text:
ages = {211--228}
}

@article{pearson_macrobenthic_1978,
	title = {Macrobenthic succession in relation to organic enrichment and pollution of the marine environment},
	volume = {16},
	issn = {1540-5834},
	doi = {10.1111/j.1540-5834.2012.00707.x},
	abstract = {None},
	number = {January},
	journal = {Oceanography and marine biology annual review},
	author = {Pearson, T.H. and Rosenberg, Rutger},
	year = {1978},
	pmid = {23425417},
	pages = {229--311}
}

@article{chanton_biogeochemical_1987,
	title = {Biogeochemical cycling in an organic-rich coastal marine basin . 7 . {Sulfur} mass balance , oxygen uptake and sulfide retention},
	volume = {5},
	author = {Chanton, Jeffrey P and Martens, Christopher S and Survey, U S Geological},
	year = {1987}
}

@article{science_c_2006,
	title = {C s a s},
	volume = {3848},
	author = {Science, Canadian and Secretariat, Advisory and Chamberlain, J and Weise, A M and Dowd, M and Grant, J and Canada, Oceans},
	year = {2006}
}

@article{gardner_nitrogen_2006,
	title = {Nitrogen fixation and dissimilatory nitrate reduction to ammonium ({DNRA}) support nitrogen dynamics in {Texas} estuaries},
	volume = {51},
	issn = {00243590},
	doi = {10.4319/lo.2006.51.1_part_2.0558},
	abstract = {We conducted continuous-flow experiments on intact sediment cores from Laguna Madre, Sabine Lake, East Matagorda Bay, and Nueces Estuary to evaluate internal nitrogen (N) sources, sinks, and retention mechanisms in Texas estuaries having different salinities. Mean ammonium (NH4+) flux ranged from slight uptake (negative values) to NH4+ production rates of about 300 µmol m-2 h-1 (units used for all N rates) and increased with salinity (p = 0.10). Net nitrate (NO3-) flux (-20 to 32) and net N2 flux (-70 to 100) did not relate to salinity. Mean net N2 flux was positive but near zero, indicating that N2 sources and sinks are nearly balanced. Total denitrification, N fixation, and potential dissimilatory NO3- reduction to NH4+ (DNRA) rates were estimated after inflow water was enriched with 15NO3- (100 µmol L-1). Total denitrification rates ranged from 0 to 90 versus N fixation rates ranging from 0 to 97. Potential DNRA, measured conservatively as 15H accumulation, ranged from 0 to 80 and related significantly to salinity (p {\textbackslash}textless 0.01). Increases in total NH4+ release after 15NO3- additions were higher but closely related (r = 0.9998) to 15NH4+ accumulation, implying exchange reactions of DNRA-regenerated 15N4+ with sediment-bound 14NH4+. The fate of NO2 was related to salinity, perhaps via sulfide effects on DNRA. Potential DNRA was high in southeastern Corpus Christi Bay in August during hypoxia when the sulfide transition zone was near the sediment surface. Nitrogen fixation and DNRA are important mechanisms that add and retain available N in Texas estuaries.},
	number = {1\_part\_2},
	journal = {Limnology and Oceanography},
	author = {Gardner, Wayne S and McCarthy, Mark J. and An, Soonmo and Sobolev, Dmitri and Sell, Karen S and Brock, David},
	year = {2006},
	pages = {558--568}
}

@article{stief_stimulation_2013,
	title = {Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: {Mechanisms} and environmental implications},
	volume = {10},
	issn = {17264170},
	doi = {10.5194/bg-10-7829-2013},
	abstract = {Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal–microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal–microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal–microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies reveal that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification–denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and transport of nitrogen.},
	number = {12},
	journal = {Biogeosciences},
	author = {Stief, P.},
	year = {2013},
	pages = {7829--7846}
}

@article{nunes_model_2003,
	title = {A model for sustainable management of shellfish polyculture in coastal bays},
	volume = {219},
	author = {Nunes, J P and Ferreira, J G and Gazeau, F and Lencart-silva, J},
	year = {2003},
	pages = {257--277}
}

@article{tomassetti_benthic_2016,
	title = {Benthic community response to sediment organic enrichment by {Mediterranean} fish farms: {Case} studies},
	volume = {450},
	abstract = {There is a great deal of scientific information about the biogeochemical processes in sediments near fish farms and how those processes may be driven under nutrient enrichment to environmental negative effects, as biodiversity decrease is observed in benthic assemblages. Within an adaptive management framework, a good monitoring program can be used to adjust farm management to avert serious and persistent impacts to the sediment. Macrobenthic community represents a good indicator able to detect environmental effects resulting from organic enrichment and, based on this, was selected to monitor Italian marine fish farms. In order to assess the environmental sediment disturbance resulting from marine aquaculture along the Italian coasts three marine fish farms were considered based on their different environmental features: two located in the Tyrrhenian Sea and one in the Adriatic Sea. The selected cage fish farms produce European sea bass Dicentrarchus labrax (L.), gilthead sea-bream Sparus aurata (L.) and meagre Argyrosomus regius (A.) The study ranges from 2001 to 2012, at different times in each fish farm, and was planned according to the fattening cycles. The samples for benthic community analyses were collected by means of a van Veen grab in selected stations located from 0 to 1000. m from the sea cages, the farthest as control stations. In total 134 stations were sampled for more of 20,000 individuals belonging to more than 450 species. Data analyses were performed with statistical methods and biotic indices were calculated. The results showed changes in benthic communities at the stations located just beneath the cages and connected with high cultured biomass. The impacted sites showed loss of biodiversity and increase of opportunistic species such as Capitella Sp. I and Nebalia strausi. Changes in the benthic communities were more or less evident in relation to substrata composition, hydrodynamic conditions and cultured biomass. The observed impact was limited to a few tens of meters around the sea cages of all the three studied fish farms.},
	journal = {Aquaculture},
	author = {Tomassetti, Paolo and Gennaro, Paola and Lattanzi, Loretta and Mercatali, Isabel and Persia, Emma and Vani, Danilo and Porrello, Salvatore},
	month = jan,
	year = {2016},
	keywords = {Benthic indicators, Biotic indices, Ecological quality status, Marine aquaculture, Seabed monitoring},
	pages = {262--272}
}

@article{wilson_early_1985,
	title = {Early organic diagenesis: {The} significance of progressive subsurface oxidation fronts in pelagic sediments},
	volume = {49},
	issn = {00167037},
	doi = {10.1016/0016-7037(85)90174-7},
	abstract = {Porewater and solid phase geochemical data at two contrasting NE Atlantic stations are reported. Station 10552, on the Cape Verde abyssal plain, is a site of slow pelagic accumulation (ca. 0.4 cm kyr-1). Molecular oxygen is present in the sediment column to at least 2 m, and probably much deeper, labile organic-carbon is almost totally consumed in the upper few centimetres of the sediment. By contrast, at station 10554 on the Madeira abyssal plain, the pelagic sequence has been interrupted by the occasional deposition of organic-rich turbidites. Porewater oxygen and nitrate profiles show that subsurface organic metabolism of the organic-carbon associated with the uppermost turbidite layer is a significant fraction of the overall metabolism in the sediment column. This metabolism occurs at a relatively thin reaction front which progresses deeper into the turbidite with time. This phenomenon exerts a controlling influence on the present nutrient profile and redox succession. In a less extreme form, substrate distributions of this latter type are not uncommon in Atlantic sediments. A model has been developed which is controlled by both oxygen and nitrate data. This model permits a vertical profile of metabolic activity to be derived, and also gives estimates of the reaction rate constants and solid phase mixing rates at these two contrasting stations. About 30\% of the total activity at station 10554 is located within the turbidite at the deepening reaction front; this is a non-steady-state condition. In fact, it is found that the integrated metabolic activity at the two stations is not dissimilar (ca. 1-2 ?? 10-13 moles cm-2 sec-1). The striking differences in redox profile are therefore primarily attributable to differences in the distribution of metabolic activity within the column. ?? 1985.},
	number = {3},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Wilson, T. R S and Thomson, J. and Colley, S. and Hydes, D. J. and Higgs, N. C. and S??rensen, J.},
	year = {1985},
	pages = {811--822}
}

@article{neubacher_short-term_2011,
	title = {Short-term hypoxia alters the balance of the nitrogen cycle in coastal sediments},
	volume = {56},
	issn = {00243590},
	url = {http://www.aslo.org/lo/toc/vol_56/issue_2/0651.html},
	doi = {10.4319/lo.2011.56.2.0651},
	abstract = {We measured denitrification, anaerobic ammonium oxidation (anammox), oxygen uptake, nutrient exchange, and pore-water profiles of oxygen in intact sediments at three sites in the southern North Sea, which we experimentally exposed to different oxygen saturations (ambient and 33\% of air-saturation for oxygen i.e., our hypoxic treatment) over 14months. Denitrification ranged from 1µmol N m2h1 to 21µmol N m2h1, anammox 0.2µmol N m2h1 to 5.7µmol N m2h1, and oxygen uptake 47µmol O2 m2h1 to 631µmol O2 m2h1. The seasonal patterns under ambient oxygen were correlated with those in the hypoxic treatment\; though, on the whole, the magnitude of flux was different. On average, under hypoxia, both the penetration and consumption of oxygen decreased by 50\%, denitrification increased by 32\%, and anammox remained constant. Anammox accounted for between 10\% and 20\% of the total N2 production, which agrees with expectations for waters of these depths (3080m). Under ambient oxygen the sediments were strong sources of nitrate to the overlying water, 12µmol NO3 m2h1 on average, but under hypoxia total N mineralization decreased by 46\% and nitrate exchanged ceased. Short-term hypoxia alters the balance between available N returned to the overlying water, primarily as NO3, and that removed from the ecosystem as N2 gas.},
	number = {2},
	journal = {Limonology And Oceanography},
	author = {Neubacher, Elke C and Parker, Ruth E and Trimmer, Mark},
	year = {2011},
	pages = {651--665}
}

@book{noauthor_yokoyama_nodate,
	title = {Yokoyama 2002 {PEARL} {FISH} {FARM} {BENTHIC} {IMPACT} {ECOLOGY}.pdf}
}

@article{koop-jakobsen_effect_2010,
	title = {The effect of increased nitrate loading on nitrate reduction via denitirification and {DNRA} in salt marsh sediments},
	volume = {55},
	issn = {00243590},
	url = {http://avto.aslo.info/lo/toc/vol_55/issue_2/0789.pdf},
	doi = {10.4319/lo.2010.55.2.0789},
	abstract = {The effects of increased nitrogen loading on denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in marsh sediments were studied in permanently submerged subtidal creek sediments and on the tidally inundated vegetated marsh platform in Plum Island Sound estuary, Massachusetts. DNRA and denitrification in surface sediments were measured at all sites using whole-core incubations and the isotope pairing technique, which allows distinction between denitrification of water column nitrate and coupled nitrification–denitrification. On the marsh platform, denitrification was also measured at depth in the rhizosphere, using a new approach that combined the push–pull method and the isotope pairing technique. In tidal creek sediments, fertilization increased denitrification of water column nitrate by approximately one order of magnitude, and coupled nitrification– denitrification threefold. Coupled nitrification–denitrification made a significant contribution to the total N2 production in the unfertilized creek but was of minor importance in the fertilized creek due to increased rates of denitrification of water column nitrate. In the surface sediment of the marsh platform, fertilization increased denitrification of water column nitrate by an order of magnitude during inundation of the marsh platform, about 12\% of the day. However, coupled nitrification–denitrification occurring at depth in the rhizosphere was the main denitrification pathway, accounting for more than 50\% of the total N2 production in the fertilized as well as in the reference marsh. DNRA was measured in the surface sediment only, where it was comparable in magnitude to denitrification in the fertilized as well as in the unfertilized marsh.},
	number = {2},
	journal = {Limnology and Oceanography},
	author = {Koop-Jakobsen, Ketil and Giblin, Anne E.},
	year = {2010},
	pages = {789--802}
}

@article{brigolin_modelling_2010,
	title = {Modelling the biomass yield and the impact of seabream mariculture in the {Adriatic} and {Tyrrhenian} {Seas} ( {Italy} )},
	doi = {10.1007/s10499-008-9232-4},
	author = {Brigolin, Daniele and Pastres, Æ Roberto and Tomassetti, Æ Paolo},
	year = {2010},
	keywords = {environmental impact assessment á, individual-based model á, mariculture impacts á site, selection á sparus aurata},
	pages = {149--163}
}

@book{noauthor_dale_nodate,
	title = {Dale et al. 2013 model includes {DNRA}.pdf}
}

@article{mortazavi_evaluating_2015,
	title = {Evaluating the impact of oyster ({Crassostrea} virginica) gardening on sediment nitrogen cycling in a subtropical estuary},
	volume = {91},
	issn = {15536955},
	doi = {10.5343/bms.2014.1060},
	abstract = {To quantify the effect of oysters on sediment N cycling, oyster-free cages and cages with adult or juvenile oysters [Crassostrea virginica (Gmelin, 1791)] were suspended above the sediments at two sites in Mobile Bay, Alabama, located in the northern Gulf of Mexico. While hydrogen sulfide (HS–) was below detection limits at Site 2, HS– exceeded 500 μM prior to the deployment at Site 1 and remained detectable in sediments in the oyster treatments. Oyster mediated N inputs were estimated at 11.4 (SE 0.4) g N m–2 and 3.2 (SE 0.2) g N m–2 in the juvenile and adult treatments, respectively. The abundances of genes associated with denitrifiers (nirK), sulfate reducers (dsrB), and bacterial and archaeal nitrifiers (bac\_amoA, arc\_amoA, respectively) varied over the course of the study, but were not affected by the treatments. Similarly, potential denitrification rates measured during the study were similar in all treatments. Net N2 fluxes, determined from N2:Ar ratios using a membrane inlet mass spectrometer were similar among treatments, despite significantly higher sediment chlorophyll-a content in the juvenile treatment. We conclude that the commonly assumed enhanced rates of N2 loss from sediments in response to deployment of oysters is not guaranteed and may depend on site-specific biogeochemistry.},
	number = {3},
	journal = {Bulletin of Marine Science},
	author = {Mortazavi, Behzad and Ortmann, Alice C. and Wang, Lei and Bernard, Rebecca J. and Staudhammer, Christina L. and Dalrymple, J. Donald and Carmichael, Ruth H. and Kleinhuizen, Alice A.},
	year = {2015},
	pages = {323--341}
}

