between methane oxidation and nitrification in coastal sediments. Geomicrobiol J 20:355–374. https://doi.org/10.1080/01490450303900
Article
Google Scholar
Casey MM, Dietl GP, Post DM, Briggs DEG (2014) The impact of eutrophication and commercial fishing on molluscan communities in Long Island Sound, USA. Biol Conserv 170:137–144. https://doi.org/10.1016/j.biocon.2013.12.037
Article
Google Scholar
Connecticut Department of Environmental Protection, New York State Department of Environmental Conservation (2000) A total maximum daily load analysis to achieve water quality standards for dissolved oxygen in Long Island Sound, Hartford, Connecticut
Cornwell JC, Kemp WM, Kana TM (1999) Denitrification in coastal ecosystems: methods, environmental controls, and ecosystem level controls, a review. Aquat Ecol 33:41–54. https://doi.org/10.1023/A:1009921414151
Article
Google Scholar
Cornwell JC, Glibert PM, Owens MS (2014) Nutrient fluxes from sediments in the San Francisco Bay Delta. Estuar Coasts 37:1120–1133. https://doi.org/10.1007/s12237-013-9755-4
Article
Google Scholar
Cornwell JC, Owens MS, Boynton WR, Harris LA (2016) Sediment-water nitrogen exchange along the potomac river estuarine salinity gradient. J Coast Res 32:776–787. https://doi.org/10.2112/JCOASTRES-D-15-00159.1
Article
Google Scholar
Dabrio CJ, Santisteban JI, Mediavilla R et al (2004) Loss on ignition: a qualitative or quantitative method for organic matter and carbonate mineral content in sediments? J Paleolimnol 32:287–299. https://doi.org/10.1023/B:JOPL.0000042999.30131.5b
Article
Google Scholar
Dalsgaard T, Nielsen LP, Brotas V et al (2000) Protocol handbook for NICE-Nitrogen Cycling in Estuaries: a project under the EU research programme: Marine Science and Technology (MAST III). Ministry of Environment and Energy National Environmental Research Institute
Delignette-Muller ML, Dutang C (2015) fitdistrplus: an R package for fitting distributions. J Stat Softw 64:1–34
Article
Google Scholar
Domangue RJ, Mortazavi B (2018) Nitrate reduction pathways in the presence of excess nitrogen in a shallow eutrophic estuary. Environ Pollut 238:599–606. https://doi.org/10.1016/j.envpol.2018.03.033
Article
Google Scholar
Domangue RJ, Mortazavi B, Jenkins MC, Kemp WM (1984) The coupling of nitrification and denitrification in two estuarine sediments. Limnol Oceanogr 29:609–619. https://doi.org/10.4319/lo.1984.29.3.0609
Article
Google Scholar
Dornblaser MM, Tucker J, Banta GT et al (1989) Obtaining undisturbed sediment cores for biogeochemical process studies using SCUBA. In: Diving for science, pp 97–104
Douglas EJ, Pilditch CA, Lohrer AM et al (2018) Sedimentary environment influences ecosystem response to nutrient enrichment. Estuar Coasts 41:1994–2008. https://doi.org/10.1007/s12237-018-0416-5
Article
Google Scholar
Duarte CM, Conley DJ, Carstensen J, Sánchez-Camacho M (2009) Return to Neverland: shifting baselines affect eutrophication restoration targets. Estuar Coasts 32:29–36. https://doi.org/10.1007/s12237-008-9111-2
Article
Google Scholar
Egger M, Rasigraf O, Sapart CJ et al (2015) Iron-mediated anaerobic oxidation of methane in brackish coastal sediments. Environ Sci Technol 49:277–283. https://doi.org/10.1021/es503663z
Article
Google Scholar
Engström P, Dalsgaard T, Hulth S, Aller RC (2005) Anaerobic ammonium oxidation by nitrite (anammox): implications for N2 production in coastal marine sediments. Geochim Cosmochim Acta 69:2057–2065. https://doi.org/10.1016/j.gca.2004.09.032
Article
Google Scholar
Eyre BD, Ferguson AJP (2002) Comparison of carbon production and decomposition, benthic nutrient fluxes and denitrification in seagrass, phytoplankton, benthic microalgae- and macroalgae-dominated warm-temperate Australian lagoons. Mar Ecol Prog Ser 229:43–59. https://doi.org/10.3354/meps229043
Article
Google Scholar
Eyre BD, Ferguson AJP (2005) Benthic metabolism and nitrogen cycling in a subtropical east Australian estuary (Brunswick): temporal variability and controlling factors. Limnol Oceanogr 50:81–96. https://doi.org/10.4319/lo.2005.50.1.0081
Article
Google Scholar
Eyre BD, Ferguson AJP (2009) Denitrification efficiency for defining critical loads of carbon in shallow coastal ecosystems. In: Eutrophication in Coastal ecosystems. Springer, Netherlands, pp 137–146. https://doi.org/10.1007/978-90-481-3385-7_12