@article{edgar_broad-scale_2005,
	title = {Broad-scale effects of marine salmonid aquaculture on macrobenthos and the sediment environment in southeastern {Tasmania}},
	volume = {327},
	issn = {00220981},
	doi = {10.1016/j.jembe.2005.06.003},
	abstract = {A comparison of sediments and associated macrobenthos at sites sampled within 20 fish farm leases distributed across southeastern Tasmania indicated major natural changes along a regional cline. Introduced taxa were strongly represented in the fauna, comprising 45\% of total macrofaunal biomass. Large differences were evident between sites affected by different levels of organic farm waste. Sites located adjacent ({\textbackslash}textless 10 m) to farm cages possessed significantly depressed sediment redox levels, a dominance of capitellid and dorvilleid polychaetes, and low macrofaunal species richness. Subtle impacts extended across farm lease areas in the form of depressed redox potential at 40 mm depth and changes to the macrobenthic community, including a prevalence of the dogwhelk Nassarius nigellus and a paucity of the heart urchin Brissus sp. and the maldanid polychaetes Asychis sp. and Rhodine sp. Minor farm effects were also evident at sites sampled 35 m outside farm lease boundaries, most notably as elevated population numbers of the polychaete Terrebellides sp., bivalve Mysella donaciformis and heart urchin Echinocardium cordatum. Amongst the univariate metrics examined, redox potential at 40 mm depth and the ratio of bivalves to total molluscs provided the most sensitive indicators of farm impacts, with the latter metric relatively insensitive to spatial variation between locations within the region studied. © 2005 Elsevier B.V. All rights reserved.},
	number = {1},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Edgar, Graham J. and Macleod, Catriona K. and Mawbey, Ron B. and Shields, Derek},
	year = {2005},
	pmid = {1470},
	keywords = {Capitella sp., Crustaceans, Environmental monitoring, Finfish aquaculture, Impact assessment, Introduced species, Molluscs, Polychaetes, Redox},
	pages = {70--90}
}

@article{vaquer-sunyer_thresholds_2008,
	title = {Thresholds of hypoxia for marine biodiversity.},
	volume = {105},
	issn = {0027-8424},
	doi = {10.1073/pnas.0803833105},
	abstract = {Hypoxia is a mounting problem affecting the world's coastal waters, with severe consequences for marine life, including death and catastrophic changes. Hypoxia is forecast to increase owing to the combined effects of the continued spread of coastal eutrophication and global warming. A broad comparative analysis across a range of contrasting marine benthic organisms showed that hypoxia thresholds vary greatly across marine benthic organisms and that the conventional definition of 2 mg O(2)/liter to designate waters as hypoxic is below the empirical sublethal and lethal O(2) thresholds for half of the species tested. These results imply that the number and area of coastal ecosystems affected by hypoxia and the future extent of hypoxia impacts on marine life have been generally underestimated.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Vaquer-Sunyer, Raquel and Duarte, Carlos M},
	year = {2008},
	pmid = {18824689},
	pages = {15452--15457}
}

@article{reid_review_2009,
	title = {A review of the biophysical properties of salmonid faeces: {Implications} for aquaculture waste dispersal models and integrated multi-trophic aquaculture},
	volume = {40},
	issn = {1355557X},
	doi = {10.1111/j.1365-2109.2008.02065.x},
	abstract = {Knowledge of the quantitative and qualitative properties of salmonid faeces is necessary for aquaculture waste dispersal models, and the design of integrated multi-trophic aquaculture (IMTA) systems. The amount and proximate composition of salmonid faeces can be estimated using a mass-balance, nutritional approach. Indigestible components of salmonid diets have the potential to affect faecal 'cohesiveness' or 'stability'. Nutrient content and density of faeces can vary depending on diet and submersion time. Faecal density has a greater influence on settling velocity than faecal size. Published settling velocity data on salmonid faeces are highly variable due to differences in fish size, rearing systems, collection time, water density, methodology, the mass fraction tested and diet. Most faecal settling data used in published salmonid waste dispersal models are rudimentary and recent information suggests that such models are highly sensitive to this input. The design of open-water IMTA systems and estimation of nutrient capture and recovery from co-cultured filter feeders is difficult due to limited information on particle size, digestibility, settleable and non-settleable mass fractions of salmonid faeces at cage environments. Implications of faecal properties on the accountability for the effects of aquaculture nutrient loading are discussed. © 2009 Blackwell Munksgaard.},
	number = {3},
	journal = {Aquaculture Research},
	author = {Reid, G. K. and Liutkus, M. and Robinson, S. M C and Chopin, T. R. and Blair, T. and Lander, T. and Mullen, J. and Page, F. and Moccia, R. D.},
	year = {2009},
	pmid = {262663000001},
	keywords = {Nutrient loading, Atlantic salmon, Environmental impact assessment, Faeces, Fish farming, Nutrition},
	pages = {257--273}
}

@article{holmer_impacts_2002,
	title = {Impacts of milkfish ({Chanos} chanos) aquaculture on carbon and nutrient fluxes in the {Bolinao} area, {Philippines}},
	volume = {44},
	issn = {0025326X},
	doi = {10.1016/S0025-326X(02)00048-6},
	abstract = {Sediment oxygen consumption, TCO2 production and nutrient fluxes across the sediment-water interface were measured in sediments within and along a transect from four fish pens with production of milkfish (Chanos chanos) in the Bolinao area, The Philippines. The four fish pens were each representing a specific period in the production cycling. There was a positive linear relationship between the rates of sedimentation inside the fish pens and the sediment oxygen consumption indicating that the benthic processes were controlled by the input of organic matter from fish production. The nutrient fluxes were generally higher inside the fish pens, and nitrate was taken up (1.7-5.8 mmolm-2d-1) whereas ammonium (1-22 mmolm-2d-1) and phosphate (0.2-4.7 mmolm-2d-1) were released from the sediments. The sediments were enriched in organic matter with up to a factor 4 compared to outside. A mass balance for one crop of milkfish was constructed based on production data and on measured fluxes of nutrients in the fish pens to assess the loss of carbon and nutrients to the environment. There was a loss to the surroundings of carbon and nitrogen of 51-68\% of the total input, whereas phosphorus was buried in the sediments inside the fish pens which acted as net sinks of phosphorus. The results obtained suggest that fish pen culture as practiced in the Bolinao area, leads to even greater impacts on benthic carbon and nutrient cycling than those found in suspended cage cultures. Copyright ?? 2002 .},
	number = {7},
	journal = {Marine Pollution Bulletin},
	author = {Holmer, Marianne and Marbá, Núria and Terrados, Jorge and Duarte, Carlos M. and Fortes, Mike D.},
	year = {2002},
	pmid = {12222893},
	keywords = {Fish farming, Carbon and nutrient cycling, Mass balances, Milkfish, Sediment},
	pages = {685--696}
}

@article{michotey_nitrogen-limited_2012,
	title = {Nitrogen-limited mangrove ecosystems conserve {N} through dissimilatory nitrate reduction to ammonium},
	volume = {62},
	doi = {10.1038/srep00419},
	number = {3},
	author = {Michotey, D and Garcia, Nicole},
	year = {2012},
	pages = {3--7}
}

@article{dowd_bio-physical_2005,
	title = {A bio-physical coastal ecosystem model for assessing environmental effects of marine bivalve aquaculture},
	volume = {183},
	doi = {10.1016/j.ecolmodel.2004.08.018},
	author = {Dowd, Michael},
	year = {2005},
	keywords = {aquaculture, benthic, box model, differential equations, nutrient cycling, pelagic coupling, regression},
	pages = {323--346}
}

@article{mahne_effects_1998,
	title = {Effects of {pH} and {Oxygen} and {Ammonium} {Concentrations} on the {Community} {Structure} of {Nitrifying} {Bacteria} from {Wastewater}},
	volume = {64},
	number = {10},
	author = {Mahne, Ivan and Megus, France},
	year = {1998},
	pages = {3584--3590}
}

@book{noauthor_bureau_nodate,
	title = {Bureau and {Hua} 2010 {Aquaculture} waste.pdf}
}

@article{murphy_microbial_2016,
	title = {Microbial nitrogen processing in hard clam ({Mercenaria} mercenaria) aquaculture sediments: the relative importance of denitrification and dissimilatory nitrate reduction to ammonium ({DNRA})},
	volume = {61},
	issn = {19395590},
	doi = {10.1002/lno.10305},
	abstract = {© 2016 Association for the Sciences of Limnology and OceanographyAs bivalve aquaculture expands worldwide, an understanding of its role in nutrient cycling is necessary to ensure ecological sustainability and determine the potential of using bivalves for nutrient mitigation. Whereas several studies, primarily of epifaunal bivalves, have assessed denitrification, few have considered nutrient regeneration processes such as dissimilatory nitrate reduction to ammonium (DNRA), which competes with denitrification for nitrate and results in nitrogen retention rather than loss. This study compares sediment nitrogen cycling including mineralization, DNRA, and denitrification within U.S. clam aquaculture sediments to nearby uncultivated sediments, seasonally. Clam aquaculture significantly increased sediment ammonium and phosphate effluxes relative to uncultivated sediments. Both DNRA and denitrification were significantly enhanced at clam beds compared to uncultivated sediments in July and November, while in May only DNRA was increased. The ratio of DNRA to denitrification was significantly higher at clam beds compared to uncultivated sediments, demonstrating that DNRA may be favored due to a ready supply of labile organic carbon relative to nitrate and perhaps sulfidic conditions. Functional gene abundances, nrfA (DNRA) and nirS (denitrification) followed similar patterns to nitrate respiration rates with highest nrfA abundances in the clam sediments and similar nirS abundances across seasons and sediment type. Ultimately clam sediments were found to be a significant source of nutrients to the water column whereas uncultivated sediments retained ammonium produced by microbial mineralization. Thus, clam cultivation may promote local eutrophication (i.e., increased primary production) by facilitating nutrient regeneration and retention of ammonium in the sediments.},
	number = {5},
	journal = {Limnology and Oceanography},
	author = {Murphy, Anna E. and Anderson, Iris C. and Smyth, Ashley R. and Song, Bongkeun and Luckenbach, Mark W.},
	year = {2016},
	pages = {1589--1604}
}

@book{noauthor_aguado-gimenez_nodate,
	title = {Aguado-{Gimenez} and {Garcia}-{Garcia} 2004 {FISH} {FARM} {BENTHIC} {IMPACT} {Notmuchchange}.pdf}
}

@article{kaspar_denitrification_1983,
	title = {Denitrification, nitrate reduction to ammonium, and inoganic nitrogen pools in intetidal sediments},
	volume = {74},
	issn = {00253162},
	doi = {10.1007/BF00413916},
	abstract = {Dissimilatory nitrate reductions and inorganic nitrogen pools in intertidal sediments of Delaware Inlet near Nelson, New Zealand, were studied between March 1981 and January 1982. The acetylene block technique was used in sediment cores to estimate rates of in situ denitrification. In the top 10.5 cm of sediment the denitrification rates were 1.2 to 11.0 mg N m-2d-1 (Juncus maritimus marsh), 1.6 to 7.9 mg N m-2d-1 (sand-flat, colonised by Euglena spp. and Oscillatoria spp.), and 1.2 to 6.0 mg N m-2d-1 (Zostera novazelandica bed). These rates were similar to those obtained in an earlier denitrification study of a Delaware Inlet mudflat. The highest in situ activity varied between the top 1.5 cm (eelgrass bed) and the 6 to 9 cm layer (sand-flat). Denitrification capacities as determined by the acetylene block technique in nitratesaturated sediment slurries generally decreased with depth and were 1943, 163, and 136 mg N m-2d-1, respectively, in the top 10.5 cm of marsh, sandflat and eelgrass bed. A comparison with another study suggested net denitrification, except in the sand-flat during blooms of N-fixing benthic microalgae when these areas are sources of bound N. A combination of the acetylene block technique and 15N techniques in both sediment slurres and intact cores showed that 70 to 95\% of the reduced nitrate was denitrified, with the rest being reduced to ammonium. The inorganic N pool in the top 10.5 cm of the mud-flat ranged from 130 mg N m-2 in autumn to 420 mg N m-2 in spring, and in the sand-flat it ranged from 100 to 287 mg N m-2. Generally, ammonium was the dominant component of this pool. In spring, nitrate concentrations increased, and in the sand-flat it transiently became the major inorganic N species. The ammonium and nitrate profiles suggest an export of inorganic nitrogen from the intertidal sediments. © 1983 Spriger-Verlag.},
	number = {2},
	journal = {Marine Biology},
	author = {Kaspar, H. F.},
	year = {1983},
	pages = {133--139}
}

@article{levin_shifts_nodate,
	title = {Shifts in a {Pacific} {Ocean} {Fish} {Assemblage}: the {Potential} {Influence} of {Exploitation} {Palabras} {Clave}: {Cambio} de fase},
	doi = {10.1111/j.1523-1739.2006.00400.x},
	abstract = {As in many regions of the world, marine fishes and invertebrates along the Pacific coast of the United States have long been subjected to overexploitation. Despite this history, however, we lack basic information on the current status of many fishes along this coastline. We used data from a quarter century of fishery-independent, coast-wide trawl surveys to study systematically the demersal fish assemblages along the U.S. Pacific coast. We documented fundamental shifts in this fish assemblage. Average fish size, across a diversity of species, has declined 45\% in 21 years. There have been major shifts in the constituent species of the assemblage, with some species achieving annual population growth rates of {\textbackslash}textgreater10\% and others declining in excess of 10\% per year. Annual rate of change in population size appeared to be a function of life history interacting with fishing pressure. Negative trends in population size were particularly apparent in rockfish (Sebastes spp.). However, across all taxa examined, trends in population size were associated with size of maturity, maximum size, and growth rate. Trends in population size were associated inversely with harvest levels, but stocks that mature late tended to decline faster than would be predicted by catch rates alone. Our results are disquieting because they raise the possibility that fishing-induced phase shifts in fish communities may affect the recovery of fishes, even after the implementation of severe fishing restrictions. Resumen: Como en muchas regiones del mundo, los peces e invertebrados marinos a lo largo de la Costa del Pacífico de los Estados Unidos han sido sujetos a la sobreexplotación. Sin embargo, a pesar de esta historia carecemos de información básica sobre el estado actual de muchos peces a lo largo de esta costa. Utilizamos datos de un cuarto de siglo de muestreos con redes de arrastre, independientes de pesquerías, para estudiar a los ensambles de peces demersales a lo largo de la Costa del Pacífico de E.U.A. Documentamos cambios fundamentales en este ensamble de peces. La talla corporal promedio, de una diversidad de especies, ha declinado 45\% en 21 años. Ha habido cambios mayores en las especies que componen el ensamble, con algunas especies alcanzando tasas de crecimiento poblacional de {\textbackslash}textgreater10\% y otras declinando más de 10\% por año. La tasa anual de cambio en el tamaño poblacional pareció ser una función de la historia de vida interactuando con la presión de pesca. Las tendencias negativas del tamaño poblacional fueron particularmente aparentes en los peces piedra (Sebastes spp.). Sin embargo, en todos los taxa examinados, las tendencias en el tamaño poblacional se asociaron con la talla a la madurez, la talla máxima y el crecimiento poblacional. Las tendencias en el tamaño poblacional se asociaron inversamente con los niveles de explotación, pero las existencias que maduran tardíamente tendieron a declinar más rápidamente que lo predicho sólo por las tasas de captura. Nuestros resultados son inquietantes porque aumentan la posibilidad de que los cambios de fase inducidos por la pesca en las comunidades de peces pueden afectar a la recuperación de los peces, aun después de la implementación de severas restricciones de pesca.},
	author = {Levin, Phillip S and Holmes, Elizabeth E and Piner, Kevin R and Harvey, Chris J},
	keywords = {body size spectrum, fisheries, marine conservation, overfishing, phase shift, rockfish, Sebastes}
}

@article{brigolin_modelling_2014-1,
	title = {Modelling biogeochemical fluxes across a {Mediterranean} fish cage farm},
	volume = {88},
	author = {Brigolin, Daniele and Meccia, Virna Loana and Venier, Chiara and Tomassetti, Paolo},
	year = {2014}
}

@article{vanderborght_vertical_1975,
	title = {Vertical distribution of nitrate concentration in interstitial water of marine sediments with nitrification and denitrification},
	volume = {20},
	issn = {00243590},
	doi = {10.4319/lo.1975.20.6.0953},
	number = {6},
	journal = {Limnology \& Oceanography},
	author = {Vanderborght, Jean-Pierre and Billen, Gilles},
	year = {1975},
	pages = {953--961}
}

@article{noauthor_no_nodate,
	title = {No {Title}},
	pages = {1--54}
}

@article{grant_marine_nodate,
	title = {{MARINE} {BIOLOGY} {High} {Intertidal} {Community} {Organization} on a {Rocky} {Headland} in {Maine}, {USA}},
	volume = {44},
	abstract = {A mosaic patchwork of the barnacle Balanus balanoides L., the mussel Mytilus edulis L., and the alga Fucus vesiculosus L. was found in the transitional region between the mid and high intertidal zones on a rocky headland on Mount Desert Island, Maine, USA. The development of the mosaic was observed by following recruitment and sur-vival of B. balanoides in denuded patches located at the same tidal level along a 60 m stretch of shore. Barnacle recruitment was least under canopies of F. vesicu-losus and greatest in open areas kept moist at low tide by surf. Barnacle survival after settlement was least under the F. vesiculosus canopy due to the whiplash effect of the algal fronds in the surf and greatest in open areas free from competition from mussels. In open areas, early mortality was correlated with settlement density. In areas of dense settlement (60 spat cm -2) up to 90\% mortality resulted within 5 months from crowding associated with growth. In older individuals crowding produced hummocks of elongated, weakly attached barnacles which were more prone to removal by surf than uncrowded barnacles. Mussels exerted competitive dominance over bar-nacles for space and the presence of mussel beds prevented further barnacle recruit-ment. Mussels suffered extensive mortality during winter storms when surf removed dense mats of weakly attached mussels. The patchy distribution of mussels and bar-nacles results from irregular rock substrata producing numerous environmental patches with respect to wave exposure and drainage at low tide, and from density-dependent mortality of both mussels and barnacles which creates patches of new colonizable space within each environmental patch.},
	number = {t977},
	journal = {Marine Biology},
	author = {Grant, W S},
	pages = {15--25}
}

@book{joye_nitrogen_2008,
	title = {Nitrogen {Cycling} in {Coastal} {Sediments}},
	isbn = {978-0-12-372522-6},
	abstract = {This chapter reviews the factors regulating sediment N-cycling, both in the bulk sediment environment and on a process level. N availability is frequently cited as the factor limiting primary production in marine systems over annual time scales though phosphorus (P), silica (Si) limitation or colimitation by N, P, and/or Si sometimes occur on seasonal time scales. In offshore waters, the presence of bioavailable iron can also regulate primary productivity, particularly that by diatoms. Sediment N pools reflect a balance between inputs (external or internal) and outputs (sedimentation, denitrification (DNF), long-term burial, or export), and this balance is affected by a variety of environmental and physiological factors. Within the sediment, N is cycled primarily by microbially mediated redox reactions between more highly oxidized forms (nitrate, NO3-, or nitrite, NO2-) and more reduced forms (ammonium, NH4-, amino acids, or organic nitrogen compounds). Gaseous products of these redox reactions may include dinitrogen, N2, nitric oxide, NO, and nitrous oxide, N2O. One characteristic of the sediment N-cycle is the coupling between aerobic and anaerobic processes. Another characteristic is that for a given species, for example, NO3-, several competing pathways and potential fates may exist. ?? 2008 Copyright ?? 2008 Elsevier Inc. All rights reserved..},
	author = {Joye, Samantha B. and Anderson, Iris C.},
	year = {2008},
	doi = {10.1016/B978-0-12-372522-6.00019-0}
}

@article{collos_acclimation_2014,
	title = {Acclimation and toxicity of high ammonium concentrations to unicellular algae},
	volume = {80},
	issn = {0025326X},
	url = {http://dx.doi.org/10.1016/j.marpolbul.2014.01.006},
	doi = {10.1016/j.marpolbul.2014.01.006},
	abstract = {A literature review on the effects of high ammonium concentrations on the growth of 6 classes of microalgae suggests the following rankings. Mean optimal ammonium concentrations were 7600, 2500, 1400, 340, 260, 100??M for Chlorophyceae, Cyanophyceae, Prymnesiophyceae, Diatomophyceae, Raphidophyceae, and Dinophyceae respectively and their tolerance to high toxic ammonium levels was 39,000, 13,000, 2300, 3600, 2500, 1200??M respectively. Field ammonium concentrations {\textbackslash}textless100??M would not likely reduce the growth rate of most microalgae. Chlorophytes were significantly more tolerant to high ammonium than diatoms, prymnesiophytes, dinoflagellates, and raphidophytes. Cyanophytes were significantly more tolerant than dinoflagellates which were the least tolerant. A smaller but more complete data set was used to estimate ammonium EC50 values, and the ranking was: Chlorophyceae{\textbackslash}textgreaterCyanophyceae, Dinophyceae, Diatomophyceae, and Raphidophyceae. Ammonia toxicity is mainly attributed to NH3 at pHs {\textbackslash}textgreater9 and at pHs {\textbackslash}textless8, toxicity is likely associated with the ammonium ion rather than ammonia. ?? 2014 Elsevier Ltd.},
	number = {1-2},
	journal = {Marine Pollution Bulletin},
	author = {Collos, Yves and Harrison, Paul J.},
	year = {2014},
	pmid = {24533997},
	keywords = {Phytoplankton, Acclimation, Ammonia/ammonium, EC50 for ammonia, PH, Toxicity},
	pages = {8--23}
}

@article{zhu_nitrogen_2017,
	title = {Nitrogen removal performance of anaerobic ammonia oxidation ({ANAMMOX}) in presence of organic matter},
	issn = {0923-9820},
	url = {http://link.springer.com/10.1007/s10532-017-9785-x},
	doi = {10.1007/s10532-017-9785-x},
	journal = {Biodegradation},
	author = {Zhu, Weiqiang and Zhang, Peiyu and Yu, Deshuang and Dong, Huiyu and Li, Jin},
	year = {2017},
	keywords = {ANAMMOX, anammox á denitrification á, Denitrific, kinetic model, matter á, Nitrogen removal, nitrogen removal á organic, Organic matter}
}

@article{martinez-garcia_effect_2015,
	title = {Effect of sediment grain size and bioturbation on decomposition of organic matter from aquaculture},
	volume = {125},
	issn = {1573515X},
	doi = {10.1007/s10533-015-0119-y},
	abstract = {Sediment grain size plays a major role in sediment biogeochemistry and sediments with different grain size are expected to react differently to organic enrichment. Through a mesocosm approach we tested the behavior of sediments with two types of predominant grain size (sandy and muddy sediments) under two levels of organic enrichment, related to mussel and fish farming. The polychaete Hediste diversicolor was used to simulate macrofauna bioturbation and bioirrigation. H. diversicolor stimulated organic matter (OM) mineralization and nutrient recycling. Muddy sediments had more OM from nature, resulting in higher sulfate reduction rates than sandy sediments. Under low levels of organic enrichment grain size did not have any effect on benthic fluxes (sediment oxygen uptake, total CO2, ammonium, nitrate, nitrite and phosphate). However, at high levels of organic enrichment, sandy sediments accumulated less OM, less sulfide and less ammonium than muddy sediments, while sediment oxygen uptake and total CO2 showed similar levels between sandy and muddy sediments. Thus, grain size should be considered a key parameter for site selection of fish farming facilities when aiming for a sustainable aquaculture industry.},
	number = {1},
	journal = {Biogeochemistry},
	author = {Martinez-Garcia, Elena and Carlsson, Marita Sundstein and Sanchez-Jerez, Pablo and Sánchez-Lizaso, José Luis and Sanz-Lazaro, Carlos and Holmer, Marianne},
	year = {2015},
	keywords = {Aquaculture, Organic enrichment, Benthic fluxes, Hediste diversicolor, Sediment biogeochemistry},
	pages = {133--148}
}

@article{bender_interstitial_2017,
	title = {Interstitial {Nitrate} {Profiles} and {Oxidation} of {Sedimentary} {Organic} {Matter} in the {Eastern} {Equatorial} {Atlantic} {Published} by : {American} {Association} for the {Advancement} of {Science} {Stable} {URL} : http://www.jstor.org/stable/1745765},
	volume = {198},
	number = {4317},
	author = {Bender, Michael L and Fanning, Kent A and Froelich, Philip N and Heath, G Ross},
	year = {2017},
	pages = {605--609}
}

@article{song_application_2016,
	title = {Application of the isotope pairing technique in sediments where anammox, denitrification, and dissimilatory nitrate reduction to ammonium coexist},
	issn = {15415856},
	doi = {10.1002/lom3.10127},
	abstract = {The isotope pairing technique (IPT) is a well-established 15N method for estimation of denitrification. Presence of anammox, the anaerobic oxidation of NH4+ to N2 with NO2– results in violation of central assumptions on which the IPT is built. It is shown that anammox activity causes overestimation of the N2 production calculated by the IPT. However, experiments with different additions of 15NO3– will reveal the problems posed by anammox. Two alternative calculation procedures are presented, which enable a more accurate quantification of anammox and denitrification activity in sediments where the processes coexist. One procedure is based on measurements of 15N-N2 production in 15NOx–-amended intact sediment cores and data addressing the contribution of anammox to total N2 production estimated from slurry incubations. The other procedure is based on measurements of 15N2 production in at least two parallel series of sediment cores incubated with different 15NOx– additions. The calculation procedure presented is used on field data from four studies where the IPT was used and the potential anammox rate measured. The IPT overestimated total 14N-N2 production rates by 0\%, 2.5\%, 31\%, and 82\% relative to the revised estimates from the 4 different sites, where anammox accounted for 0\%, 6\%, 18\%, and 69.8\%, respectively, of N2 production. The overestimation of true denitrification was, however, up to several hundred percent. Our analysis suggests however that the IPT does not seriously overestimate N2 production in estuarine sediments because anammox accounts for {\textbackslash}textless6\% of N2 production in such sediments, according to present knowledge.},
	journal = {Limnology and Oceanography: Methods},
	author = {Song, G. D. and Liu, S. M. and Kuypers, M. M M and Lavik, G.},
	year = {2016},
	pages = {801--815}
}