Eyre BD, Oakes JM, Middelburg JJ (2016) Fate of microphytobenthos nitrogen in subtropical subtidal sediments: a 15N pulse-chase study. Limnol Oceanogr 61:2108–2121. https://doi.org/10.1002/lno.10356
Article
Google Scholar
Fagherazzi S, Mariotti G, Banks AT et al (2014) The relationships among hydrodynamics, sediment distribution, and chlorophyll in a mesotidal estuary. Estuar Coast Shelf Sci 144:54–64. https://doi.org/10.1016/j.ecss.2014.04.003
Article
Google Scholar
Fear J, Gallo T, Hall N et al (2004) Predicting benthic microalgal oxygen and nutrient flux responses to a nutrient reduction management strategy for the eutrophic Neuse River Estuary, North Carolina, USA. Estuar Coast Shelf Sci 61:491–506. https://doi.org/10.1016/j.ecss.2004.06.013
Article
Google Scholar
Ferguson A, Eyre B (2007) Seasonal discrepancies in denitrification measured by isotope pairing and N2: Ar techniques. Mar Ecol Prog Ser 350:19–27. https://doi.org/10.3354/meps07152
Article
Google Scholar
Ferguson A, Eyre B, Gay J (2004) Benthic nutrient fluxes in euphotic sediments along shallow sub-tropical estuaries, northern New South Wales, Australia. Aquat Microb Ecol 37:219–235. https://doi.org/10.3354/ame037219
Article
Google Scholar
Finke N, Vandieken V, Jorgensen BB (2007) Acetate, lactate, propionate, and isobutyrate as electron donors for iron and sulfate reduction in Arctic marine sediments, Svalbard. FEMS Microbiol Ecol 59:10–22. https://doi.org/10.1111/j.1574-6941.2006.00214.x
Article
Google Scholar
Fisher TR, Peele ER, Ammerman JW, Harding LW (1992) Nutrient limitation of phytoplankton in Chesapeake Bay. Mar Ecol Prog Ser 82:51–63. https://doi.org/10.3354/meps082051
Article
Google Scholar
Foster SQ, Fulweiler RW (2014) Spatial and historic variability of benthic nitrogen cycling in an anthropogenically impacted estuary. Front Mar Sci 1:56. https://doi.org/10.3389/fmars.2014.00056
Article
Google Scholar
Foster SQ, Fulweiler RW (2016) Sediment nitrous oxide fluxes are dominated by uptake in a temperate estuary. Front Mar Sci 3:1–13. https://doi.org/10.3389/fmars.2016.00040
Article
Google Scholar
Foster SQ, Fulweiler RW (2019a) Estuarine sediments exhibit dynamic and variable biogeochemical responses to hypoxia. J Geophys Res Biogeosci 12:737–758
Article
Google Scholar
Foster SQ, Fulweiler RW (2019b) Nutrient and dissolved gas fluxes across the sediment-water interface under normoxic conditions in Waquoit Bay, Massachusetts (USA). https://doi.org/10.6084/m9.figshare.7371095.v2
Fulweiler RW, Heiss E (2014) (Nearly) A decade of directly measured sediment N2 fluxes: what can Narragansett Bay tell us about the global ocean nitrogen budget? Oceanography 27:184–195. https://doi.org/10.5670/oceanog.2014.22
Article
Google Scholar
Fulweiler RW, Nixon SW (2009) Responses of benthic-pelagic coupling to climate change in a temperate estuary. Hydrobiologia 629:147–156. https://doi.org/10.1007/s10750-009-9766-0
Article
Google Scholar
Fulweiler RW, Nixon SW, Buckley BA, Granger SL (2007) Reversal of the net dinitrogen gas flux in coastal marine sediments. Nature 448:180–182. https://doi.org/10.1038/nature05963
Article
Google Scholar
Fulweiler RW, Nixon SW, Buckley BA, Granger SL (2008) Net sediment N2 fluxes in a coastal marine system-experimental manipulations and a conceptual model. Ecosystems 11:1168–1180. https://doi.org/10.1007/s10021-008-9187-3
Article
Google Scholar
Fulweiler RW, Nixon SW, Buckley BA (2010) Spatial and temporal variability of benthic oxygen demand and nutrient regeneration in an anthropogenically impacted New England estuary. Estuar Coasts 33:1377–1390. https://doi.org/10.1007/s12237-009-9260-y
Article
Google Scholar
Fulweiler RW, Brown SM, Nixon SW, Jenkins BD (2013) Evidence and a conceptual model for the co-occurrence of nitrogen fixation and denitrification in heterotrophic marine sediments. Mar Ecol Prog Ser 482:57–68. https://doi.org/10.3354/meps10240
Article
Google Scholar
Gelesh L, Marshall K, Boicourt W, Lapham L (2016) Methane concentrations increase in bottom waters during summertime anoxia in the highly eutrophic estuary, Chesapeake Bay, USA. Limnol Oceanogr 61:S253–S266. https://doi.org/10.1002/lno.10272
Article
Google Scholar
Giblin AE, Hopkinson CS, Tucker J, et al (1995) Metabolism, nutrient cycling and denitrification in Boston Harbor and Massachusetts Bay Sediments in 1994. Massachusetts Water Resour. Auth