@article{an_dissimilatory_2002,
	title = {Dissimilatory nitrate reduction to ammonium ({DNRA}) as a nitrogen link, versus denitrification as a sink in a shallow estuary ({Laguna} {Madre}/{Baffin} {Bay}, {Texas})},
	volume = {237},
	issn = {01718630},
	doi = {10.3354/meps237041},
	abstract = {Rates of nitrate (NO3 –) reduction to nitrogen gas (N2) and ammonium (NH4 +) were measured in August and December 1999 on intact cores (Laguna Madre and Baffin Bay, Texas) using flowing seawater enriched with 15NO3 –. The combination of membrane inlet mass spectrometry (MIMS) and high performance liquid chromatography (HPLC) allowed accurate and simple estimation of these 2 dissimilatory pathways of NO3 – reduction. NO3 – enrichment (∼100 μM 15NO3 –) did not stimulate denitrification (mean ± SE = 55 ± 16 and 69 ± 15 [Aug 99], –11 ± 16 and 11 ± 18 [Dec 99] μmolN m–2 h–1 before and after 15NO3 – addition, respectively; n = 8). However, 15NH4 + production rates increased after the 15NO3 – addition (69 ± 14 [Aug 99], 50 ± 9 [Dec 99] μmolN m–2 h–1), comprised about 1/3 of total NH4 + flux, and were comparable to denitrification rates. A larger portion of added 15NO3 – was converted to 15NH4 + (15 to 75\%) than to N2 (29+ 30N2; 5 to 29\%) on both sampling dates. High dissimilatory NO3 – reduction to NH4 + (DNRA) and low denitrification suggest that sulfide may influence the processes. High sulfide concentrations inhibit nitrification and denitrification but may enhance DNRA by providing an electron donor. Inhibited denitrification and enhanced DNRA may preserve available nitrogen in Laguna Madre/Baffin Bay, which has limited water exchange with other bodies of water.},
	journal = {Marine Ecology Progress Series},
	author = {An, Soonmo and Gardner, Wayne S.},
	year = {2002},
	keywords = {Denitrification, DNRA, Brown tide, Dissimilatory nitrate reduction to ammonium, Laguna Madre/Baffin Bay, Nitrogen conservation},
	pages = {41--50}
}

@article{laverock_bioturbation:_2011,
	title = {Bioturbation: impact on the marine nitrogen cycle.},
	volume = {39},
	issn = {0300-5127},
	doi = {10.1042/BST0390315},
	abstract = {Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into deeper sediment layers and allows the exchange of solutes between the sediment and water column. Burrows can effectively extend the oxic/anoxic interface into deeper sediment layers, thus providing a unique environment for nitrogen-cycling microbial communities. Recent studies have shown that the abundance and diversity of micro-organisms can be far greater in burrow wall sediment than in the surrounding surface or subsurface sediment; meanwhile, bioturbated sediment supports higher rates of coupled nitrification-denitrification reactions and increased fluxes of ammonium to the water column. In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study.},
	number = {1},
	journal = {Biochemical Society transactions},
	author = {Laverock, Bonnie and Gilbert, Jack a and Tait, Karen and Osborn, a Mark and Widdicombe, Steve},
	year = {2011},
	pmid = {21265795},
	keywords = {bioturbation, abbreviation used, anoxic interface, microbial community structure, nitrogen cycle, nutrient flux, oxic, srb, sulfate-reducing bacteria},
	pages = {315--320}
}

@article{ferreira_analysis_2009,
	title = {Analysis of coastal and offshore aquaculture : {Application} of the {FARM} model to multiple systems and shell fi sh species},
	volume = {289},
	issn = {0044-8486},
	url = {http://dx.doi.org/10.1016/j.aquaculture.2008.12.017},
	doi = {10.1016/j.aquaculture.2008.12.017},
	number = {1-2},
	journal = {Aquaculture},
	author = {Ferreira, J G and Sequeira, A and Hawkins, A J S and Newton, A and Nickell, T D and Pastres, R and Forte, J and Bodoy, A and Bricker, S B},
	year = {2009},
	pages = {32--41}
}

@article{seitzinger_denitrification_1988,
	title = {Denitrification in freshwater and coastal marine ecosystems: {Ecological} and geochemical significance},
	volume = {33},
	issn = {00243590},
	doi = {10.4319/lo.1988.33.4_part_2.0702},
	abstract = {Denitrification occurs in essentially all river, lake, and coastal marine ecosystems that have been studied. In general, the range ofdenitrification rates measured in coastal marine sediments is greater than that measured in lake or river sediments. In various estuarine and coastal marine sediments, rates commonly range between 50 and 250 pmol N m–:! h-l, with extremes from 0 to 1,067. Rates of denitrification in lake sediments measured at near-ambient conditions range from 2 to 17 1 pmol N m-2 h-l. Denitrification rates in river and stream sediments range from 0 to 345 pmol N m-2 h-l. The higher rates are from systems that receive substantial amounts of anthropogenic nutrient input. In lakes, denitrification also occurs in low oxygen hypolimnetic waters, where rates generally range from 0.2 to 1.9 pmol N liter-' d-l. In lakes where denitrification rates in both the water and sediments have been measured, denitrification is greater in the sediments. The major source of nitrate for denitrification in most river, lake, and coastal marine sediments underlying an aerobic water column is nitrate produced in the sediments, not nitrate diffusing into the sediments from the overlying water. During the mineralization of organic matter in sediments, a major portion of the mineralized nitrogen is lost from the ecosystem via denitrification. In freshwater sediments, denitrification appears to remove a larger percentage of the mineralized nitrogen. N, fluxes accounted for 76-100\% of the sediment-water nitrogen flux in rivers and lakes, but only 15-70\% in estuarine and coastal marine sediments. Benthic N,O fluxes were always small compared to N, fluxes. The loss of nitrogen via denitrification exceeds the input of nitrogen via N, fixation in almost all river, lake, and coastal marine ecosystems in which both processes have been measured. Denitrification is also important relative to other inputs of fixed N in both freshwater and coastal marine ecosystems. In the two rivers where both denitrification measurements and N input data were available, denitrification removed an amount of nitrogen equivalent to 7 and 35\% of the external nitrogen loading. In six lakes and six estuaries where data are available, denitrification is estimated to remove an amount of nitrogen equivalent to between 1 and 36\% of the input to the lakes and between 20 and 50\% of the input to the estuaries.},
	number = {4, part 2},
	journal = {Limnology and Oceanography},
	author = {Seitzinger, Sybil P.},
	year = {1988},
	pages = {702--724}
}

@article{nizzoli_effect_2010,
	title = {Effect of organic enrichment and thermal regime on denitrification and dissimilatory nitrate reduction to ammonium ({DNRA}) in hypolimnetic sediments of two lowland lakes},
	volume = {44},
	issn = {00431354},
	url = {http://dx.doi.org/10.1016/j.watres.2010.02.002},
	doi = {10.1016/j.watres.2010.02.002},
	abstract = {We analyzed benthic fluxes of inorganic nitrogen, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) rates in hypolimnetic sediments of lowland lakes. Two neighbouring mesotrophic (Ca' Stanga; CS) and hypertrophic (Lago Verde; LV) lakes, which originated from sand and gravel mining, were considered. Lakes are affected by high nitrate loads (0.2-0.7 mM) and different organic loads. Oxygen consumption, dissolved inorganic carbon, methane and nitrogen fluxes, denitrification and DNRA were measured under summer thermal stratification and late winter overturn. Hypolimnetic sediments of CS were a net sink of dissolved inorganic nitrogen (-3.5 to -4.7 mmol m-2 d-1) in both seasons due to high nitrate consumption. On the contrary, LV sediments turned from being a net sink during winter overturn (-3.5 mmol m-2 d-1) to a net source of dissolved inorganic nitrogen under summer conditions (8.1 mmol m-2 d-1), when significant ammonium regeneration was measured at the water-sediment interface. Benthic denitrification (0.7-4.1 mmol m-2 d-1) accounted for up to 84-97\% of total NO3- reduction and from 2 to 30\% of carbon mineralization. It was mainly fuelled by water column nitrate. In CS, denitrification rates were similar in winter and in summer, while in LV summer rates were 4 times lower. DNRA rates were generally low in both lakes (0.07-0.12 mmol m-2 d-1). An appreciable contribution of DNRA was only detected in the more reducing sediments of LV in summer (15\% of total NO3- reduction), while during the same period only 3\% of reduced NO3- was recycled into ammonium in CS. Under summer stratification benthic denitrification was mainly nitrate-limited due to nitrate depletion in hypolimnetic waters and parallel oxygen depletion, hampering nitrification. Organic enrichment and reducing conditions in the hypolimnetic sediment shifted nitrate reduction towards more pronounced DNRA, which resulted in the inorganic nitrogen recycling and retention within the bottom waters. The prevalence of DNRA could favour the accumulation of mineral nitrogen with detrimental effects on ecosystem processes and water quality. ?? 2010 Elsevier Ltd. All rights reserved.},
	number = {9},
	journal = {Water Research},
	author = {Nizzoli, Daniele and Carraro, Elisa and Nigro, Valentina and Viaroli, Pierluigi},
	year = {2010},
	pmid = {20206960},
	keywords = {Denitrification, DNRA, Sediment, Lake, Thermal stratification and overturn, Trophic state},
	pages = {2715--2724}
}

@article{asche_salmon_2013,
	title = {Salmon {Aquaculture}: {Larger} {Companies} and {Increased} {Production}},
	volume = {17},
	issn = {1365-7305},
	url = {http://www.tandfonline.com/doi/abs/10.1080/13657305.2013.812156},
	doi = {10.1080/13657305.2013.812156},
	number = {3},
	journal = {Aquaculture Economics \& Management},
	author = {Asche, Frank and Roll, Kristin H. and Sandvold, Hilde N. and Sørvig, Arne and Zhang, Dengjun},
	year = {2013},
	pages = {322--339}
}

@article{black_scientific_2008,
	title = {The scientific basis of marine fish farm regulation},
	volume = {20},
	number = {2},
	journal = {Science Diliman},
	author = {Black, Kenneth D and Cromey, Christopher J},
	year = {2008},
	pages = {11--22}
}

@book{noauthor_ward_nodate,
	title = {Ward {Nitrification} {CH}1 {Overview}.pdf}
}

@book{noauthor_zhulay_nodate,
	title = {Zhulay et al. 2015 {FALLOWING} {RECOVERY} {ECOLOGY}.pdf}
}

@article{hu_nutrient_2001,
	title = {Nutrient release and sediment oxygen demand in a eutrophic land-locked embayment in {Hong} {Kong}},
	volume = {26},
	issn = {01604120},
	doi = {10.1016/S0160-4120(01)00014-9},
	abstract = {Tolo Harbour is a large eutrophic land-locked estuarine embayment in Hong Kong. The rapid urbanization, commercio-industrial activities and lack of legislative control around the Tolo catchment produced large quantities of untreated or partially treated municipal sewage, agricultural wastes and cottage industrial effluents which were discharged into Tolo Harbour via rivers and watercourses. Control measures were implemented to reduce the external nutrient loading into the harbour since the early 1980s. Nutrient data for the period 1982 to 1997 were analyzed for temporal trends. Over the period of observation, the total inorganic nitrogen and total phosphorus both show an increasing trend, despite a decade of efforts in reducing nutrient loading. The release rates of potentially mobile nitrogen (N) and phosphorus (P) from the sediments collected from Tolo Harbour were determined by N and P release experiments under oxic conditions. The experimental results showed that the sediment released significant amount of nutrients, especially orthophosphates and ammonia nitrogen. The maximum release rates were 15.0 and 206.0 mg/m2/day, respectively. Although the external nutrient loading has been reduced, nutrients could gradually be released back into the water column from the contaminated sediments and delay improvement of the water quality. © 2001 Elsevier Science Ltd. All rights reserved.},
	number = {5-6},
	journal = {Environment International},
	author = {Hu, W. F. and Lo, W. and Chua, H. and Sin, S. N. and Yu, P. H F},
	year = {2001},
	pmid = {11392753},
	keywords = {Eutrophication, Nutrients, Sediment, Estuarine pollution, Hong Kong, Nitrogen pollution, Nutrient release, Phosphorus pollution, Sediment oxygen demand},
	pages = {369--375}
}

@article{radiarta_gis-based_2008,
	title = {{GIS}-based multi-criteria evaluation models for identifying suitable sites for {Japanese} scallop ({Mizuhopecten} yessoensis) aquaculture in {Funka} {Bay}, southwestern {Hokkaido}, {Japan}},
	volume = {284},
	issn = {00448486},
	url = {http://dx.doi.org/10.1016/j.aquaculture.2008.07.048},
	doi = {10.1016/j.aquaculture.2008.07.048},
	abstract = {Production from Japanese scallop (Mizuhopecten yessoensis) aquaculture is increasing, and supports coastal communities. To ensure both success and long-term sustainability of providing scallop productions, finding suitable sites is an important step in any aquaculture operation. This study was conducted to identify the most suitable sites for hanging culture of Japanese scallop using geographic information system (GIS)-based multi-criteria evaluation models. Remote sensing data (Sea-viewing Wide Field-of-view Sensor (SeaWiFS), Moderate Resolution Imaging Spectroradiometer (MODIS) and Advanced Land Observing Satellite (ALOS)) were used to extract most of the parameters. Seven thematic layers were grouped into two basic requisite for scallop aquaculture, namely biophysical (sea temperature, chlorophyll, suspended sediment and bathymetry) and social-infrastructural (distance to town, pier and land-based facilities). A constraint layer was used to exclude the areas from suitability maps that cannot be allowed to develop scallop aquaculture, including harbor, area near town/industrial and river mouth. A series of GIS models was developed to identify the most suitable areas for scallop culture using multi-criteria evaluation known as weighted linear combination. Suitability scores were ranked on a scale from 1 (least suitable) to 8 (most suitable), and about 56\% of the total potential area with bottom depths less than 60??m had the higher scores (scores 7 and 8). These areas were shown to have the optimum condition for scallop culture in this region. The final suitability model outputs were compared with field verification data and found to be consistent. ?? 2008 Elsevier B.V. All rights reserved.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Radiarta, I. Nyoman and Saitoh, Sei Ichi and Miyazono, Akira},
	year = {2008},
	keywords = {GIS, Site selection, Funka Bay, Multi-criteria evaluation, Remote sensing, Scallop aquaculture},
	pages = {127--135}
}

@article{hamersley_anaerobic_2007,
	title = {Anaerobic ammonium oxidation in the {Peruvian} oxygen minimum zone},
	volume = {52},
	issn = {0024-3590},
	doi = {10.4319/lo.2007.52.3.0923},
	abstract = {We investigated the microbial pathways of nitrogen (N) loss in an April 2005 transect through the Peruvian oxygen minimum zone (OMZ) at 12uS latitude using short anaerobic incubations with 15N-labeled substrates and molecular–ecological and lipid–biomarker studies. In incubations with 15NH4+ , immediate production of 14N15N, but not 15N15N, indicated that N2 was produced by the pairing of labeled 15NH4+ with in situ 14NO2- via anaerobic ammonium oxidation (anammox). Supporting this finding, we also found anammox-related 16S ribosomal ribonucleic acid gene sequences similar to those previously known from other marine water columns in which anammox activity was measured. We identified and enumerated anammox bacteria via fluorescence in situ hybridization and quantitative polymerase chain reaction and found ladderane membrane lipids specific to anammox bacteria wherever anammox activity was measured by our isotope tracer method. However, in incubations with 15NO3- or 15NO2- , in which denitrification would have been expected to produce 15N15N by pairing of oxidized 15N ions, 15N15N production was not detected before 24 h, showing that denitrification of fixed N to N2 was not taking place in our samples. At the time and locality of our study, anammox, rather than denitrification, was responsible for N2 production in the Peruvian OMZ waters.},
	number = {3},
	journal = {Limnol. Oceanogr.},
	author = {Hamersley, M Robert and Lavik, Gaute and Woebken, Dagmar and Rattray, Jayne E and Lam, Phyllis and Hopmans, Ellen C and Damsté, Jaap S Sinninghe and Krüger, Siegfried and Graco, Michelle and Gutiérrez, Dimitri and Kuypers, Marcel M M},
	year = {2007},
	pages = {923--933}
}

@article{mccarthy_anaerobic_2015,
	title = {Anaerobic ammonium oxidation (anammox) in the marine environment},
	volume = {156},
	issn = {09232508},
	doi = {10.1016/j.resmic.2005.01.011},
	abstract = {Oceanographers noticed already many years ago that far less ammonium accumulated in anoxic fjords and basins, than would be expected from the stoichiometry of heterotrophic denitrification. It was suggested that this 'missing' ammonium was oxidized with nitrate to free N(2). Since then several other workers have argued based on chemical profiles that ammonium is oxidized anaerobically in oxygen deficient marine sediments and waters with either nitrate or manganese oxides as electron acceptor. While there is as yet no direct evidence for the anaerobic ammonium oxidation with manganese oxides in either sediments or anoxic water columns, more and more evidence is being provided for anaerobic ammonium oxidation with nitrite/nitrate. The first direct evidence for the anaerobic oxidation of ammonium was provided in a waste water bioreactor, where so-called 'anammox' bacteria belonging to the Order Planctomycetales directly oxidize ammonium to N(2) with nitrite as the electron acceptor. Although the anammox process was generally seen as a promising process for waste water treatment. it was believed to be insignificant in the natural environment due to the extremely slow generation times (more than 2 weeks) of the anammox organisms. However, recent studies provide direct evidence for anaerobic oxidation of ammonium by nitrate and/or nitrite in marine sediments, oxygen minimum zones, anoxic fjords and basins as well as Arctic sea ice. Phylogenetic analysis of 16S ribosomal RNA sequences show that the bacteria involved are closely related to anammox bacteria from waste water bioreactors. The combined biogeochemical and microbiological data available indicates that anammox may contribute significantly to the loss of reactive nitrogen in the ocean.},
	number = {6},
	journal = {Research in Microbiology},
	author = {McCarthy, Mark J. and Newell, Silvia E. and Carini, Stephen A. and Gardner, Wayne S. and Kuypers, M M M and Lavik, G and Thamdrup, Bo and Dalsgaard, Tage and Thamdrup, Bo and Canfield, Donald E.},
	year = {2015},
	pmid = {15862442},
	keywords = {Denitrification, Anammox, DNRA, Gulf of Mexico, Hypoxia, N fixation, anammox, denitrification, anaerobic ammonium oxidation, fluidized-bed reactor, nitrogen cycle, Anaerobic ammonium oxidation, anammox bacteria, autotrophic nitrogen-removal, benguela upwelling system, costa-rica, golfo-dulce, in-situ detection, marine, n-2 production, organic-carbon, oxidizing bacteria, review, Review, suboxic},
	pages = {457--464}
}

@article{froelich_early_1978,
	title = {Early oxidation of organic matter in pelagic sediments of the eastern equatorial {Atlantic} : suhoxic diagenesis},
	author = {Froelich, P N and Klinkhammer, G P and Bender, M L and Luedtke, N A and Heath, G R and Cullen, Doug and Dauphin, Paul and Hammond, Doug and Hartman, Blayne},
	year = {1978}
}

@article{childs_sediment_2002,
	title = {Sediment denitrification in the {Gulf} of {Mexico} zone of hypoxia},
	volume = {240},
	issn = {01718630},
	doi = {10.3354/meps240285},
	abstract = {The largest zone of anthropogenic bottom water hypoxia in the Western Hemisphere occurs seasonally in the northern Gulf of Mexico between the Mississippi River delta and the coast of eastern Texas. This zone of hypoxia reaches its greatest extent in the summer months and is a consequence of seasonal stratification of the water column combined with the decomposition of organic matter derived from accelerated rates of primary production. This enhanced productivity is driven primarily by the input of inorganic nitrogen from the Mississippi River. There are 3 likely sinks for fixed nitrogen within this zone of hypoxia: sequestration in the sediment, dispersion and dilution into the Gulf of Mexico, and denitrification. We assessed potential denitrification rates at 7 stations in the zone of hypoxia during the summer of 1999. Those data are compared with bottom water nitrate, ammonium and dissolved oxygen (DO) concentrations. No denitrification was observed in the water column. Denitrification potential rates in the surface sediments were unexpectedly low and ranged between 39.8 and 108.1 mumol m(-1) h(-1). The highest rates were observed at stations with bottom water DO concentrations between 1 and 3 mg l(-1). Denitrification activity was significantly lower at stations where DO was lower than 1 mg l(-1) or higher than 3 mg l(-1). Nutrient data for these stations demonstrate that as anoxia is approached, the dominant species of nitrogen shifts from nitrate to ammonium. The shift in nitrogen species suggests competition between microbial populations in the sediment community. The lower denitrification rates at stations with bottom water DO {\textbackslash}textless1 mg l(-1) may be due to nitrate limitation or an increase in the competitive advantage of microorganisms capable of dissimilatory nitrate reduction to ammonium (DNRA). Suppression of denitrification at low DO by any mechanism will increase the residence time of bioavailable nitrogen. This trend could act as a positive feedback mechanism in the formation of hypoxic bottom waters.},
	number = {1992},
	journal = {Marine Ecology Progress Series},
	author = {Childs, Carl R. and Rabalais, Nancy N. and Turner, R. Eugene and Proctor, Lita M.},
	year = {2002},
	keywords = {Denitrification, Gulf of Mexico, Hypoxia, Sediment},
	pages = {285--290}
}

@book{noauthor_dugdale_nodate,
	title = {Dugdale et al. 2007 {NH}4 {BLOOMS}.pdf}
}

@article{ansell_sedimentation_1974,
	title = {Sedimentation of organic detritus in {Lochs} {Etive} and {Creran}, {Argyll}, {Scotland}},
	volume = {27},
	issn = {00253162},
	doi = {10.1007/BF00391951},
	abstract = {The rates of sedimentation of organic detritus were measured at 3 stations in two Scottish sea lochs, Loch Etive and Loch Creran, using sedimentation jars exposed at various depths. Details are given of the seasonal and depth distribution of sedimenting material, and its composition for a 1-year period. Differences in the pattern of sedimenting material collected at different depths and in the seasonal patterns of sedimentation at the different stations suggested that, in each case there were differences in the relative importance of detritus from various sources. At all stations, phytoplankton production made a relatively small contribution to the total detritus collected, either directly as dead cells, or indirectly as the faeces of zooplankton organisms. Near the head of Loch Etive there were contributions by filamentous algae and Enteromorpha sp., but a major source of detritus was terrestrial debris, mainly carried into the loch in the waters of the River Etive. In the lower basin of Loch Etive, terrestrial detritus also contributed to the total sedimenting near the surface, but at greater depths much of the material collected in the sedimentation jars probably resulted from short-term resuspension and re-deposition of bottom material, reflecting a net transport of fine sediment from the shallower to the deeper areas of the loch. Secondarily resuspended material was also a major source of material collected in the jars exposed in Loch Creran.},
	number = {3},
	journal = {Marine Biology},
	author = {Ansell, A. D.},
	year = {1974},
	pages = {263--273}
}

@article{cranford_benthic_2009,
	title = {Benthic organic enrichment from suspended mussel ({Mytilus} edulis) culture in {Prince} {Edward} {Island}, {Canada}},
	volume = {292},
	issn = {00448486},
	url = {http://dx.doi.org/10.1016/j.aquaculture.2009.04.039},
	doi = {10.1016/j.aquaculture.2009.04.039},
	abstract = {The effects of increased biodeposition within mussel (Mytilus edulis) farms on the benthic environment were investigated using surface sediment samples collected from 11 coastal embayments in Prince Edward Island (PEI), Canada. The degree of organic enrichment, determined using geochemical indicators (total free sulfides (S), redox potentials (EhNHE), water content (WC) and organic matter (OM)), was significantly greater in mussel leases compared to reference sites located both outside lease boundaries and in inlets not used to culture mussel (MANOVA, p {\textbackslash}textless 0.001). Post-hoc tests showed that mean WC and OM, EhNHE potentials and S concentration were all significantly different between lease and reference sites (p ??? 0.009). Temporal changes in organic enrichment conditions were detected by comparing our 2001 data to those previously reported from a 1997 survey of the same sampling sites (MANOVA, p {\textbackslash}textless 0.001). This multivariate effect resulted primarily from a 39\% increase in mean S concentration between 1997 and 2001 (p = 0.029). Surface sediment variables at reference sites were similar between years. Benthic conditions were discriminated along an oxic-anoxic enrichment gradient using multidimensional scaling analysis. Mussel lease sites sampled in 1997 were clustered within predefined oxic sediment classifications along with the majority of reference sites, but were grouped farther along the enrichment gradient in 2001. The significant increase in hypoxic and sulfidic sediments within mussel farms between 1997 and 2001 is consistent with the 43\% increase in PEI mussel production-a classic response to excessive organic biodeposition in shallow coastal inlets with relatively low dispersive capacity. Crown Copyright ?? 2009.},
	number = {3-4},
	journal = {Aquaculture},
	author = {Cranford, P. J. and Hargrave, B. T. and Doucette, L. I.},
	year = {2009},
	keywords = {Biodeposits, Benthic impacts, Redox, Shellfish culture, Sulfide},
	pages = {189--196}
}

@article{dortch_interaction_1990,
	title = {The interaction between ammonium and nitrate uptake in phytoplankton},
	volume = {61},
	issn = {0171-8630},
	doi = {10.3354/meps061183},
	abstract = {A thorough review of field studies shows that the reduction of nitrate uptake rate in the presence of ammonium is rarely so severe, and that it is a highly variable phenomenon. To simplify quantification of the interaction between nitrate and ammonium uptake, it is proposed that it be divided into an indirect interaction, preference, and a direct effect, inhibition. In order to determine preference and inhibition it is necessary to measure uptake of each inorganic nitrogen source alone and in the presence of increasing concentrations of the other nitrogen source. Preference for ammonium uptake is manifested primarily in a higher V sub(max) and lower K sub(s) for ammonium uptake than for nitrate uptake and is accentuated by low light and low nitrogen availability. However, although ammonium is the preferred nitrogen source for uptake,},
	number = {September},
	journal = {Marine Ecology Progress Series},
	author = {Dortch, Q},
	year = {1990},
	pmid = {2338},
	pages = {183--201}
}

@article{carlsson_effects_2012,
	title = {Effects of mussel farms on the benthic nitrogen cycle on the {Swedish} west coast},
	volume = {2},
	issn = {1869-215X},
	doi = {10.3354/aei00039},
	abstract = {The biogeochemical impact of 3 long-line mussel farms (M1, M2 and M3) in Lysekil, Sweden, was investigated from before farm establishment until 1.5 yr after operation had begun. Sedimentation, benthic N flux, total oxygen uptake (TOU) and sulfate reduction rate (SRR) were all significantly increased below the mussel lines at all 3 farms. Effects of increased sedimentation rates were revealed by sediment profile imaging and were highest at Stn M2. These effects increased significantly with time of farm operation, indicating the accumulation of organic matter within sediments over time. Furthermore, more total particulate organic N deposited at farm stations was recycled into the water column compared to at reference stations (similar to 45 versus similar to 13\%), indicating an increased release of dissolved inorganic N from sediment below the mussel farms. At one station (M2) with the highest increase in sedimentation rate, denitrification seemed inhibited, while at another station (M3), with a less pronounced increase in sedimentation rate, denitrification was in fact stimulated, accounting for 13\% of total sediment N removal. Calculations based on estimated values of N removal through mussel harvest and direct measurements of N input through changes in sedimentation, N regeneration from sediment to the water column through benthic fluxes and changes in denitrification showed, in all cases, a net removal of N from the system, as only 26 to 40\% of the total amount of harvested N had been added to the sediments during the growth period.},
	number = {2},
	journal = {Aquaculture Environment Interactions},
	author = {Carlsson, Ms and Engström, P and Lindahl, O and Ljungqvist, L and Petersen, Jk and Svanberg, L and Holmer, M},
	year = {2012},
	keywords = {resale or republication not, denitrification, nitrogen, benthic mineralization, mussel farm, of the publisher, permitted without written consent},
	pages = {177--191}
}