Giblin AE, Tobias C, Song B et al (2013) The importance of dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen cycle of coastal ecosystems. Oceanography 26:124–131. https://doi.org/10.5670/oceanog.2013.54
Article
Google Scholar
Glud RN (2008) Oxygen dynamics of marine sediments. Mar Biol Res 4:243–289. https://doi.org/10.1080/17451000801888726
Article
Google Scholar
Gobler CJ, Buck NJ, Sieracki ME, Sañudo-Wilhelmy SA (2006) Nitrogen and silicon limitation of phytoplankton communities across an urban estuary: the East River-Long Island Sound system. Estuar Coast Shelf Sci 68:127–138. https://doi.org/10.1016/j.ecss.2006.02.001
Article
Google Scholar
Goebel NL, Kremer JN (2007) Temporal and spatial variability of photosynthetic parameters and community respiration in Long Island Sound. Mar Ecol Prog Ser 329:23–42. https://doi.org/10.3354/meps329023
Article
Google Scholar
Grasshoff K, Kremling K, Ehrhardt M (2009) Methods of seawater analysis, 3rd edn. Wiley-VCH, Weinheim
Google Scholar
Grenz C, Moreno MO, Soetaert K et al (2019) Spatio-temporal variability in benthic exchanges at the sediment-water interface of a shallow tropical coastal lagoon (south coast of Gulf of Mexico). Estuar Coast Shelf Sci 218:368–380. https://doi.org/10.1016/j.ecss.2019.01.012
Article
Google Scholar
Groffman PM, Butterbach-Bahl K, Fulweiler RW et al (2009) Challenges to incorporating spatially and temporally explicit phenomena (hotspots and hot moments) in denitrification models. Biogeochemistry 93:49–77. https://doi.org/10.1007/s10533-008-9277-5
Article
Google Scholar
Hardison AK, Canuel EA, Anderson IC, Veuger B (2010) Fate of macroalgae in benthic systems: carbon and nitrogen cycling within the microbial community. Mar Ecol Prog Ser 414:41–55. https://doi.org/10.3354/meps08720
Article
Google Scholar
Hardison AK, Algar CK, Giblin AE, Rich JJ (2015) Influence of organic carbon and nitrate loading on partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and N2 production. Geochim Cosmochim Acta 164:146–160. https://doi.org/10.1016/j.gca.2015.04.049
Article
Google Scholar
Hardy CD (1972) Movement and quality of Long Island Sound waters, 1971. Marine Sciences Research Center, State University of New York, Albany
Google Scholar
Heiri O, Lotter AF, Lemcke G (2001) Loss on ignition as a method for estimating organic and carbonate content in sediments: Reproducibility and comparability of results. J Paleolimnol 25:101–110. https://doi.org/10.1023/A:1008119611481
Article
Google Scholar
Heiss EM, Fields L, Fulweiler RW (2012) Directly measured net denitrification rates in offshore New England sediments. Cont Shelf Res 45:78–86. https://doi.org/10.1016/j.csr.2012.06.002
Article
Google Scholar
Hopkinson CS, Smith EM (2005) Estuarine respiration: an overview of benthic, pelagic, and whole system respiration. Respir Aquat Ecosyst. https://doi.org/10.1093/acprof:oso/9780198527084.003.0008
Article
Google Scholar
Hopkinson CS, Giblin AEA, Tucker J (2001) Benthic metabolism and nutrient regeneration on the continental shelf of Eastern Massachusetts, USA. Mar Ecol Prog Ser 224:1–19. https://doi.org/10.3354/meps224001
Article
Google Scholar
Howarth R, Chan F, Conley DJ et al (2011) Coupled biogeochemical cycles: eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems. Front Ecol Environ 9:18–26. https://doi.org/10.1890/100008
Article
Google Scholar
Humphries AT, Ayvazian SG, Carey JC et al (2016) Directly measured denitrification reveals oyster aquaculture and restored oyster reefs remove nitrogen at comparable high rates. Front Mar Sci 3:1–10. https://doi.org/10.3389/fmars.2016.00074
Article
Google Scholar
Ji Q, Frey C, Sun X et al (2018) Nitrogen and oxygen availabilities control water column nitrous oxide production during seasonal anoxia in the Chesapeake Bay. Biogeosciences 15:6127–6138. https://doi.org/10.5194/bg-15-6127-2018
Article
Google Scholar
Jilbert T, Slomp CP, Gustafsson BG, Boer W (2011) Beyond the Fe-P-redox connection: preferential regeneration of phosphorus from organic matter as a key control on Baltic Sea nutrient cycles. Biogeosciences 8:1699–1720. https://doi.org/10.5194/bg-8-1699-2011
Article
Google Scholar
Johnson KS, Petty RL (1983) Determination of nitrate and nitrite in seawater by flow injection analysis1. Limnol Oceanogr 28:1260–1266. https://doi.org/10.4319/lo.1983.28.6.1260