@article{fulweiler_reversal_2007,
	title = {Reversal of the net dinitrogen gas flux in coastal marine sediments},
	volume = {448},
	issn = {1476-4687},
	doi = {10.1038/nature05963},
	abstract = {The flux of nitrogen from land and atmosphere to estuaries and the coastal ocean has increased substantially in recent decades. The observed increase in nitrogen loading is caused by population growth, urbanization, expanding water and sewer infrastructure, fossil fuel combustion and synthetic fertilizer consumption 1,2 . Most of the nitrogen is removed by denitrification in the sedi-ments of estuaries and the continental shelf, leading to a reduction in both cultural eutrophication and nitrogen pollution of the open ocean 3,4 . Nitrogen fixation, however, is thought to be a negligible process in sub-tidal heterotrophic marine systems 5 . Here we report sediment core data from Narragansett Bay, USA, which demonstrate that heterotrophic marine sediments can switch from being a net sink to being a net source of nitrogen. Mesocosm and core incubation experiments, together with a historic data set of mean annual chlorophyll production 6,7 , support the idea that a climate-induced decrease in primary production has led to a decrease in organic matter deposition to the benthos and the observed reversal of the net sediment nitrogen flux. Our results suggest that some estuaries may no longer remove nitrogen from the water column. Instead, nitrogen could be exported to the continental shelf and the open ocean and could shift the effect of anthropogenic nitrogen loading beyond the immediate coastal zone. Climate change has altered the phenology or seasonal sequencing of events in a variety of ecosystems 8,9 . In the marine environment, the timing of phytoplankton production is particularly important because it affects both pelagic and benthic ecology 10,11 . For shallow systems, organic matter deposited to the benthos determines fauna abundance as well as rates of biogeochemical cycling 12,13 . In turn, the fluxes of nutrients off the sediment surface can influence water-column phytoplankton production, especially when pelagic nutrient concentrations are low. The impact of climate change on this benthic–pelagic coupling has previously been unknown. Long-term warming 14,15 has resulted in the loss of the winter– spring diatom bloom in most years and a decrease in mean annual chlorophyll production between the 1970s and 1990s in Narragansett Bay, Rhode Island (41.3u N, 071.1u W) 6 . This decrease has continued through 2005 and there is also a marked decrease in summer chloro-phyll concentrations (Fig. 1). The exact mechanism behind this decline is not known, but it is believed to be the result of increased year-round grazing 15 or an increase in cloudy days, which negatively affects the onset of the winter–spring bloom 16 (Supplementary Discussion). Nitrogen inputs have remained constant for the last twenty-five years 17 . Combining the chlorophyll observations with associated Secchi disk data (a proxy for light penetration depth) 18 in a simple empirical model that relates carbon fixation by marine phytoplankton to chlorophyll, optical depth, and surface irradiance 19 suggests that primary production in the mid-bay may have declined by 40\% in the last thirty years. Recent measurements in the bay have also shown a marked decrease in sediment denitrification, sediment oxygen consumption, and in the fluxes of ammonium and phosphate from sediments to the overlying water compared with extensive mea-surements made in the 1970s and 1980s 7 . As in most estuaries, denitrification has traditionally been a dom-inant nitrogen process in the sediments, removing between 15–25\% of the nitrogen load from land and atmosphere to the bay 3,20 . But during the summer of 2006, using the N 2 /Ar technique 21,22 , we observed a dramatic change in the net sediment N 2 flux by mid-bay sediments (Fig. 2). High rates of N-fixation were also found in triplicate cores collected in July and August at three other stations throughout the bay (Table 1). The N-fixation was seasonal, and by mid-September the sediments were once again dominated by denit-rification. These N-fixation rates are remarkable for two reasons. They represent some of the highest rates measured for a marine system 23 , and this is the first demonstration that heterotrophic marine sediments can switch from being a net sink to being a major net source of nitrogen. We hypothesized that the decrease in primary production led to a decrease in organic matter deposition to the benthos and the observed reversal of the net sediment N 2 flux (Supplementary Discussion). We tested this hypothesis using core incubations and nine large (4 m 2) benthic mesocosms containing sediment and associated fauna from mid-bay. The mesocosm experiment was designed to quantify the response of the benthos to different levels of organic deposition. Estimates of the proportion of phytoplankton blooms that fall to the bottom in coastal waters vary widely, with larger values for winter–spring blooms and},
	number = {July},
	journal = {Nature},
	author = {Fulweiler, R W and Nixon, S W and Buckley, B A and Granger, S L},
	year = {2007},
	pmid = {17625562},
	pages = {180--182}
}

@article{giblin_effects_2010,
	title = {The {Effects} of {Salinity} on {Nitrogen} {Losses} from an {Oligohaline} {Estuarine} {Sediment}},
	volume = {33},
	issn = {15592723},
	doi = {10.1007/s12237-010-9280-7},
	abstract = {Benthic respiration, sediment-water nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in the upper section of the Parker River Estuary from 1993 to 2006. This site experiences large changes in salinity over both short and long time scales. Sediment respiration ranged from 6 to 52 mmol m(-2) day(-1) and was largely controlled by temperature. Nutrient fluxes were dominated by ammonium fluxes, which ranged from a small uptake of -0.3 to an efflux of over 8.2 mmol N m(-2) day(-1). Ammonium fluxes were most highly correlated with salinity and laboratory experiments demonstrated that ammonium fluxes increased when salinity increased. The seasonal pattern of DNRA closely followed salinity. DNRA rates were extremely low in March, less than 0.1 mmol m(-2) day(-1), but increased to 2.0 mmol m(-2) day(-1) in August. In contrast, denitrification rates were inversely related to salinity, ranging from 1 mmol m(-2) day(-1) during the spring and fall to less than 0.2 mmol m(-2) day(-1) in late summer. Salinity appears to exert a major control on the nitrogen cycle at this site, and partially decouples sediment ammonium fluxes from organic matter decomposition.},
	number = {5},
	journal = {Estuaries and Coasts},
	author = {Giblin, Anne E. and Weston, Nathaniel B. and Banta, Gary T. and Tucker, Jane and Hopkinson, Charles S.},
	year = {2010},
	keywords = {Ammonium, Denitrification, Dissimilatory nitrate reduction to ammonium (DNRA), Estuary, Benthic fluxes, Benthic respiration, Salinity, Sediments},
	pages = {1054--1068}
}

@article{sorensen_comparison_2017,
	title = {A {Comparison} of {Oxygen} , {Nitrate} , and {Sulfate} {Respiration} in {Coastal} {Marine} {Sediments} {Stable} {URL} : http://www.jstor.org/stable/4250563 {Microbial} {Ecology} 5 : 105-115 ( 1979 ) {MIaRBoAl} {ECc} {LOc}},
	volume = {5},
	number = {2},
	author = {Sørensen, Jan and Jørgensen, Bo Barker and Revsbech, Niels Peter and Ecology, Source Microbial},
	year = {2017},
	pages = {105--115}
}

@article{berner_sulfate_1978,
	title = {Sulfate {Reduction} and {Rate} of {Deposition} of {Marine}-{Sediments}},
	volume = {37},
	issn = {0012821X},
	doi = {10.1016/0012-821X(78)90209-1},
	number = {3},
	journal = {Earth and Planetary Science Letters},
	author = {Berner, R A},
	year = {1978},
	pages = {492--498}
}

@article{tiedje_ecology_1988,
	title = {Ecology of denitrification and dissimilatory nitrate reduction to ammonium},
	abstract = {4.1 INTRODUCTION 4.2 DEFINITIONS 4.2.1 Chemodenitrification 4.2.2 Respiratory Denitrification 4.2.3 Nonrespiratory N20 Production 4.2.4 Dissimilatory Nitrate Reduction to Ammonium 4.3 IMPORTANCE OF DISSIMILATORY NITRATE REDUCING PROCESSES 4.4 DISSIMILATORY NITRATE REDUCING ORGANISMS AND THEIR PHYSIOLOGY 4.4.1 Denitrification (Respiratory) 4.4.1.1 Growth 4.4.1.2 Organisms 4.4.1.3 Special Oxygen Physiology 4.4.1.4 Pollutant Metabolism 4.4.1.5 Regulation of Intermediate Production 4.4.2 Dissimilatory Nitrate Reduction to Ammonium 4.4.2.1 General Features 4.4.2.2 Organisms 4.4.2.3 Physiology 4.5 POPULATION ECOLOGY OF DISSIMILArOHY NITRATE REDUCTION 4.5.1 Denitrification 4.5.1.1 What Denitrifier Populations Are Found? 4.5.1.2 What Selects Denitrifier Populations? 4.5.1.3 Adaptive Traits of Denitrifiers 4.5.1.4 Survival of Denitrifying Activity 4.5.2 Dissimilatory Nitrate Reduction to Ammonium (DNRA) 4.5.2.1 What DNRA Populations Are Found 4.5.2.2 What Selects DNRA Populations? 4.6 REGULATION OF DENITRIFICATION IN THE ENVIRONMENT 4.6.1 Characteristics of Oxygen Regulation 4.6.1.1 Oxygen as a Dominant Regulator 4.6.1.2 Oxygen Threshold for Denitrification 4.6.1.3 Synthesis of Denitrifying Enzymes 4.6.1.4 Effect of Oxygen on the Different Steps in the Denitrification Sequence 4.6.2 Conceptual Model of Environmental Regulation of Denitrification 4.6.3 Regulatory Factors 4.6.3.1 Oxygen 4.6.3.2 Nitrate 4.6.3.3 Carbon as Electron Donor 4.6.3.4 Effect of Macrofeatures: Burrows and Roots 4.7 SUMMARY OF METHODS USED TO MEASURE DENITRIFICATION REFERENCES},
	number = {April},
	journal = {Environmental Microbiology of Anaerobes},
	author = {Tiedje, J.M.},
	year = {1988},
	pages = {179--244}
}

@article{nogaro_influence_2014,
	title = {Influence of bioturbation on denitrification and dissimilatory nitrate reduction to ammonium ({DNRA}) in freshwater sediments},
	volume = {120},
	issn = {1573515X},
	doi = {10.1007/s10533-014-9995-9},
	abstract = {Intensive agriculture leads to increased nitrogen fluxes (mostly as nitrate, NO3 -) to aquatic ecosystems, which in turn creates ecological problems, including eutrophication and associated harmful algal blooms. These problems have focused scientific attention on understanding the controls on nitrate reduction processes such as denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Our objective was to determine the effects of nutrient-tolerant bioturbating invertebrates (tubificid oligochaetes) on nitrogen cycling processes, specifically coupled nitrification-denitrification, net denitrification, DNRA, and biogeochemical fluxes (O2, NO3 -, NH4 +, CO2, N2O, and CH4) in freshwater sediments. A mesocosm experiment determined how tubificid density and increasing NO3 - concentrations (using N15 isotope tracing) interact to affect N cycling processes. At the lowest NO3 - concentration and in the absence of bioturbation, the relative importance of denitrification to DNRA was similar (i.e., 49.6 and 50.4 ± 8.1 \%, respectively). Increasing NO3 - concentrations in the control cores (without fauna) stimulated denitrification, but did not enhance DNRA, which significantly altered the relative importance of denitrification compared to DNRA (94.6 vs. 5.4 ± 0.9 \%, respectively). The presence of tubificid oligochaetes enhanced O2, NO3 -, NH4 + fluxes, greenhouse gas production, and N cycling processes. The relative importance of denitrification to DNRA shifted towards favoring denitrification with both the increase in NO3 - concentrations and the increase of bioturbation activity. Our study highlights that understanding the interactions between nutrient-tolerant bioturbating species and nitrate contamination is important for determining the nitrogen removal capacity of eutrophic freshwater ecosystems. © 2014 Springer International Publishing Switzerland.},
	number = {1-3},
	journal = {Biogeochemistry},
	author = {Nogaro, Geraldine and Burgin, Amy J.},
	year = {2014},
	keywords = {Eutrophication, Nitrogen cycle, Isotope pairing technique, Lake sediment, Nitrate ammonification, Tubificid oligochaete},
	pages = {279--294}
}

@article{longdill_integrated_2008,
	title = {An integrated {GIS} approach for sustainable aquaculture management area site selection},
	volume = {51},
	issn = {09645691},
	url = {http://fcm.ens.uabc.mx/ georges/SIG-OCEANO/articulo/_4 An integrated GIS approach for sustainable aquaculture management area site selection.pdf},
	doi = {10.1016/j.ocecoaman.2008.06.010},
	abstract = {Within New Zealand, growth in the aquaculture industry has led to the diversification of aquaculture sites from more sheltered bays and harbours toward open coast locations. Coastal zone managers, along with the aquaculture industry, aim to ensure the long-term sustainability of any ‘new' sites selected. Through targeted data collection programmes and the subsequent implementation of Geographic Information System (GIS) based models, the most suitable and sustainable locations for Aquaculture Management Areas (AMAs) can be identified. This approach is applied within the Bay of Plenty, New Zealand, with specific reference to suspended mussel (Perna canaliculus) aquaculture. Within the region, areas where maximum sustainability may be achieved make up 18\% of the total area considered, with conflicting uses and other constraints accounting for 46\%. Whilst further site and development specific studies are required to determine explicit carrying capacities, the effort required has been considerably reduced by eliminating unsuitable locations and identifying those where sustainability can be maximised.},
	number = {8-9},
	journal = {Ocean \& Coastal Management},
	author = {Longdill, Peter C. and Healy, Terry R. and Black, Kerry P.},
	year = {2008},
	pages = {612--624}
}

@article{henderson_use_2001,
	title = {Use of hydrodynamic and benthic models for managing environmental impacts of marine aquaculture},
	volume = {17},
	author = {Henderson, By A and Gamito, S and Karakassis, I and Pederson, P and Smaal, A},
	year = {2001},
	pages = {163--172}
}

@article{jones_archaeology_2016,
	title = {The archaeology of fish and fishing on the central coast of {California}: {The} case for an under-exploited resource},
	issn = {02784165},
	doi = {10.1016/j.jaa.2015.11.002},
	journal = {Journal of Anthropological Archaeology},
	author = {Jones, Terry L. and Gobalet, Kenneth W. and Codding, Brian F.},
	year = {2016}
}

@book{noauthor_guo_nodate,
	title = {Guo and {Li} 2003 {N} from {Fish} {Farming} effect on communities {FW} {LAKE}.pdf}
}

@article{sutherland_characterization_2001,
	title = {Characterization of suspended particulate matter surrounding a salmonid net-pen in the {Broughton} {Archipelago}, {British} {Columbia}},
	volume = {58},
	issn = {10543139},
	url = {http://icesjms.oxfordjournals.org/cgi/content/abstract/58/2/404},
	doi = {10.1006/jmsc.2000.1043},
	abstract = {A field study was carried out on the central coast of British Columbia in March 1999 to determine particle fluxes arising from a salmonid net-pen during feeding. Water samples were collected within, beside, and at two depths relative to a net-pen and analysed for suspended particulate matter (SPM), major and minor elemental abundance, carbon/nitrogen content, and stable carbon isotopes. Sediment traps were also deployed immediately beside the bottom of the net-pen. The highest mean concentration of SPM (0.6 mg l-1) during the feeding cycle was observed within the central region of the net-pen. Approximately 87\% and 30\% of the mean SPM were observed at depth and beside the net-pen, respectively, suggesting that transport of suspended particulates was predominantly in the vertical direction. Sediment trap deployments revealed that sedimentation fluxes of total SPM, carbon, and nitrogen were higher below the farm than at the control site located 500 m away. Major and minor elemental analyses of feed pellets and sediment trap contents showed that calcium, phosphorus, sulphur, and strontium were removed within the net-pen system. The feed-specific carbon isotope signature (\{delta\}13C=-21.4 to -22.0\{per thousand\}) was not evident in the trap samples deployed beside the bottom of the net-pen (\{delta\}13C=-23.4\{per thousand\}), suggesting the relative absence of feed pellet particles, isotopic alteration through fish assimilation and/or dilution of the isotope signature with other carbon sources. However, a feed-signature was evident in samples collected in the upper water column (depth 5 m), suggesting that \{delta\}13C might serve as a useful tracer of feed particles.},
	number = {2},
	journal = {ICES J. Mar. Sci.},
	author = {Sutherland, T F and Martin, a J and Levings, C D},
	year = {2001},
	keywords = {sediment, benthic impacts, particulate-waste-deposition, salmon aquaculture, waste dispersion},
	pages = {404--410}
}

@book{noauthor_gilbert_nodate,
	title = {gilbert et al.2016 phytoplankton and comm comp.pdf}
}

@article{vadas_experimental_1986,
	title = {Experimental evaluation of aggregation behavior in the sea urchin {Strongyiocentrotus} droebachiensis},
	volume = {90},
	abstract = {Introduction Defensive aggregation by Strongylocentrotus droe-bachiensis has been invoked as the fulcrum for the transfor-mation of macroalgal beds into coralline barrens in the northwest Atlantic. We critically examined some of the mechanisms contributing to aggregation behavior by ex-perimentally manipulating sea urchins, purported pred-ators and food during autumn 1983 and spring 1984 both in the laboratory and field. We utilized several approaches to examine a range of sea urchin responses to the presence of food, tethered predators, caged predators, crushed con-specifics in the field and predators in laboratory tanks. Some of the field cages had the property of allowing free passage to sea urchins while retaining lobsters; this allowed distinctions to be made between artifacts caused by cage walls or topographic barriers and unrestricted behavioral responses of sea urchins. The results falsified the hypoth-esis that aggregations of S. droebachiensis are elicited by predators. Except in the presence of algae, sea urchins al-ways avoided decapod predators (but not sea stars) and fled from the vicinity of injured conspecifics. However, avoidance behavior was subordinate to feeding responses, demonstrated by mass migrations of sea urchins into cages (with lobsters) to feed on algae. We reaffirmed by ob-servation and manipulation previous studies which showed that sea urchins aggregate only in the presence of food. Two types of sea urchin groupings were delineated: (1) sur-ficial two dimensional associations, often caused by to-pographic or other features which inhibited dispersal and (2) cohesive three-dimensional aggregations induced by food.},
	journal = {Marine Biology},
	author = {Vadas, R L and Elner, R W and Garwood, P E and Babb, G},
	year = {1986},
	pages = {433--448}
}

@article{hu_nutrient_2001-1,
	title = {Nutrient release and sediment oxygen demand in a eutrophic land-locked embayment in {Hong} {Kong}},
	volume = {26},
	issn = {01604120},
	doi = {10.1016/S0160-4120(01)00014-9},
	abstract = {Tolo Harbour is a large eutrophic land-locked estuarine embayment in Hong Kong. The rapid urbanization, commercio-industrial activities and lack of legislative control around the Tolo catchment produced large quantities of untreated or partially treated municipal sewage, agricultural wastes and cottage industrial effluents which were discharged into Tolo Harbour via rivers and watercourses. Control measures were implemented to reduce the external nutrient loading into the harbour since the early 1980s. Nutrient data for the period 1982 to 1997 were analyzed for temporal trends. Over the period of observation, the total inorganic nitrogen and total phosphorus both show an increasing trend, despite a decade of efforts in reducing nutrient loading. The release rates of potentially mobile nitrogen (N) and phosphorus (P) from the sediments collected from Tolo Harbour were determined by N and P release experiments under oxic conditions. The experimental results showed that the sediment released significant amount of nutrients, especially orthophosphates and ammonia nitrogen. The maximum release rates were 15.0 and 206.0 mg/m2/day, respectively. Although the external nutrient loading has been reduced, nutrients could gradually be released back into the water column from the contaminated sediments and delay improvement of the water quality. © 2001 Elsevier Science Ltd. All rights reserved.},
	number = {5-6},
	journal = {Environment International},
	author = {Hu, W. F. and Lo, W. and Chua, H. and Sin, S. N. and Yu, P. H F},
	year = {2001},
	pmid = {11392753},
	keywords = {Eutrophication, Nutrients, Sediment, Estuarine pollution, Hong Kong, Nitrogen pollution, Nutrient release, Phosphorus pollution, Sediment oxygen demand},
	pages = {369--375}
}

@article{bostock_aquaculture:_2010,
	title = {Aquaculture: global status and trends},
	volume = {365},
	issn = {0962-8436},
	url = {http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2010.0170},
	doi = {10.1098/rstb.2010.0170},
	abstract = {Aquaculture contributed 43 per cent of aquatic animal food for human consumption in 2007 (e.g. fish, crustaceans and molluscs, but excluding mammals, reptiles and aquatic plants) and is expected to grow further to meet the future demand. It is very diverse and, contrary to many per-ceptions, dominated by shellfish and herbivorous and omnivorous pond fish either entirely or partly utilizing natural productivity. The rapid growth in the production of carnivorous species such as salmon, shrimp and catfish has been driven by globalizing trade and favourable economics of larger scale intensive farming. Most aquaculture systems rely on low/uncosted environmental goods and services, so a critical issue for the future is whether these are brought into company accounts and the consequent effects this would have on production economics. Failing that, increased competition for natural resources will force governments to allocate strategically or leave the market to determine their use depending on activities that can extract the highest value. Further uncertainties include the impact of climate change, future fisheries supplies (for competition and feed supply), practical limits in terms of scale and in the economics of integration and the development and acceptability of new bio-engineering technologies. In the medium term, increased output is likely to require expansion in new environments, further intensification and efficiency gains for more sustainable and cost-effective production. The trend towards enhanced intensive systems with key monocultures remains strong and, at least for the foreseeable future, will be a significant contributor to future supplies. Dependence on external feeds (including fish), water and energy are key issues. Some new species will enter production and policies that support the reduction of resource footprints and improve integration could lead to new developments as well as reversing decline in some more traditional systems. 1. THE AQUACULTURE SECTOR: KEY FEATURES AND TRENDS (a) Output, value and regional overview (i) Current status Global aquaculture (figure 1) has grown dramatically over the past 50 years to around 52.5 million tonnes (68.3 million including aquatic plants) in 2008 worth US\$98.5 billion (US\$106 billion including aquatic plants) and accounting for around 50 per cent of the world's fish food supply. Asia dominates this prod-uction, accounting for 89 per cent by volume and 79 per cent by value, with China by far the largest producer (32.7 million tonnes in 2008). The rapid growth in this region has been driven by a variety of factors, including pre-existing aquaculture practices, population and economic growth, relaxed regulatory framework and expanding export opportunities. Aquaculture development in Europe and North America was rapid during the 1980s – 1990s but has since stagnated, probably owing to regulatory restric-tions on sites and other competitive factors, although as markets for fish and seafood they have continued to grow.},
	number = {1554},
	journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
	author = {Bostock, John and McAndrew, B. and Richards, Randolph and Jauncey, Kim and Telfer, Trevor and Lorenzen, Kai and Little, David and Ross, Lindsay and Handisyde, Neil and Gatward, Iain and Corner, Richard},
	year = {2010},
	pmid = {20713392},
	keywords = {aquaculture, competitiveness, development, integration, resources},
	pages = {2897--2912}
}

@article{joyner-matos_hydrogen_2010,
	title = {Hydrogen {Sulfide} {Induces} {Oxidative} {Damage} to {RNA} and {DNA} in a {Sulfide}-{Tolerant} {Marine} {Invertebrate}},
	volume = {83},
	doi = {10.1086/597529},
	number = {2},
	author = {Joyner-matos, Joanna and Predmore, Benjamin L and Stein, Jenny R and Leeuwenburgh, Christiaan and Julian, David},
	year = {2010},
	pages = {356--365}
}

@article{subasinghe_global_2009,
	title = {Global aquaculture and its role in sustainable development},
	volume = {1},
	issn = {17535123},
	doi = {10.1111/j.1753-5131.2008.01002.x},
	abstract = {Aquaculture is the fastest growing food-producing sector in the world. It is developing, expanding and intensifying in almost all regions of the world. The global population is increasing, thus, the demand for aquatic food products is also increasing. Production from capture fisheries has levelled off and most of the main fishing areas have reached their maximum potential. Sustaining fish supplies from capture fisheries will, therefore, not be able to meet the growing global demand for aquatic food and aquaculture is considered to be an oppor- tunity to bridge the supply and demand gap of aquatic food in most regions of the world. However, in our efforts to achieve this potential, the sector will face significant challenges. Key development trends indicate that the sector contin- ues to intensify and diversify and is continuing to use new species and modify its systems and practices. Markets, trade and consumption preferences strongly influence the growth of the sector, with clear demands for the production of safe and quality products. As a consequence, increasing emphasis is placed on enhanced enforcement of regulation and better governance of the sector. It is increasingly realized that sustainable development and responsible production of aquaculture, in the long run, cannot be achieved without the full participa- tion of the producers in the decision-making and regulation process, which has led to efforts to empower farmers and their associations and move toward increasing self-regulation. These factors are all contributing to an improvement in the management of the sector, typically through the promotion of ‘better management' practices of producers. This review discusses the role of aquacul- ture, as at large a small-scale farmer driven production sector, in the quest for sustainable development, reducing poverty and improving food security on a global scale.},
	journal = {Reviews in Aquqculture},
	author = {Subasinghe, Rohana and Soto, Doris and Jia, Jiansan},
	year = {2009},
	keywords = {aquaculture, sustainability, fish, fishfarming, mariculture, seafood},
	pages = {2--9}
}

@article{grant_model_2005,
	title = {A model of aquaculture biodeposition for multiple estuaries and field validation at blue mussel ( {Mytilus} edulis ) culture sites in eastern {Canada}},
	volume = {62},
	issn = {0706-652X},
	url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f05-033#.VGqe4vnF-TR},
	doi = {10.1139/f05-033},
	abstract = {Development of mariculture in Canadian waters has outpaced the ability of regulators to adequately assess environmental impacts and coexistence with other resource users. In eastern Canada, suspended longline culture of blue mussels (Mytilus edulis) leads to depletion of seston and subsequent biodeposition of feces and pseudofeces. Based on the need to evaluate aquaculture effects over multiple farms, a model was developed to compare the rate of mussel egestion with the scale of culture and tidal flushing of particulate waste from estuarine waters. Egestion was calculated using a bioenergetic submodel, and tidal flushing was determined with a tidal prism method. A short-term field program of particle sensing and sediment trapping was undertaken in Tracadie Bay and Savage Harbour (Prince Edward Island) to examine model assumptions and for validation. A finite element model was used to verify tidal prism calculations. Expressing model output as sedimentation rate, predicted biodeposition in Tracadie Bay was...},
	number = {6},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Grant, Jon and Cranford, Peter and Hargrave, Barry and Carreau, Michel and Schofield, Bryan and Armsworthy, Shelley and Burdett-Coutts, Victoria and Ibarra, Diego},
	year = {2005},
	pages = {1271--1285}
}

@article{holmer_pelagic_2014,
	title = {Pelagic and {Benthic} {Nutrient} {Regeneration} {Processes} in {Mussel} {Cultures} ({Mytilus} edulis) in a {Eutrophic} {Coastal} {Area} ({Skive} {Fjord}, {Denmark})},
	issn = {15592723},
	doi = {10.1007/s12237-014-9864-8},
	abstract = {Page 1. Pelagic and Benthic Nutrient Regeneration Processes ... Estuaries and Coasts DOI 10.1007 / s12237 - 014 - 9864 - 8 Page 2. ... Furthermore, the benthic effects of sedi- mentation of biodeposits were examined by measuring sedi- ment oxygen uptake and SRR. ... \${\textbackslash}backslash\$n},
	journal = {Estuaries and Coasts},
	author = {Holmer, Marianne and Thorsen, Sandra Walløe and Carlsson, Marita Sundstein and Kjerulf, Petersen Jens},
	year = {2014},
	keywords = {Eutrophication, Sediment, Mitigation of nutrients, Nutrient removal, Sedimentation},
	pages = {1629--1641}
}