Article
Google Scholar
Jones RD, Morita RY (1983) Methane oxidation by Nitrosococcus oceanus and Nitrosomonas europaea. Appl Environ Microbiol 45:401–410. https://doi.org/10.1128/aem.45.2.401-410.1983
Article
Google Scholar
Jordan TE, Cornwell JC, Boynton WR et al (2008) Changes in phosphorus biogeochemistry along an estuarine salinity gradient: the iron conveyer belt. Limnol Oceanogr 53:172–184. https://doi.org/10.4319/lo.2008.53.1.0172
Article
Google Scholar
Joshi SR, Kukkadapu RK, Burdige DJ et al (2015) Organic matter remineralization predominates phosphorus cycling in the mid-bay sediments in the Chesapeake Bay. Environ Sci Technol 49:5887–5896. https://doi.org/10.1021/es5059617
Article
Google Scholar
Kana TM, Darkangelo C, Duane MH et al (1994) Membrane Inlet mass spectrometer for rapid high-precision determination of N2, O2, and Ar in environmental water samples. Anal Chem 66:4166-4170. https://doi.org/10.1021/ac00095a009
Article
Google Scholar
Kemp WM, Sampou P, Caffrey J et al (1990) Ammonium recycling versus denitrification in Chesapeake Bay sediments. Limnol Oceanogr 35:1545–1563. https://doi.org/10.4319/lo.1990.35.7.1545
Article
Google Scholar
Kemp WM, Testa JM, Conley DJ et al (2009) Temporal responses of coastal hypoxia to nutrient loading and physical controls. Biogeosciences 6:2985–3008. https://doi.org/10.5194/bg-6-2985-2009
Article
Google Scholar
Kessler AJ, Roberts KL, Bissett A, Cook PLM (2018) Biogeochemical controls on the relative importance of denitrification and dissimilatory nitrate reduction to ammonium in estuaries. Global Biogeochem Cycles 32:1045–1057. https://doi.org/10.1029/2018GB005908
Article
Google Scholar
Knittel K, Boetius A (2009) Anaerobic oxidation of methane: Progress with an unknown process. Annu Rev Microbiol 63:311–334. https://doi.org/10.1146/annurev.micro.61.080706.093130
Article
Google Scholar
Kostka J, Thamdrup B, Glud R, Canfield D (1999) Rates and pathways of carbon oxidation in permanently cold Arctic sediments. Mar Ecol Prog Ser 180:7–21. https://doi.org/10.3354/meps180007
Article
Google Scholar
Laursen AE, Seitzinger SP (2002) The role of denitrification in nitrogen removal and carbon mineralization in Mid-Atlantic Bight sediments. Cont Shelf Res 22:1397–1416. https://doi.org/10.1016/S0278-4343(02)00008-0
Article
Google Scholar
Lee YJ, Lwiza KMM (2008) Characteristics of bottom dissolved oxygen in Long Island Sound, New York. Estuar Coast Shelf Sci 76:187–200. https://doi.org/10.1016/j.ecss.2007.07.001
Article
Google Scholar
Lenth R, Singmann H, Love J et al (2018) Emmeans: estimated marginal means, aka least-squares means. R Packag version 1:3
Google Scholar
Li M, Lee YJ, Testa JM et al (2016) What drives interannual variability of hypoxia in Chesapeake Bay: climate forcing versus nutrient loading? Geophys Res Lett 43:2127–2134. https://doi.org/10.1002/2015GL067334
Article
Google Scholar
Li Y, Meseck SL, Dixon MS, Wikfors GH (2018) The East River tidal strait, New York City, New York, a high-nutrient, low-chlorophyll coastal system. Int Aquat Res 10:65–77. https://doi.org/10.1007/s40071-018-0189-2
Article
Google Scholar
Li S, Christensen A, Twilley RR (2020) Benthic fluxes of dissolved oxygen and nutrients across hydrogeomorphic zones in a coastal deltaic floodplain within the Mississippi River delta plain. Biogeochemistry 149:115–140. https://doi.org/10.1007/s10533-020-00665-8
Article
Google Scholar
Liu C, Hou L, Liu M et al (2019) Coupling of denitrification and anaerobic ammonium oxidation with nitrification in sediments of the Yangtze Estuary: importance and controlling factors. Estuar Coast Shelf Sci 220:64–72. https://doi.org/10.1016/j.ecss.2019.02.043
Article
Google Scholar
Lopez G, Carey D, Carlton JT et al (2014) Biology and Ecology of Long Island Sound. In: Latimer J, Tedesco M, Swanson R et al (eds) Long Island Sound. Springer, New York, pp 285–479
Chapter
Google Scholar
Lyons WB, Fitzgerald WF (1980) Trace metal fluxes to nearshore Long Island Sound sediments. Mar Pollut Bull 11:157–161. https://doi.org/10.1016/0025-326X(80)90142-3
Article
Google Scholar
Mackin J, Swider K (1989) Organic matter decomposition pathways and oxygen consumption in coastal marine sediments. J Mar Res. https://doi.org/10.1357/002224089785076154
Article
Google Scholar
Marchant HK, Holtappels M, Lavik G et al (2016) Coupled nitrification-denitrification leads to extensive N loss in subtidal permeable sediments. Limnol Oceanogr 61:1033–1048. https://doi.org/10.1002/lno.10271
Article
Google Scholar
Martens CS, Berner RA (1974) Methane production in the interstitial waters of sulfate-depleted marine sediments. Science 185:1167–1169. https://doi.org/10.1126/science.185.4157.1167
Article
Google Scholar
Martens CS, Val Klump J (1980) Biogeochemical cycling in an organic-rich coastal marine basin-I. Methane sediment-water exchange processes. Geochim Cosmochim Acta 44:471–490. https://doi.org/10.1016/0016-7037(80)90045-9
Article
Google Scholar
Mecray EL, Buchholtz ten Brink MR (2000) Contaminant distribution and accumulation in the surface sediments of Long Island Sound. J Coast Res 16:575–590
Google Scholar
Morford J, Kalnejais L, Martin W et al (2003) Sampling marine pore waters for Mn, Fe, U, Re and Mo: modifications on diffusional equilibration thin film gel probes. In: Journal of experimental marine biology and ecology. Elsevier, pp 85–103. https://doi.org/10.1016/S0022-0981(02)00521-X
Mortazavi B, Riggs AA, Caffrey JM et al (2012) The contribution of benthic nutrient regeneration to primary production in a shallow Eutrophic Estuary, Weeks Bay, Alabama. Estuar Coasts 35:862–877. https://doi.org/10.1007/s12237-012-9478-y
Article
Google Scholar
Mortimer CH (1941) The exchange of dissolved substances between mud and water in lakes. J Ecol 29:280. https://doi.org/10.2307/2256395
Article
Google Scholar
Moseman-Valtierra S, Gonzalez R, Kroeger KD et al (2011) Short-term nitrogen additions can shift a coastal wetland from a sink to a source of N2O. Atmos Environ 45:4390–4397. https://doi.org/10.1016/j.atmosenv.2011.05.046
Article
Google Scholar
Mouret A, Anschutz P, Deflandre B et al (2016) Spatial heterogeneity of benthic biogeochemistry in two contrasted marine environments (Arcachon Bay and Bay of Biscay, SW France). Estuar Coast Shelf Sci 179:51–65. https://doi.org/10.1016/j.ecss.2015.09.001
Article
Google Scholar
Murray RH, Erler DV, Eyre BD (2015) Nitrous oxide fluxes in estuarine environments: response to global change. Glob Chang Biol 21:3219–3245. https://doi.org/10.1111/gcb.12923
Article
Google Scholar
Myhre G, Shindell D, Bréon F-M et al (2013) Anthropogenic and natural radiative forcing. In: Stocker TF, Qin D, Plattner G-K et al (eds) Climate change 2013: the physical science basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge, UK, pp 659–740. https://doi.org/10.1017/CBO9781107415324.018
Myllykangas JP, Hietanen S, Jilbert T (2020) Legacy effects of eutrophication on modern methane dynamics in a Boreal estuary. Estuar Coasts 43:189–206. https://doi.org/10.1007/s12237-019-00677-0
Article
Google Scholar
Myllykangas JP, Rissanen AJ, Hietanen S, Jilbert T (2020) Influence of electron acceptor availability and microbial community structure on sedimentary methane oxidation in a boreal estuary. Biogeochemistry 148:291–309. https://doi.org/10.1007/s10533-020-00660-z
Article
Google Scholar
Nieuwenhuize J, Maas YEM, Middelburg JJ (1994) Rapid analysis of organic carbon and nitrogen in particulate materials. Mar Chem 45:217–224. https://doi.org/10.1016/0304-4203(94)90005-1
Article
Google Scholar
Nixon SW (1981) Remineralization and nutrient cycling in coastal marine ecosystems. In: Estuaries and nutrients. Humana Press, pp 111–138. https://doi.org/10.1007/978-1-4612-5826-1_6
Nixon SW, Fulweiler RW, Buckley BA et al (2009) The impact of changing climate on phenology, productivity, and benthic-pelagic coupling in Narragansett Bay. Estuar Coast Shelf Sci 82:1–18. https://doi.org/10.1016/j.ecss.2008.12.016
Article
Google Scholar
Nowicki BL (1994) The effect of temperature, oxygen, salinity, and nutrient enrichment on estuarine denitrification rates measured with a modified nitrogen gas flux technique. Estuar Coast Shelf Sci 38:137–156. https://doi.org/10.1006/ecss.1994.1009
Article
Google Scholar
O’Donnell J, Wilson RE, Lwiza K et al (2014) The physical oceanography of Long Island Sound. In: Latimer JS, Tedesco MA, Swanson RL et al (eds) Long Island Sound: prospects for the Urban Sea. Springer, New York, pp 79–158
Chapter
Google Scholar
O’Meara TA, Hewitt JE, Thrush SF et al (2020) Denitrification and the role of macrofauna across estuarine gradients in nutrient and sediment loading. Estuar Coasts 43:1394–1405. https://doi.org/10.1007/s12237-020-00728-x
Article
Google Scholar
Oremland RS, Taylor BF (1978) Sulfate reduction and methanogenesis in marine sediments. Geochim Cosmochim Acta 42:209–214. https://doi.org/10.1016/0016-7037(78)90133-3
Article
Google Scholar
O’Shea ML, Brosnan TM (2000) Trends in indicators of eutrophication in western Long Island Sound and the Hudson-Raritan Estuary. Estuaries 23:877–901. https://doi.org/10.2307/1353004
Article
Google Scholar
Otte JM, Blackwell N, Ruser R et al (2019) N2O formation by nitrite-induced (chemo)denitrification in coastal marine sediment. Sci Rep 9:10691. https://doi.org/10.1038/s41598-019-47172-x
Article
Google Scholar
Oviatt C, Smith L, Krumholz J et al (2017) Managed nutrient reduction impacts on nutrient concentrations, water clarity, primary production, and hypoxia in a north temperate estuary. Estuar Coast Shelf Sci 199:25–34. https://doi.org/10.1016/j.ecss.2017.09.026
Article
Google Scholar
Owens MS, Cornwell JC (2016) The benthic exchange of O2, N2 and dissolved nutrients using small core incubations. J Vis Exp. https://doi.org/10.3791/54098
Article
Google Scholar
Parker CA, O’Reilly JE, O’Riley J (1991) Oxygen depletion in Long Island Sound: a historical perspective. Estuaries 14:248–264. https://doi.org/10.2307/1351660
Article
Google Scholar
Percuoco VP, Kalnejais LH, Officer LV (2015) Nutrient release from the sediments of the Great Bay Estuary, N.H. USA. Estuar Coast Shelf Sci 161:76–87. https://doi.org/10.1016/j.ecss.2015.04.006
Article
Google Scholar
Pérez-Villalona H, Cornwell JC, Ortiz-Zayas JR, Cuevas E (2015) Sediment denitrification and nutrient fluxes in the San José Lagoon, a Tropical Lagoon in the highly urbanized San Juan Bay Estuary, Puerto Rico. Estuar Coasts 38:2259–2278. https://doi.org/10.1007/s12237-015-9953-3
Article
Google Scholar
Poppe LJ, Knebel HJ, Mlodzinska ZJ et al (2000) Distribution of surficial sediment in Long Island Sound and adjacent waters: texture and total organic carbon. J Coast Res 16:567–574
Google Scholar
Portmann RW, Daniel JS, Ravishankara AR (2012) Stratospheric ozone depletion due to nitrous oxide: influences of other gases. Philos Trans R Soc B 367:1256–1264. https://doi.org/10.1098/rstb.2011.0377
Article
Google Scholar
Pratt DR, Lohrer AM, Pilditch CA, Thrush SF (2014) Changes in ecosystem function across sedimentary gradients in estuaries. Ecosystems 17:182–194. https://doi.org/10.1007/s10021-013-9716-6
Article
Google Scholar
R Core Team (2020) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Google Scholar
Raffaelli D, Bell E, Weithoff G et al (2003) The ups and downs of benthic ecology: considerations of scale, heterogeneity and surveillance for benthic-pelagic coupling. J Exp Mar Bio Ecol 285–286:191–203. https://doi.org/10.1016/S0022-0981(02)00527-0
Article
Google Scholar
Ravishankara AR, Daniel JS, Portmann RW (2009) Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 326:123–125. https://doi.org/10.1126/science.1176985
Article
Google Scholar
Ray N, Henning M, Fulweiler R (2019) Nitrogen and phosphorus cycling in the digestive system and shell biofilm of the eastern oyster Crassostrea virginica. Mar Ecol Prog Ser 621:95–105. https://doi.org/10.3354/meps13007
Article
Google Scholar
Ray NE, Al-Haj AN, Fulweiler RW (2020) Sediment biogeochemistry along an oyster aquaculture chronosequence. Mar Ecol Prog Ser 646:13–27. https://doi.org/10.3354/meps13377
Article
Google Scholar
Reading MJ, Tait DR, Maher DT et al (2020) Land use drives nitrous oxide dynamics in estuaries on regional and global scales. Limnol Oceanogr 65:1–18. https://doi.org/10.1002/lno.11426
Article
Google Scholar
Reeburgh WS (2007) Oceanic methane biogeochemistry. Chem Rev 107:486–513
Article
Google Scholar
Reed HE, Martiny JBH (2013) Microbial composition affects the functioning of estuarine sediments. ISME J 7:868–879. https://doi.org/10.1038/ismej.2012.154
Article
Google Scholar
Reimers CE, Ruttenberg KC, Canfield DE et al (1996) Porewater pH and authigenic phases formed in the uppermost sediments of the Santa Barbara Basin. Geochim Cosmochim Acta 60:4037–4057. https://doi.org/10.1016/S0016-7037(96)00231-1
Article
Google Scholar
Renaud PE, Morata N, Carroll ML et al (2008) Pelagic-benthic coupling in the western Barents Sea: processes and time scales. Deep Res Part II Top Stud Oceanogr 55:2372–2380. https://doi.org/10.1016/j.dsr2.2008.05.017
Article
Google Scholar
Rice E, Stewart G (2013) Analysis of interdecadal trends in chlorophyll and temperature in the Central Basin of Long Island Sound. Estuar Coast Shelf Sci 128:64–75. https://doi.org/10.1016/j.ecss.2013.05.002
Article
Google Scholar
Riekenberg PM, Oakes JM, Eyre BD (2020) A shift in the pool of retained microphytobenthos nitrogen under enhanced nutrient availability. Water Res 187:116438. https://doi.org/10.1016/j.watres.2020.116438
Article
Google Scholar
Riemann B, Carstensen J, Dahl K et al (2016) Recovery of Danish coastal ecosystems after reductions in nutrient loading: a holistic ecosystem approach. Estuaries Coasts 39:82–97. https://doi.org/10.1007/s12237-015-9980-0
Article
Google Scholar
Riley GA (1941) Plankton studies. III.: Long Island Sound. Kraus Reprint
Roberts KL, Eate VM, Eyre BD et al (2012) Hypoxic events stimulate nitrogen recycling in a shallow salt-wedge estuary: the Yarra River estuary, Australia. Limnol Oceanogr 57:1427–1442. https://doi.org/10.4319/lo.2012.57.5.1427
Article
Google Scholar
Rowe GT, Clifford CH, Smith KL, Hamilton PL (1975) Benthic nutrient regeneration and its coupling to primary productivity in coastal waters. Nature 255:215–217. https://doi.org/10.1038/255215a0
Article
Google Scholar
Rozan TF, Taillefert M, Trouwborst RE et al (2002) Iron-sulfur-phosphorus cycling in the sediments of a shallow coastal bay: implications for sediment nutrient release and benthic macroalgal blooms. Limnol Oceanogr 47:1346–1354. https://doi.org/10.4319/lo.2002.47.5.1346
Article
Google Scholar
Ruttenberg KC, Berner RA (1993) Authigenic apatite formation and burial in sediments from non-upwelling, continental margin environments. Geochim Cosmochim Acta 57:991–1007. https://doi.org/10.1016/0016-7037(93)90035-U
Article
Google Scholar
Rysgaard S, Christensen PB, Nielsen LP (1995) Seasonal variation in nitrification and denitrification in estuarine sediment colonized by benthic microalgae and bioturbating infauna. Mar Ecol Prog Ser 126:111–121. https://doi.org/10.3354/meps126111
Article
Google Scholar
Rysgaard S, Risgaard-Petersen N, Niels Peter S et al (1994) Oxygen regulation of nitrification and denitrification in sediments. Limnol Oceanogr 39:1643–1652. https://doi.org/10.4319/lo.1994.39.7.1643
Article
Google Scholar
Ryther JH, Dunstan WM (1971) Nitrogen, phosphorus, and eutrophication in the coastal marine environment 1008–1013. Science 171:1008–1013. https://doi.org/10.1126/science.171.3975.1008
Article
Google Scholar
Sakamoto Y, Ishiguro M, Kitagawa G (1986) Akaike information criterion statistics. Reidel, Dordrecht
Google Scholar
Sanders T, Schöl A, Dähnke K (2018) Hot spots of nitrification in the elbe estuary and their impact on nitrate regeneration. Estuar Coasts 41:128–138. https://doi.org/10.1007/s12237-017-0264-8
Article
Google Scholar
Sawicka JE, Brüchert V (2017) Annual variability and regulation of methane and sulfate fluxes in Baltic Sea estuarine sediments. Biogeosciences 14:325–339. https://doi.org/10.5194/bg-14-325-2017
Article
Google Scholar
Seitzinger SP (1988) Denitrification in freshwater and coastal marine ecosystems: ecological and geochemical significance. Limnol Oceanogr 33:702–724. https://doi.org/10.4319/lo.1988.33.4part2.0702
Article
Google Scholar
Seitzinger SP, Giblin AE (1996) Estimating denitrification in North Atlantic continental shelf sediments. Biogeochemistry 35:235–260. https://doi.org/10.1007/BF02179829
Article
Google Scholar
Seitzinger SP, Nixon SW, Pilson MEQ (1984) Denitrification and nitrous oxide production in a coastal marine ecosystem. Limnol Oceanogr 29:73–83. https://doi.org/10.4319/lo.1984.29.1.0073
Article
Google Scholar
Seitzinger SP, Kroeze C, Styles RV (2000) Global distribution of N2O emissions from aquatic systems: natural emissions and anthropogenic effects. Chemosphere 2:267–279. https://doi.org/10.1016/S1465-9972(00)00015-5
Article
Google Scholar
Seitzinger S, Harrison JA, Böhlke JK et al (2006) Denitrification across landscapes and waterscapes: a synthesis. Ecol Appl 16:2064–2090
Article
Google Scholar
Shen LD, Hu B, Liu S et al (2016) Anaerobic methane oxidation coupled to nitrite reduction can be a potential methane sink in coastal environments. Appl Microbiol Biotechnol 100:7171–7180. https://doi.org/10.1007/s00253-016-7627-0
Article
Google Scholar
Smith CJ, DeLaune RD, Patrick WH (1983) Nitrous oxide emission from Gulf Coast wetlands. Geochim Cosmochim Acta 47:1805–1814. https://doi.org/10.1016/0016-7037(83)90028-5
Article
Google Scholar
Snyder JT, Whitney MM, Dam HG et al (2019) Citizen science observations reveal rapid, multi-decadal ecosystem changes in eastern Long Island Sound. Mar Environ Res 146:80–88. https://doi.org/10.1016/j.marenvres.2019.03.007
Article
Google Scholar
Solorzano L (1969) Determinatiom of ammonia in natural waters by the phenolhypochlorite method. Limnol Oceanogr 14:799–801
Article
Google Scholar
Staniec A, Vlahos P (2017) Timescales for determining temperature and dissolved oxygen trends in the Long Island Sound (LIS) estuary. Cont Shelf Res 151:1–7. https://doi.org/10.1016/j.csr.2017.09.013
Article
Google Scholar
Stockdale A, Davison W, Zhang H (2009) Micro-scale biogeochemical heterogeneity in sediments: a review of available technology and observed evidence. Earth 92:81–97
Google Scholar
Sundby B, Gobeil C, Silverberg N, Alfonso M (1992) The phosphorus cycle in coastal marine sediments. Limnol Oceanogr 37:1129–1145. https://doi.org/10.4319/lo.1992.37.6.1129
Article
Google Scholar
Thomas E, Gapotchenko T, Varekamp JC et al (2000) Benthic foraminifera and environmental changes in Long Island Sound. J Coast Res 16:641–655
Google Scholar
Tucker J, Kelsey S, Giblin A, Hopkinson C (2008) 2007 Annual benthic nutrient flux monitoring report. Boston: Massachusetts Water Resources Authority. Report ENQUAD
Tucker J, Kelsey S, Giblin A (2010) 2009 Benthic nutrient flux annual report. Boston: Massachusetts Water Resources Authority. Report 2010-10
Tucker J, Giblin AE, Hopkinson CS et al (2014) Response of benthic metabolism and nutrient cycling to reductions inwastewater loading to Boston Harbor, USA. Estuar Coast Shelf Sci 151:54–68. https://doi.org/10.1016/j.ecss.2014.09.018
Article
Google Scholar
Vaquer-Sunyer R, Duarte CM (2008) Thresholds of hypoxia for marine biodiversity. Proc Natl Acad Sci USA 105:15452–15457. https://doi.org/10.1073/pnas.0803833105
Article
Google Scholar
Varekamp JC, McElroy AE, Mullaney JR, Breslin VT (2014) Metals, organic compounds, and nutrients in long island sound: sources, magnitudes, trends, and impacts. Springer, New York, pp 203–283
Book
Google Scholar
Vlahos P, Whitney MM (2017) Organic carbon patterns and budgets in the Long Island Sound estuary. Limnol Oceanogr 62:S46–S57. https://doi.org/10.1002/lno.10638
Article
Google Scholar
Vlahos P, Whitney MM, Menniti C et al (2020) Nitrogen budgets of the Long Island Sound estuary. Estuar Coast Shelf Sci 232:106493. https://doi.org/10.1016/j.ecss.2019.106493
Article
Google Scholar
Wallmann K (2003) Feedbacks between oceanic redox states and marine productivity: a model perspective focused on benthic phosphorus cycling. Global Biogeochem Cycles 17:1968. https://doi.org/10.1029/2002gb001968
Article
Google Scholar
Wells NS, Chen J-J, Maher DT et al (2020) Changing sediment and surface water processes increase CH4 emissions from human-impacted estuaries. Geochim Cosmochim Acta 280:130–147. https://doi.org/10.1016/j.gca.2020.04.020
Article
Google Scholar
Welsh BL, Eller FC (1991) Mechanisms controlling summertime oxygen depletion in western Long Island Sound. Estuaries 14:265–278. https://doi.org/10.2307/1351661
Article
Google Scholar
Westrich JT, Berner RA (1988) The effect of temperature on rates of sulfate reduction in marine sediments. Geomicrobiol J 6:99–117. https://doi.org/10.1080/01490458809377828
Article
Google Scholar
Wolfe DA, Monahan R, Stacey PE et al (1991) Environmental quality of Long Island Sound: assessment and management issues. Estuaries 14:224–236. https://doi.org/10.1007/BF02689356
Article
Google Scholar
Woodland RJ, Thomson JR, Mac Nally R et al (2015) Nitrogen loads explain primary productivity in estuaries at the ecosystem scale. Limnol Oceanogr 60:1751–1762. https://doi.org/10.1002/lno.10136
Article
Google Scholar
Xiao K-Q, Beulig F, Kjeldsen KU et al (2017) Concurrent methane production and oxidation in surface sediment from Aarhus Bay, Denmark. Front Microbiol 8:1198. https://doi.org/10.3389/fmicb.2017.01198
Article
Google Scholar
Zuur A, Ieno EN, Walker N et al (2009) Mixed effects models and extensions in ecology with R. Springer, New York
Book
Google Scholar