@book{paerl_nitrogen_2008,
	title = {Nitrogen and {Marine} {Eutrophication}},
	isbn = {978-0-12-372522-6},
	abstract = {Researchers have recognized growing imbalance between new nitrogen (N) inputs and N losses in the marine environment through human activities, especially in estuarine and coastal waters where N overenrichment has fueled accelerated primary production, or eutrophication, which is an increase in the rate of supply of organic matter to an ecosystem. This chapter focuses on this imbalance in organic matter specifically nitrogen and its effects on ecology. From a food web perspective, eutrophication is a condition where nutrient-enhanced primary production exceeds the ability of higher ranked consumers to utilize it. Characterized this condition as "too much of good thing," or overfertilization of N-limited marine ecosystems with new N, the bulk of it being anthropogenic. Symptoms of N-driven eutrophication include: subtle increases in plant production, changes in primary producer community composition, rapidly accelerating algal growth, visible discoloration or blooms, losses in water clarity, and increased consumption of oxygen leading to ecosystem-scale oxygen depletion (hypoxia, anoxia), which is stressful to resident fauna and flora, and can lead to elimination of habitats. Lastly, excessive N enrichment, relative to other nutrient inputs, can alter nutrient input balances and cycling, including shifts to phosphorus and silicon limitation of primary production in receiving estuarine and coastal waters Anthropogenic or cultural eutrophication has been closely linked to population densities in coastal watersheds A significant, and in many instances increasing, proportion of new N input can also be attributed to remote sources delivered through airsheds and subsurface aquifers outside the immediate watershed. © 2008 Copyright © 2008 Elsevier Inc. All rights reserved..},
	author = {Paerl, Hans W. and Piehler, Michael F.},
	year = {2008},
	doi = {10.1016/B978-0-12-372522-6.00011-6}
}

@book{ward_nitrification_2008,
	title = {Nitrification in {Marine} {Systems}},
	isbn = {978-0-12-372522-6},
	abstract = {This chapter presents new information on the NH3-oxidizing Archaea, which were unknown at the times of the earlier reviews. The most important organisms in aerobic nitrification are nitrifying bacteria and the NH3 oxidizing Archaea (AOA). Until very recently, the known nitrifiers were restricted to the Proteobacterial phylum. There are two functionally distinct groups of nitrifiers: those that oxidize NH4+ to NO2- (NH3-oxidizing bacteria and Archaea, NH3-oxidizing bacteria (AOB) and AOA) and those that oxidize nitrite to NO3- (NO2- -oxidizing bacteria, NOB). No organism is known to carry out both reactions. These unique metabolic traits are not without costs; the chemolithoautotrophic lifestyle enables nitrifiers to exploit a unique niche in natural systems, but also confers constraints such as slow growth and inflexible nutritional requirements. A new group of aerobic NO3- oxidizing nitrifiers was recently discovered, first by detection of NH3 oxidizing genes of apparent Archaeal origin in environmental metagenomic libraries and subsequently verified with the cultivation of a strain of Archaea (NH3-oxidizing Archaea, AOA) that oxidizes NH3 to NO2-, apparently using a pathway very much like that known in AOB. It now seems likely that AOA are more abundant than AOB in marine systems, and are also prevalent in soils. ?? 2008 Copyright ?? 2008 Elsevier Inc. All rights reserved..},
	author = {Ward, Bess B.},
	year = {2008},
	doi = {10.1016/B978-0-12-372522-6.00005-0},
	pmid = {25246403}
}

@article{porubsky_benthic_2009-1,
	title = {Benthic metabolism and the fate of dissolved inorganic nitrogen in intertidal sediments},
	volume = {83},
	issn = {02727714},
	url = {http://dx.doi.org/10.1016/j.ecss.2009.04.012},
	doi = {10.1016/j.ecss.2009.04.012},
	abstract = {We determined patterns of benthic metabolism and examined the relative importance of denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) as sinks for nitrate (NO3-) in intertidal sediments in the presence and absence of benthic microalgal (BMA) activity. By influencing the activity of BMA, light regulated the metabolic status of the sediments, and, in turn, exerted strong control on sediment nitrogen dynamics and the fate of inorganic nitrogen. A pulsed addition of 15N-labeled NO3- tracked the effect and fate of dissolved inorganic nitrogen (DIN) in the system. Under illuminated conditions, BMA communities influenced benthic fluxes directly, via DIN uptake, and indirectly, by altering the oxygen penetration depth. Under dark hypoxic and anoxic conditions, the fate of water column NO3- was determined largely by three competing dissimilatory reductive processes; DNF, DNRA, and, on one occasion, anaerobic ammonium oxidation (anammox). Mass balance of the added 15N tracer illustrated that DNF accounted for a maximum of 48.2\% of the 15NO3- reduced while DNRA (a minimum of 11.4\%) and anammox (a minimum of 2.2\%) accounted for much less. A slurry experiment was employed to further examine the partitioning between DNF and DNRA. High sulfide concentrations negatively impacted rates of both processes, while high DOC:NO3- ratios favored DNRA over DNF. ?? 2009 Elsevier Ltd. All rights reserved.},
	number = {4},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Porubsky, W. P. and Weston, N. B. and Joye, S. B.},
	year = {2009},
	keywords = {anammox, denitrification, benthic microalgae, dissimilatory nitrate reduction to ammonium, intertidal sediments},
	pages = {392--402}
}

@book{noauthor_marchant_nodate,
	title = {Marchant et al. 2016 coupled nitrification and denitrification.pdf}
}

@book{noauthor_burkholder_nodate,
	title = {Burkholder and {Shumway} 2011 {AQUACULTURE} {SHELLFISH} {EUTROPHICATION} {Chapter}.pd.pdf}
}

@article{perez_water_2003,
	title = {Water quality requirements for marine fish cage site selection in tenerife ({Canary} {Islands}): {Predictive} modelling and analysis using {GIS}},
	volume = {224},
	issn = {00448486},
	doi = {10.1016/S0044-8486(02)00274-0},
	abstract = {Site selection is a key factor in any aquaculture operation, affecting both success and sustainability. The correct choice of site in any aquatic farming operation is vitally important since it can greatly influence economic viability by determining capital outlay, and, by affecting running costs, rates of productions and mortality factors. It is impractical to try control water quality parameters in cage culture systems, therefore culture of any species must be established in geographical regions having adequate water quality and exchange. This study used GIS and related technology to build a spatial database using those water quality variables which were considered to have an influence in developing marine fish-cage culture of seabass and seabream in Tenerife (Canary Islands). The water quality variables identified were: temperature, turbidity (runoff soil erosion and sewage), disease stress (sewage) and possibility of waste feedback from fish-cages (bathymetry). Variables were grouped in a logical model and combined to generate outputs showing the most suitable areas for siting cage culture. Most areas of the coastline of Tenerife were identified as being suitable or very suitable, and none was identified as totally unsuitable. Sensitivity to parameter changes was tested in order to evaluate the model, by changing one parameter at a time. Values chosen were ± 5\%, 10\% and 15\% of the reference situation. This analysis shows that the model was especially sensitive to sea temperature and suspended solids. © 2002 Elsevier Science B.V. All rights reserved.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Pérez, O. M. and Ross, L. G. and Telfer, T. C. and Del Campo Barquin, L. M.},
	year = {2003},
	keywords = {GIS, Aquaculture, Site selection, Tenerife, Water quality, Cage},
	pages = {51--68}
}

@article{mazzola_initial_1999,
	title = {Initial fish-farm impact on meiofaunal assemblages in coastal sediments of the {Western} {Mediterranean}},
	issn = {0025326X},
	doi = {10.1016/S0025-326X(99)00142-3},
	abstract = {We studied the initial impact of organic loads due to the biodeposition of a new fish farm in a non-impacted coastal area of the Tyrrhenian Sea (Western Mediterranean). Sediment chemistry and meiofaunal assemblages were investigated from July 1997 to February 1998 on a monthly basis at two stations: the first was located under the fish farm, while the second was at about 1 km distance, and served as control. Variations in the biochemical composition of the sedimentary organic matter and meiofaunal community structure were also related to changes in reared fish biomass. The presence of the cage-induced rapid changes in the benthic compartment: the sediments reached rapidly (i.e., after only 6 weeks) reducing conditions. A significant accumulation of biopolymeric carbon was observed beneath the cage both at the beginning of this study and 5-7 months after cage disposal and appeared to be related to the fish-farm production cycle. Sedimentary proteins and lipids resulted to be good descriptors of medium-term fish-farm impact. Changes in the sediment conditions beneath the cage determined a significant reduction of the total meiofaunal density (on average for 70\%). Most meiofaunal taxa, including nematodes, copepods and ostracods displayed a significant decrease in the farm sediments within 3 months after cage installation. Kinorhynchs appeared extremely sensitive to reducing conditions of the sediments and disappeared almost completely, whereas polychaete densities remained unvaried. After initial impact meiofaunal assemblages responded to organic enrichment recovering, at least partially, their apparent structural characteristics. These data indicate that studies carried out several months after cage deployment might underestimate the actual impact on benthic assemblages. Copyright (C) 1999 Elsevier Science Ltd.},
	journal = {Marine Pollution Bulletin},
	author = {Mazzola, A. and Mirto, S. and Danovaro, R.},
	year = {1999},
	keywords = {Carbohydrates, Fish farming impact, Lipids, Mediterranean sea, Meiofauna, Proteins}
}

@article{eyre_denitrification_2009,
	title = {Denitrification efficiency for defining critical loads of carbon in shallow coastal ecosystems},
	volume = {629},
	issn = {00188158},
	doi = {10.1007/s10750-009-9765-1},
	abstract = {Denitrification efficiency [DE; (N2 - N/(DIN + N2 - N) 9 100\%)] as an indicator of change associated with nutrient over-enrichment was evaluated for 22 shallow coastal ecosystems in Australia. The rate of carbon decomposition (which can be considered a proxy for carbon loading) is an important control on the efficiency with which coastal sediments in depositional mud basins with low water column nitrate concentrations recycle nitrogen as N2. The relationship between DE and carbon loading is due to changes in carbon and nitrate (NO3) supply associated with sediment biocomplexity. At the DE optimum (500–1,000 lmol m-2 h-1), there is an overlap of aerobic and anaerobic respiration zones (caused primarily by the existence of anaerobic micro-niches within the oxic zone, and oxidized burrow structures penetrating into the anaerobic zone), which enhances denitrification by improving both the organic carbon and nitrate supply to denitrifiers. On either side of the DE optimum zone, there is a reduction in denitrification sites as the sediment loses its three-dimensional complexity. At low organic carbon loadings, a thick oxic zone with low macrofauna biomass exists, resulting in limited anoxic sites for denitrification, and at high carbon loadings, there is a thick anoxic zone and a resultant lack of oxygen for nitrification and associated NO3 production. We propose a trophic scheme for defining critical (sustainable) carbon loading rates and possible thresholds for shallow coastal ecosystems based on the relationship between denitrification efficiency and carbon loading for 17 of the 22 Australian coastal ecosystems. The denitrification efficiency “optimum” occurs between carbon loadings of about 50 and 100 g C m-2 year-1. Coastal managers can use this simple trophic scheme to classify the current state of their shallow coastal ecosystems and for determining what carbon loading rate is necessary to achieve any future state.},
	number = {1},
	journal = {Hydrobiologia},
	author = {Eyre, Bradley D. and Ferguson, Angus J P},
	year = {2009},
	keywords = {Eutrophication, Trophic state, Carbon loading, Critical loads, Indicator, Nutrient enrichment, Threshold},
	pages = {137--146}
}

@article{cathalot_spatial_2012,
	title = {Spatial and {Temporal} {Variability} of {Benthic} {Respiration} in a {Scottish} {Sea} {Loch} {Impacted} by {Fish} {Farming}: {A} {Combination} of {In} {Situ} {Techniques}},
	volume = {18},
	issn = {13806165},
	doi = {10.1007/s10498-012-9181-4},
	abstract = {The effects of fish farm activities on sediment biogeochemistry were investigated in Loch Creran (Western Scotland) from March to October 2006. Sediment oxygen uptake rates (SOU) were estimated along an organic matter gradient generated from an Atlantic salmon farm using a combination of in situ techniques: microelectrodes, planar optode and benthic chamber incubations. Sulphide (H2S) and pH distributions in sediment porewater were also measured using in situ microelectrodes, and dissolved inorganic carbon (DIC) fluxes were measured in situ using benthic chambers. Relationships between benthic fluxes, vertical distribution of oxidants and reduced compounds in the sediment were examined as well as bacterial abundance and biomass. Seasonal variations in SOU were relatively low and mainly driven by seasonal temperature variations. The effect of the fish farm on sediment oxygen uptake rate was clearly identified by higher total and diffusive oxygen uptake rates (TOU and DOU, respectively) on impacted stations (TOU: 70 ± 25 mmol O2 m-2 day-1; DOU: 70 ± 32 mmol O2 m-2 day-1 recalculated at the summer temperature), compared with the reference station (TOU: 28.3 ± 5.5 mmol O2 m-2 day-1; DOU: 21.5 ± 4.5 mmol O2 m-2 day-1). At the impacted stations, planar optode images displayed high centimetre scale heterogeneity in oxygen distribution underlining the control of oxygen dynamics by small-scale processes. The organic carbon enrichment led to enhanced sulphate reduction as

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib