text:
@article{porubsky_benthic_2009,
	title = {Benthic metabolism and the fate of dissolved inorganic nitrogen in intertidal sediments},
	volume = {83},
	issn = {02727714},
	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.},
	number = {4},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Porubsky, W.P. and Weston, N.B. and Joye, S.B.},
	year = {2009},
	pages = {392--402}
}

@article{noauthor_loyola_2015,
	title = {{LOYOLA} {UNIVERSITY} {CHICAGO} {THE} {INFLUENCE} {OF} {EASTERN} {OYSTER} ( {CRASSOSTREA} {VIRGINICA} ) {REEF} {RESTORATION} {ON} {NITROGEN} {CYCLING} {IN} {A} {EUTROPHIC} {ESTUARY} {A} {THESIS} {SUBIMTTED} {TO} {THE} {FACULTY} {OF} {THE} {GRADUATE} {SCHOOL} {IN} {CANDIDACY} {FOR} {THE} {DEGREE} {OF} {MASTER} {OF} {SCIENCE} {PROGR}},
	number = {May},
	year = {2015}
}

@article{domingues_ammonium_2011,
	title = {Ammonium, nitrate and phytoplankton interactions in a freshwater tidal estuarine zone: {Potential} effects of cultural eutrophication},
	volume = {73},
	issn = {10151621},
	doi = {10.1007/s00027-011-0180-0},
	abstract = {Nitrate and ammonium are the most important nitrogen sources for phytoplankton growth. Differential utilization of inorganic nitrogenous compounds by phytoplankton has been observed and may have significant impacts on primary productivity at local scales. We used enrichment experiments with natural phytoplankton populations from the freshwater tidal zone of the Guadiana estuary, a coastal ecosystem increasingly subjected to anthropogenic influences, to study the effects of nitrate and ammonium on N-consumption and phytoplankton growth. In addition, we used combined additions of nitrate and ammonium to understand the inhibitory effect of ammonium over nitrate uptake. Ammonium concentrations in the freshwater tidal reaches of the Guadiana estuary throughout the sampling period were too low to exert an inhibitory effect on nitrate uptake or a toxic effect on phytoplankton growth. Nitrate was clearly the main nitrogen source for phytoplankton at the study site. Overall, nitrate seemed to become limiting at concentrations lower than 20 mu M and N-limitation was particularly significant during summer. A trend of decreasing nitrate uptake with increasing ammonium concentrations and uptake suggested an overall preference for ammonium. However, preference for ammonium was group-specific, and it was observed mainly in green algae and cyanobacteria. In fact, cyanobacteria relied only on ammonium as their N-source. On the contrary, diatoms preferred nitrate, and did not respond to ammonium additions. The increasing eutrophication in the Guadiana estuary and particularly increased inputs of nitrogen as ammonium due to urban waste effluents may result in a shift in phytoplankton community composition, towards a dominance of cyanobacteria and green algae.},
	number = {3},
	journal = {Aquatic Sciences},
	author = {Domingues, Rita B. and Barbosa, Ana B. and Sommer, Ulrich and Galvão, Helena M.},
	year = {2011},
	keywords = {Ammonium, Guadiana estuary, Nitrate, Nitrogen, Nutrient limitation, Phytoplankton},
	pages = {331--343}
}

@article{sequeira_trade-offs_2008,
	title = {Trade-offs between shellfish aquaculture and benthic biodiversity: {A} modelling approach for sustainable management},
	volume = {274},
	issn = {00448486},
	doi = {10.1016/j.aquaculture.2007.10.054},
	abstract = {This paper presents an ecosystem modelling approach aimed at improving shellfish aquaculture management by explicitly considering natural benthic biodiversity. This methodology uses a combination of benthic field survey data, sediment and bathymetric mapping, physiological models and dynamic ecosystem modelling. The Wild species Integration for Shellfish Ecoaquaculture (WISE) approach helps to understand the baseline food requirements for maintaining natural benthic biodiversity of suspension-feeding organisms, thus informing managers on potential upper thresholds for shellfish aquaculture. WISE was tested in four coastal systems in Europe and China, including bays, estuaries and sea loughs with widely differing aquaculture activities. In the European systems, where the aquaculture industry is developing, species diversity and abundance are much higher and suspension-feeding wild species play an important role in the consumption of food resources. Densities of wild individuals were estimated to be 13 ind m- 2 in Sanggou Bay (total: 2 ?? 109), 33??ind m- 2 in Xiangshan Gang (total: 122 ?? 109), 95??ind m- 2 in Carlingford Lough (total: 4.62 ?? 109) and 175??ind m- 2 in Loch Creran (total: 2.62 ?? 109). Total clearance rates by wild populations were calculated as 5\% of the total volume d- 1 in Sanggou Bay (75 ?? 106??m3 d- 1), 11\% d- 1 in Xiangshan Gang (434 ?? 106??m3 d- 1), 40\% d- 1 in Loch Creran (93 - 99 ?? 106??m3 d- 1) and 45\%??d- 1 in Carlingford Lough (170-250 ?? 106??m3 d- 1). In relative terms, wild populations play a more important role than cultivated shellfish in clearing suspended particles from the European systems due to the much lower aquaculture activity. 56\% and 76\% of total primary production in Loch Creran and Carlingford Lough, respectively, are consumed annually by wild organisms, while less than 50\% is consumed in Chinese systems (45\% in Sanggou Bay and 2.9\% in Xiangshan Gang). Integration of the WISE approach within broader ecological modelling illustrates some of the trade-offs between commercial aquaculture and the conservation of biodiversity, showing that rates of and capacities for shellfish culture are reduced when both wild and cultured suspension-feeding species are considered in relation to the available seston. When food resources are partitioned between wild and cultivated species, there is a decrease in individual length and weight (9 to 22\% reduction in shell length and 24 to 52\% reduction in total fresh weight for the Pacific oyster; reductions of 6\% in length and 20\% in weight for blue mussel; reductions of 4\% in length and 13\% in individual weight for bivalves in Xiangshan Gang), resulting in a lower aquaculture production (e.g. for Pacific oyster, a reduction of 12.5\% in Carlingford Lough, 34\% in Loch Creran and of 9\% for bivalves in Xiangshan Gang). ?? 2007 Elsevier B.V. All rights reserved.},
	number = {2-4},
	journal = {Aquaculture},
	author = {Sequeira, A. and Ferreira, J. G. and Hawkins, A. J S and Nobre, A. and Louren??o, P. and Zhang, X. L. and Yan, X. and Nickell, T.},
	year = {2008},
	pmid = {741},
	keywords = {Biodiversity, China, Coastal systems, Conservation, Ecoaquaculture, Ecological modeling, Europe, GIS, Resource partitioning, Sustainable shellfish aquaculture, Wild species},
	pages = {313--328}
}

@article{nixon_coastal_1995,
	title = {Coastal marine eutrophication: a definition, social causes, and future concerns},
	volume = {41},
	issn = {0078-5326},
	url = {http://www.tandfonline.com/doi/abs/10.1080/00785236.1995.10422044%5Cn%3CGo to ISI%3E://A1995QQ83600010},
	doi = {10.1080/00785236.1995.10422044},
	abstract = {There is a need in the marine research and management communities for a clear operational definition of the term, eutrophication. I propose the following: eutrophication (noun) - an increase in the rate of supply of organic matter to an ecosystem. This definition is consistent with historical usage and emphasizes that eutrophication is a process, not a trophic state. A simple trophic classification for marine systems is also proposed: [GRAPHICS] Various factors may increase the supply of organic matter to coastal systems, but the most common is clearly nutrient enrichment. The major causes of nutrient enrichment in coastal areas are associated directly or indirectly with meeting the requirements and desires of human nutrition and diet. The deposition of reactive nitrogen emitted to the atmosphere as a consequence of fossil fuel combustion is also an important anthropogenic factor. The intensity of nitrogen emission from fertilizer, livestock waste, and fossil fuel combustion varies widely among the countries of the world. It is strongest in Europe, the northeastern United States, India/Pakistan, Japan/Korea, and the Caribbean. This geographical distribution corresponds with many areas where coastal marine eutrophication has become a recent concern. Demographic and social trends suggest that past practices leading to coastal nutrient enrichment are likely to be repeated in the coming decades in the developing countries of Asia, Africa, and Latin America.},
	number = {September},
	journal = {Ophelia},
	author = {Nixon, Scott W.},
	year = {1995},
	pages = {199--219}
}

@article{moore_recovery_1991,
	title = {Recovery of a sewage sludge dumping ground . 11 . {Macrobenthic} community},
	volume = {75},
	number = {March 1985},
	author = {Moore, D C and Rodger, G K},
	year = {1991}
}

@article{lindemann_effect_2016,
	title = {Effect of {Eastern} {Oysters} ({Crassostrea} virginica) and {Seasonality} on {Nitrite} {Reductase} {Gene} {Abundance} ({nirS}, {nirK}, {nrfA}) in an {Urban} {Estuary}},
	volume = {39},
	issn = {15592731},
	doi = {10.1007/s12237-015-9989-4},
	abstract = {The influence of oysters on nitrogen (N) cycling has received increased research attention. Previous work focused on fluxes of N solutes and gases, but the effects on microbes responsible for N transformations are unknown. In May 2010, we deployed eastern oysters (Crassostrea virginica) in mesh cages above sand-filled boxes at four sites across a nutrient gradient in Jamaica Bay, New York City. In fall and winter, we used quantitative PCR to measure abundance of 16S rRNA and nitrite reductase genes for denitrification (nirS and nirK) and dissimilatory nitrate reduction to ammonium (nrfA) in sediment. We measured water column nutrients and chlorophyll a, sediment C:N and organic matter (OM), exchangeable ammonium (NH4 +), ammonification, nitrification, and denitrification potential (DNP). Oysters did not affect gene abundance in fall, when we predicted that their influence would be strongest, or in winter. However, gene abundance was significantly different among sites and seasons. Factors which explained 16S rRNA, nirS, and nirK gene abundance included sediment OM, water column N, and chlorophyll a, similar to previous research. Abundance of nrfA was lower than that of nir genes and positively related to sediment C:N, suggesting OM lability may drive the balance between nir and nrfA. Finally, nirS and nirK abundance was unrelated to DNP, which is consistent with variable results from the literature. More studies that combine molecular techniques with N transformation rates in the context of oyster reefs are needed. Results will advance models which predict the ecosystem effects of reef conservation and restoration under variable environmental conditions.},
	number = {1},
	journal = {Estuaries and Coasts},
	author = {Lindemann, Samantha and Zarnoch, Chester B. and Castignetti, Domenic and Hoellein, Timothy J.},
	year = {2016},
	keywords = {Biodeposits, Bivalves, Denitrification, Eutrophication, Oyster reef habitat},
	pages = {218--232}
}

@article{perez_geographical_2005,
	title = {Geographical information systems-based models for offshore floating marine fish cage aquaculture site selection in {Tenerife}, {Canary} {Islands}},
	volume = {36},
	issn = {1355557X},
	doi = {10.1111/j.1365-2109.2005.01282.x},
	abstract = {The present study focuses on the development of a standard methodology for selection of suitable sites for o¡shore (exposed) marine ¢sh-cage farming ({\textbackslash}poundsoating cages) of seabream (Sparus aurata)and sea- bass (Dicentrarchus labrax) in an island environment, using Tenerife as an example. Site selection is a key factor in any aquaculture operation, a¡ecting both success and sustainability and can solve con{\textbackslash}poundsicts be- tween di¡erent activities, making a rational use of the coastal space. Site selection was achieved by using geographical information systems (GIS)-based models and related technology to support the deci- sion-making process. The framework for spatialmul- ticriteria decision analysis used in this study began with a recognition and de¢nition of the decision pro- blem. Subsequently,31production functions (factors and constraints) were identi¢ed, de¢ned and subdi- vided into eight submodels. These were then inte- grated into a GIS database in the form of thematic layers and later scored for standardization. At this stage, the database was veri¢ed by ¢eld sampling to establish the quality of data used. The decision ma- ker's preferences were incorporated into the decision model by assigning weights of relative importance to the evaluation under consideration. These, together with the thematic layers, were incorporated using multicriteria evaluation techniques and simple over- lays to provide an overall assessment of possible alternatives. The integration, manipulation and pre- sentation of the results by means of GIS-based mod- els in this sequential and logical {\textbackslash}poundsow of steps proved to be very e¡ective for helping the decision-making process of site selection. Tenerife has very favourable environmental conditions for culture of marine ¢sh and there are no totally unsuitable sites for cage farming identi¢ed in this study. On the other hand, there are few very suitable sites (high scores) either, principally due to the heavy use of the coastline and the con{\textbackslash}poundsicts between di¡erent users. From the 228 km2 of available area for sitingcages inthe coast- al regions with depth less than 50m, the total area suitable for siting cages (scores 6{\textasciicircum}8) was 37 km2. There are only 0.51km2 of very suitable areas (score 8) and approximately 5.37 km2 of suitable (score 7), most of these being located in the southeast of the is- land.These relatively small areas of suitability should be put into the context of thewider use of the coastal environment aroundTenerife.},
	number = {10},
	journal = {Aquaculture Research},
	author = {Pérez, Oscar M. and Telfer, Trevor C. and Ross, Lindsay G.},
	year = {2005},
	keywords = {GIS, Aquaculture, Cage culture, Site selection, Tenerife},
	pages = {946--961}
}

@book{noauthor_silvert_nodate,
	title = {Silvert 1992 {Enviro} impacts finfish aquaculture marine.pdf}
}

@article{v_effects_1988,
	title = {Effects of {Sea} {Cage} {Salmon} {Farming} on {Sediment} {Nitrification} and {Dissimilatory} {Nitrate} {Reductions}},
	volume = {70},
	author = {V, Elsevier Science Publishers B},
	year = {1988},
	pages = {333--344}
}

@article{debruyn_modelling_2004,
	title = {Modelling the diagenetic fate of persistent organic pollutants in organically enriched sediments},
	volume = {179},
	issn = {03043800},
	doi = {10.1016/j.ecolmodel.2004.05.009},
	abstract = {The fate of persistent organic pollutants (POPs) in aquatic ecosystems is intimately linked to the cycling of organic matter. In this paper, we present a model of the effect of organic matter decomposition on the distribution of persistent organic pollutants in sediments. The model predicts a diagenetic (sediment-ageing) magnification of chemical concentrations in sediments enriched with labile organic matter. We predict two- to four-fold diagenetic magnification across a wide range of realistic parameter values, and higher levels (up to 20-fold) for labile organic matter in systems with low burial rates (i.e., residence times on the order of years). As an illustration, we apply our model to understand the fate of waste organic matter and associated PCBs discharged by marine fish farms. The available data support both the spatial pattern (as a function of burial rate) and the range of sediment PCB concentrations predicted by our model. This model explains why equilibrium models fail to predict the very high sediment-water partitioning coefficients often observed in the field. Effectively, diagenetic processes impose an additional biomagnification step at the bottom of the detritus-based food web, increasing the exposure to POPs of organisms at higher trophic levels. ?? 2004 Elsevier B.V. All rights reserved.},
	number = {3},
	journal = {Ecological Modelling},
	author = {DeBruyn, Adrian M H and Gobas, Frank A P C},
	year = {2004},
	keywords = {Aquaculture, Chemical fate, Desorption, Diagenesis, PCBs, Persistent organic pollutants},
	pages = {405--416}
}

@article{noauthor_nitrogen_2016,
	title = {Nitrogen {Fixation} in a {Coral} {Reef} {Community} {Author} ( s ): {W} . {J} . {Wiebe} , {R} . {E} . {Johannes} and {K} . {L} . {Webb} {Published} by : {American} {Association} for the {Advancement} of {Science} {Stable} {URL} : http://www.jstor.org/stable/1739936 {REFERENCES} {Linked} references ar},
	volume = {188},
	number = {4185},
	year = {2016},
	pages = {257--259}
}

@article{brandes_new_2007,
	title = {New developments in the marine nitrogen cycle},
	volume = {107},
	issn = {00092665},
	doi = {10.1021/cr050377t},
	abstract = {ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.},
	number = {2},
	journal = {Chemical Reviews},
	author = {Brandes, Jay A. and Devol, Allan H. and Deutsch, Curtis},
	year = {2007},
	pmid = {17300141},
	pages = {577--589}
}

@article{jacobsen_comparing_2016,
	title = {Comparing model predictions for ecosystem-based management 1},
	volume = {73},
	issn = {0706-652X},
	url = {http://www.nrcresearchpress.com/doi/full/10.1139/cjfas-2014-0561#.V2l2JI-cFMs},
	doi = {10.1139/cjfas-2014-0561},
	abstract = {Ecosystem modeling is becoming an integral part of fisheries management, but there is a need to identify differences between predictions derived from models employed for scientific and management purposes. Here, we compared two models: a biomass-based food-web model (Ecopath with Ecosim (EwE)) and a size-structured fish community model. The models were compared with respect to predicted ecological consequences of fishing to identify commonalities and differences in model predictions for the California Current fish community. We compared the models regarding direct and indirect responses to fishing on one or more species. The size-based model predicted a higher fishing mortality needed to reach maximum sustainable yield than EwE for most species. The size-based model also predicted stronger top-down effects of predator removals than EwE. In contrast, EwE predicted stronger bottom-up effects of forage fisheries removal. In both cases, the differences are due to the presumed degree of trophic overlap between...},
	language = {en},
	number = {4},
	journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	author = {Jacobsen, Nis S. and Essington, Timothy E. and Andersen, Ken H. and Shuter, Brian},
	month = apr,
	year = {2016},
	pages = {666--676}
}

@article{trimmer_anaerobic_2003,
	title = {Anaerobic {Ammonium} {Oxidation} {Measured} in {Sediments} along the {Thames} {Estuary} , {United} {Kingdom} {Anaerobic} {Ammonium} {Oxidation} {Measured} in {Sediments} along the {Thames} {Estuary} , {United} {Kingdom}},
	volume = {69},
	doi = {10.1128/AEM.69.11.6447},
	number = {11},
	author = {Trimmer, Mark and Nicholls, Joanna C and Deflandre, Bruno},
	year = {2003},
	pages = {6447--6454}
}

@article{heisler_eutrophication_2008,
	title = {Eutrophication and harmful algal blooms: {A} scientific consensus},
	volume = {8},
	issn = {15689883},
	doi = {10.1016/j.hal.2008.08.006},
	abstract = {In January 2003, the US Environmental Protection Agency sponsored a "roundtable discussion" to develop a consensus on the relationship between eutrophication and harmful algal blooms (HABs), specifically targeting those relationships for which management actions may be appropriate. Academic, federal, and state agency representatives were in attendance. The following seven statements were unanimously adopted by attendees based on review and analysis of current as well as pertinent previous data:(1)Degraded water quality from increased nutrient pollution promotes the development and persistence of many HABs and is one of the reasons for their expansion in the U.S. and other nations;(2)The composition-not just the total quantity-of the nutrient pool impacts HABs;(3)High-biomass blooms must have exogenous nutrients to be sustained;(4)Both chronic and episodic nutrient delivery promote HAB development;(5)Recently developed tools and techniques are already improving the detection of some HABs, and emerging technologies are rapidly advancing toward operational status for the prediction of HABs and their toxins;(6)Experimental studies are critical to further the understanding about the role of nutrients in HABs expression, and will strengthen prediction and mitigation of HABs; and(7)Management of nutrient inputs to the watershed can lead to significant reduction in HABs. Supporting evidence and pertinent examples for each consensus statement are provided herein. ?? 2008 Elsevier B.V.},
	number = {1},
	journal = {Harmful Algae},
	author = {Heisler, J. and Glibert, P. M. and Burkholder, J. M. and Anderson, D. M. and Cochlan, W. and Dennison, W. C. and Dortch, Q. and Gobler, C. J. and Heil, C. A. and Humphries, E. and Lewitus, A. and Magnien, R. and Marshall, H. G. and Sellner, K. and Stockwell, D. A. and Stoecker, D. K. and Suddleson, M.},
	year = {2008},
	keywords = {Eutrophication, HABs, Harmful algal blooms, Management of nutrients, Nutrient composition, Nutrient loading, Nutrient pollution, US EPA, Water quality},
	pages = {3--13}
}

@article{tide_eutrophication_2006,
	title = {Eutrophication and occurrences of harmful algal blooms in the {Seto} {Inland} {Sea} , {Japan}},
	volume = {1},
	issn = {1882-627X},
	doi = {10.3800/pbr.1.71},
	number = {2},
	journal = {Environmental Studies},
	author = {Tide, Red},
	year = {2006},
	keywords = {age, algicidal bacteria, eutrophication, fish-kill, fishery dam-, harmful algal blooms, mitigation, red tides, seaweeds, seto inland sea, toxic blooms, viruses},
	pages = {71--84}
}

@article{mccarthy_denitrification_2015,
	title = {Denitrification {Dominates} {Sediment} {Nitrogen} {Removal} and {Is} {Enhanced} by {Bottom}-{Water} {Hypoxia} in the {Northern} {Gulf} of {Mexico}},
	volume = {38},
	issn = {15592731},
	doi = {10.1007/s12237-015-9964-0},
	abstract = {Nutrient loads from the Mississippi River watershed are associated with seasonal development of bottom-water hypoxia in the northern Gulf of Mexico. Microbial nitrogen (N) transformations at the sediment-water interface are important in determining system productivity and the development and maintenance of hypoxia. Intact sediment cores were incubated in a continuous-flow system with stable isotope tracers to identify and quantify important N sources (e.g., N fixation), sinks (e.g., denitrification and anammox), and links (e.g., dissimilatory nitrate reduction to ammonium, DNRA). Microbial N sinks on the Louisiana-Texas continental shelf remove up to 68 \% of the total N load from the Mississippi River watershed, and up to 29 \% of this N removal (mean = 11.8 +/- 1.7 \%) may be due to anammox. The highest N-2 production rates and ammonium effluxes were observed at low bottom-water oxygen concentrations, and sediments were a significant source of ammonium to the water column at all times. DNRA and heterotrophic N fixation were not consistent pathways for total sediment N fluxes, but their potential importance to N balance and productivity in the system warrants further study and inclusion in ecosystem models. Physical disturbance from passage of two hurricanes in 2008 resulted in lower N cycling rates and sediment oxygen consumption, with sediment processes migrating into the water column. Denitrification is the dominant N sink in the northern Gulf of Mexico and provides a valuable ecosystem service by mitigating N loads from the Mississippi River watershed, particularly during seasonal bottom-water hypoxia events.},
	number = {6},
	journal = {Estuaries and Coasts},
	author = {McCarthy, Mark J. and Newell, Silvia E. and Carini, Stephen A. and Gardner, Wayne S.},
	year = {2015},
	keywords = {Denitrification, Anammox, DNRA, Gulf of Mexico, Hypoxia, N fixation},
	pages = {2279--2294}
}

@article{mortimer_anoxic_2004,
	title = {Anoxic nitrification in marine sediments},
	volume = {276},
	issn = {01718630},
	doi = {10.3354/meps276037},
	abstract = {Nitrate peaks are found in pore-water profiles in marine sediments at depths considerably\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nbelow the conventional zone of oxic nitrification. These have been interpreted to represent nonsteady-\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nstate effects produced by the activity of nitrifying bacteria, and suggest that nitrification\${\textbackslash}backslash\$r\${\textbackslash}backslash\$noccurs throughout the anoxic sediment region. In this study, ΣNO3 peaks and molecular analysis of\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nDNA and RNA extracted from anoxic sediments of Loch Duich, an organic-rich marine fjord, are consistent\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nwith nitrification occurring in the anoxic zone. Analysis of ammonia oxidiser 16S rRNA gene\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nfragments amplified from sediment DNA indicated the abundance of autotrophic ammonia-oxidising\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nbacteria throughout the sediment depth sampled (40 cm), while RT-PCR analysis indicated their\${\textbackslash}backslash\$r\${\textbackslash}backslash\$npotential activity throughout this region. A large non-steady-state pore-water ΣNO3 peak at ∼21 cm\${\textbackslash}backslash\$r\${\textbackslash}backslash\$ncorrelated with discontinuities in this ammonia-oxidiser community. In addition, a subsurface nitrate\${\textbackslash}backslash\$r\${\textbackslash}backslash\$npeak at ∼8 cm below the oxygen penetration depth, correlated with the depth of a peak in nitrification\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nrate, assessed by transformation of 15N-labelled ammonia. The source of the oxidant required to\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nsupport nitrification within the anoxic region is uncertain. It is suggested that rapid recycling of N is\${\textbackslash}backslash\$r\${\textbackslash}backslash\$noccurring, based on a coupled reaction involving Mn oxides (or possibly highly labile Fe oxides)\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nburied during small-scale slumping events. However, to fully investigate this coupling, advances in\${\textbackslash}backslash\$r\${\textbackslash}backslash\$nthe capability of high-resolution pore-water techniques are required.},
	number = {1},
	journal = {Marine Ecology Progress Series},
	author = {Mortimer, Robert J G and Harris, Sansha J. and Krom, Michael D. and Freitag, Thomas E. and Prosser, James I. and Barnes, Jonathan and Anschutz, Pierre and Hayes, Peter J. and Davies, Ian M.},
	year = {2004},
	keywords = {16sRNA, Anoxic nitrification, Diffusive Equilibrium in Thin films (DET)},
	pages = {37--51}
}

@article{mason_historical_2004,
	title = {{HISTORICAL} {PATTERNS} {FROM} 74 {YEARS} {OF} {COMMERCIAL} {LANDINGS} {FROM} {CALIFORNIA} {WATERS}},
	volume = {45},
	abstract = {California's commercial fisheries harvested many dif-ferent species of finfish and invertebrates from 1928 to 2001. A time series of the landings from waters off California was created to examine changes in the species composition, weight, and value of the landings. Small coastal pelagic fishes dominated the landings weight until the late 1980s, when landings of invertebrates increased. Tunas, groundfish, salmon, crabs, sea urchins, and squid have all contributed significantly to the value of the land-ings. Value and landings were affected by domestic and international market conditions. The availability of cer-tain species, especially coastal pelagics, has varied in response to decadal-scale changes in environmental con-ditions, and tunas, herring, and squid varied with in-teryear environmental warming from California El Niño events. The depletion and subsequent regulation of many of the stocks, including several rockfish, have contributed to declines in their landings over time. Invertebrates be-came more important in both the weight and value of landings in the 1990s. The declining trend in the total value of landings, despite increased total landings, raises concern for the future of the fishing economy.},
	journal = {MASON: COMMERCIAL LANDINGS PATTERNS CalCOFI Rep},
	author = {Mason, Janet E},
	year = {2004}
}

@article{kalantzi_benthic_2006,
	title = {Benthic impacts of fish farming: {Meta}-analysis of community and geochemical data},
	volume = {52},
	issn = {0025326X},
	doi = {10.1016/j.marpolbul.2005.09.034},
	abstract = {A number of 41 papers dealing with the benthic effects of fish farming were reviewed and the values of the variables studied were extracted to be used in a meta-analysis of effects. The papers used covered a wide range of farmed species, geographic regions, management practices and specific site characteristics (e.g., depth, exposure, and sediment type). Therefore, the total data-set may not be considered as biased towards a particular set of conditions as is often the case with data collected in a single study. More than 120 biological and geochemical variables were monitored, occasionally using different sampling and analytical protocols for the same variables. The rank correlation analysis between all possible pairs of variables in the data set showed a large number of significant positive or negative correlations, reflecting the response of these variables to benthic organic enrichment. The use of stepwise regression showed that most biological and geochemical variables are determined by a combination of distance from the farm with bottom depth and/or latitude. Results of stepwise regression, repeated separately for each type of sediment, showed that although the general pattern was similar among different types of sediments, the coefficients varied considerably indicating changes of the distance affected by settling particulate organic material for different sediment types. The overall conclusion is that the complicated interactions between variables and the lack of data, such as current speed, induce difficulties in setting common or uniform environmental quality standards for benthic effects of fish farming and these should take into account the existing considerable differences between geographic regions, depth zones and sediment types. ?? 2005 Elsevier Ltd. All rights reserved.},
	number = {5},
	journal = {Marine Pollution Bulletin},
	author = {Kalantzi, Ioanna and Karakassis, Ioannis},
	year = {2006},
	pmid = {16257014},
	keywords = {Benthic enrichment, Biogeochemistry, Cage aquaculture, Mariculture, Meta-analysis, Sediment types},
	pages = {484--493}
}

@article{behrendt_vertical_2013,
	title = {Vertical activity distribution of dissimilatory nitrate reduction in coastal marine sediments},
	volume = {10},
	issn = {17264170},
	doi = {10.5194/bg-10-7509-2013},
	abstract = {The relative importance of two dissimilatory nitrate reduction pathways, denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA), was investigated in intact sediment cores from five different coastal marine field sites (Dorum, Aarhus Bight, Mississippi Delta, Limfjord and Janssand). The vertical distribution of DEN activity was examined using the acetylene inhibition technique combined with N2O microsensor measurements, whereas NH4+ production via DNRA was measured with a recently developed gel probe-stable isotope technique. At all field sites, dissimilatory nitrate reduction was clearly dominated by DEN (59–131\% of the total NO3− reduced) rather than by DNRA, irrespective of the sedimentary inventories of electron donors such as organic carbon, sulfide, and iron. Highest ammonium production via DNRA, accounting for up to 8.9\% of the total NO3− reduced, was found at a site with very high concentrations of total sulfide and NH4+ within and below the layer in which NO3− reduction occurred. Sediment from two field sites, one with low and one with high DNRA activity in the core incubations, was also used for slurry incubations. Now, in both sediments high DNRA activity was detected accounting for 37–77\% of the total NO3− reduced. These contradictory results might be explained by enhanced NO3− availability for DNRA bacteria in the sediment slurries compared to the core-incubated sediments in which diffusion of NO3− from the water column may only reach DEN bacteria, but not DNRA bacteria. The true partitioning of dissimilatory nitrate reduction between DNRA and DEN may thus lie in between the values found in whole core (underestimation of DNRA) and slurry incubations (overestimation of DNRA).},
	number = {11},
	journal = {Biogeosciences},
	author = {Behrendt, A. and De Beer, D. and Stief, P.},
	year = {2013},
	pages = {7509--7523}
}

@article{hyun_impacts_2013,
	title = {Impacts of long-line aquaculture of {Pacific} oysters ({Crassostrea} gigas) on sulfate reduction and diffusive nutrient flux in the coastal sediments of {Jinhae}-{Tongyeong}, {Korea}},
	volume = {74},
	issn = {0025326X},
	url = {http://dx.doi.org/10.1016/j.marpolbul.2013.07.004},
	doi = {10.1016/j.marpolbul.2013.07.004},
	abstract = {We investigated the environmental impacts of long-line aquaculture of Pacific oysters (Crassostrea gigas) on sediment geochemistry and carbon oxidation by sulfate reduction and diffusive benthic nutrient flux in a coastal ecosystem in Korea. Inventories of the NH4+ and HPO42- at the farm site were 7.7-11.5 and 1.8-8.0 times higher, respectively, than those at a reference site. Sulfate reduction rates (SRRs) at the oyster farm were 2.4-5.2 times higher than SRRs at the reference site. The SRRs at the farm site were responsible for 48-99\% (average 70\%) of the total C oxidation in the sediment. The diffusive benthic fluxes of NH4+ and HPO42- at the oyster farm were comparable to 30-164\% and 19-58\%, respectively, of the N and P demands for primary production, and were responsible for the enhanced benthic microalgal biomass on the surface sediment. © 2013 Elsevier Ltd.},
	number = {1},
	journal = {Marine Pollution Bulletin},
	author = {Hyun, Jung Ho and Kim, Sung Han and Mok, Jin Sook and Lee, Jae Seong and An, Sung Uk and Lee, Won Chan and Jung, Rae Hong},
	year = {2013},
	pmid = {23896400},
	keywords = {Benthic nutrient flux, Benthic-pelagic coupling, Crassostrea gigas, Fe and P cycles, Long-line oyster culture, Sulfate reduction},
	pages = {187--198}
}

@article{crawford_environmental_2003,
	title = {Environmental management of marine aquaculture in {Tasmania}, {Australia}},
	volume = {226},
	issn = {00448486},
	doi = {10.1016/S0044-8486(03)00473-3},
	abstract = {Marine farming is an important rural industry in coastal bays and estuaries of Tasmania. The two main species cultured are the introduced Pacific oyster, Crassostrea gigas, and Atlantic salmon, Salmo salar. Legislation has been introduced to assist the development of aquaculture, and this includes requirements for environmental management, such as baseline assessments and routine monitoring of leases. Local impacts on the seabed around salmon farms are monitored using video footage, analysis of benthic invertebrate infauna, and chemical measures (redox and organic matter). Monitoring of shellfish farms is minimal because our research has shown that shellfish culture is having little impact on the environment. Research related to management of aquaculture wastes is ongoing. Studies include investigating appropriate inexpensive measures for an industry-wide long-term monitoring program. Mitigation measures against excessive loadings of organic matter from fish farms, mainly by fallowing, i.e. rotating the position of fish pens around a lease, are currently being researched. Rates of recovery of a heavily impacted salmon lease area after the removal of fish have also been studied. A new project is investigating system-wide effects of salmon farming on the environment, in particular, increased release of nutrients into waterways. This includes monitoring dissolved oxygen, nutrients and phytoplankton, modelling the system, and investigating ecological indicators of eutrophication. ?? 2003 Elsevier B.V. All rights reserved.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Crawford, Christine},
	year = {2003},
	pmid = {1491},
	keywords = {Atlantic salmon, Environmental management, Marine farming, Monitoring, Organic enrichment, Pacific oysters},
	pages = {129--138}
}

@article{brandes_new_nodate,
	title = {New {Developments} in the {Marine} {Nitrogen} {Cycle}},
	doi = {10.1021/cr050377t},
	author = {Brandes, Jay A and Devol, Allan H and Deutsch, Curtis}
}

@article{glibert_cooccurrence_1999,
	title = {Cooccurrence of {Elevated} {Urea} {Levels} and {Dinoflagellate} {Blooms} in {Temperate} {Estuarine} {Aquaculture} {Ponds} †},
	volume = {65},
	number = {12},
	author = {Glibert, Patricia M},
	year = {1999},
	pages = {5594--5596}
}

@article{navarro_effect_2008,
	title = {Effect of salmon cage aquaculture on the pelagic environment of temperate coastal waters: {Seasonal} changes in nutrients and microbial community},
	volume = {361},
	issn = {01718630},
	doi = {10.3354/meps07357},
	abstract = {The effects of salmon farm inputs on pelagic nutrient concentrations and planktonic mi- crobial abundance and biomass were investigated in Loch Fyne, a temperate fjordic environment off the west coast of Scotland. The concentration of photosynthetic pigments and inorganic and organic nutrients, and the abundance and biomass of the autotrophic and heterotrophic microorganisms, were determined over a complete annual cycle from 3 depths (5, 15 and 25–30 m) at 4 stations located at differing proximities to the fish farm. Ammonium and dissolved organic nitrogen concentrations and heterotrophic microbial abundance and biomass were significantly higher at the stations nearest to the fish farm, suggesting that these and other nutrients derived from the fish farm may be directly or indirectly enhancing heterotrophic microbial activity. This in turn suggests that the heterotrophic microbial food web was responsible, at least in part, for processing matter and energy released into the pelagic environment from the salmon farm. By contrast, pigment concentrations, including chlorophyll a, tended to be similar at all stations, supporting the conclusions of previous studies that failed to estab- lish a clear relationship between fish farm inputs and phytoplankton biomass. As such, the response of the heterotrophic microbial community is probably a more appro-priate indicator than chlorophyll concentration of local ecological effects of fish farms in temperate coastal waters. KEY},
	journal = {Marine Ecology Progress Series},
	author = {Navarro, Nuria and Leakey, Raymond J G and Black, Kenneth D.},
	year = {2008},
	keywords = {Bacteria, Chlorophyll, Fish farm, Nutrients, Plankton community},
	pages = {47--58}
}

@article{brigolin_modelling_2014,
	title = {Modelling biogeochemical fluxes across a {Mediterranean} fish cage farm},
	volume = {5},
	doi = {10.3354/aei00093},
	author = {Brigolin, Daniele and Meccia, Virna Loana and Venier, Chiara and Tomassetti, Paolo and Porrello, Salvatore and Pastres, Roberto},
	year = {2014},
	keywords = {cage farming, ecosystem approach to aquaculture, individual-based model, marine spatial planning, nutrient budgets, particle tracking model},
	pages = {71--88}
}

@article{porubsky_field_2011,
	title = {Field measurements and modeling of groundwater flow and biogeochemistry at {Moses} {Hammock}, a backbarrier island on the {Georgia} coast},
	volume = {104},
	issn = {01682563},
	doi = {10.1007/s10533-010-9484-8},
	abstract = {A combination of field measurements, laboratory experiments and model simulations were used to characterize the groundwater biogeochemical dynamics along a shallow monitoring well transect on a coastal hammock. A switch in the redox status of the dissolved inorganic nitrogen (DIN) pool in the well at the upland/saltmarsh interface occurred over the spring-neap tidal transition: the DIN pool was dominated by nitrate during spring tide and by ammonium during neap tide. A density-dependent reaction-transport model was used to investigate the relative importance of individual processes to the observed N redox-switch. The observed N redox-switch was evaluated with regard to the roles of nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), ammonium adsorption, and variations in inflowing water geochemistry between spring and neap tides. Transport was driven by measured pressure heads and process parameterizations were derived from field observations, targeted laboratory experiments, and the literature. Modeling results suggest that the variation in inflow water chemistry was the dominant driver of DIN dynamics and highlight the importance of spring-neap tide variations in the high marsh, which influences groundwater biogeochemistry at the marsh-upland transition. © 2010 Springer Science+Business Media B.V.},
	number = {1-3},
	journal = {Biogeochemistry},
	author = {Porubsky, W. P. and Joye, S. B. and Moore, W. S. and Tuncay, K. and Meile, C.},
	year = {2011},
	keywords = {Hammock groundwater, Nitrogen cycle, Reaction transport modeling, Spring-neap tide cycle, Upland-marsh transition},
	pages = {69--90}
}

@article{laurent_parameterization_2016,
	title = {Parameterization of biogeochemical sediment-water fluxes using in situ measurements and a diagenetic model},
	volume = {13},
	issn = {17264189},
	doi = {10.5194/bg-13-77-2016},
	number = {1},
	journal = {Biogeosciences},
	author = {Laurent, A. and Fennel, K. and Wilson, R. and Lehrter, J. and Devereux, R.},
	year = {2016},
	pages = {77--94}
}

@article{ah_supplemental_nodate,
	title = {Supplemental material},
	number = {d},
	journal = {Animals},
	author = {Ah, Animals},
	pages = {1--15}
}

@article{deal_galactolipids_2003,
	title = {Galactolipids rather than phlorotannins as herbivore deterrents in the brown seaweed {Fucus} vesiculosus},
	volume = {136},
	doi = {10.1007/s00442-003-1242-3},
	abstract = {The first investigation of seaweed chemical defense against herbivores involved the brown seaweed Fucus vesiculosus and suggested defense via phlorotan-nins. The first demonstration of seaweed induction of secondary metabolites in response to herbivory also involved the genus Fucus and assumed a defensive function for phlorotannins. Many other investigations correlate herbivore feeding preference with changing levels of phlorotannins in this genus and others, but few directly test the effects of phlorotannins. No studies have assessed Fucus chemical defenses using bioassay-guided separation to investigate the complete complement of compounds deterring herbivores. We investigated the deterrence of F. vesiculosus chemical extracts using herbivore bioassays to guide our chemical investigations. Although crude extracts from F. vesiculosus strongly deterred feeding by the sea urchin Arbacia punctulata, phlorotannins from this extract did not deter feeding at 2 or 4 natural concentration by dry mass. Feeding deterrence was due to: (1) a polar galactolipid in the ethyl acetate-soluble extract, and (2) a non-phenolic compound, or compounds, in the water-soluble extract. Although this is the first evidence of galactolipids deterring herbivores, such defenses could be geographi-cally and taxonomically widespread. The galactolipid we discovered in Fucus occurs in marine dinoflagellates, and a related metabolite that deters herbivory has recently been discovered in a tropical green seaweed. We were unable to identify the second deterrent compound, but deterrence occurred in a fraction containing carbohy-drates, including sulfated sugars, but no phlorotannins. Given the polarity of these chemical deterrents, they could co-occur with and confound bioassays of phlorotan-nins if investigators test phlorotannin-containing algal extracts without further purification.},
	journal = {Oecologia},
	author = {Deal, Michael S and Hay, Mark E and Wilson, Dean and Fenical, William},
	year = {2003},
	keywords = {Arbacia punctulata ·, Glycerolipids ·, Plant-herbivore interactions ·, Polyphenolics ·, Seaweed chemical defenses},
	pages = {107--114}
}

@article{hogslund_intertidal_2014,
	title = {Intertidal community composition along rocky shores in {South}- west {Greenland}: a quantitative approach},
	doi = {10.1007/s00300-014-1541-7},
	abstract = {The intertidal communities on rocky shores are directly subjected to climatic changes in air and water temperatures and to derived effects of climate change, such as changes in freshwater run-off and ice dynamics. Global warming occurs at elevated rates in Greenland and results in changing species distributions with range expansions to the north and new species entering terrestrial habitats from the south. There is, however, no quantitative knowledge of past or present species distribution in the littoral zone of Southern Greenland, an area which represents an important gateway for northern range expansions of temperate spe-cies. This study provides baseline information on abun-dances of macroorganisms in the eulittoral Southern Greenland. This knowledge will pave the way for future studies on the impact of climate change and anthropogenic activities on these communities. Nine sites, situated at different exposure levels, were investigated. A total of 22 taxa were recorded, suggesting low species richness. Pa-tellid limpets and predators such as dogwhelks, starfish and crabs were absent. Total standing stock ranged from 0 to 31,898 g m -2 . Species composition and biomasses were related to locally generated wave exposure, oceanic swells and ice scouring. The high standing stock at sheltered sites indicated that neither light, temperature nor nutrients, constrained buildup of biomass in this environment. Inshore seasonal measurements of water and air tempera-tures were recorded for the first time in the region, dis-playing low water temperatures and high variation in air temperatures, indicating lack of insulating stable sea ice in the area. Possible impacts of ongoing temperature changes are discussed based on recorded temperatures and meteo-rological data from the past 30 years.},
	author = {Høgslund, Signe and Sejr, Mikael K and Jozef, @bullet and @bullet, Wiktor Jr and Blicher, Martin E and Wegeberg, Susse},
	year = {2014},
	keywords = {Air temperature Á, Arctic Á, Biomass Á, Climate change Á, Greenland Á, Intertidal Á, Rocky shore Á, Sea surface temperature}
}

@article{weise_shellfish-depomod:_2009,
	title = {Shellfish-{DEPOMOD}: {Modelling} the biodeposition from suspended shellfish aquaculture and assessing benthic effects},
	volume = {288},
	issn = {00448486},
	url = {http://dx.doi.org/10.1016/j.aquaculture.2008.12.001},
	doi = {10.1016/j.aquaculture.2008.12.001},
	abstract = {By predicting the dispersal of particulate aquaculture wastes around farm sites, numerical modelling can provide an effective tool to assess the spatial extent of environmental effects. The present paper describes how the aquaculture waste model DEPOMOD (Cromey, C.J., Nickell, T.D., Black, K.D. 2002a. DEPOMOD - modelling the deposition and biological effects of waste solids from marine cage farms. Aquaculture 214, 211-239.), originally developed for finfish aquaculture sites, was adapted and validated for suspended shellfish aquaculture. Field data were collected for species-specific model input parameters (mussel biodeposition rates and particle settling velocities) and several finfish model parameters (farm representation and calculation of aquaculture wastes) were adjusted for the shellfish scenario. Shellfish-DEPOMOD was tested at three coastal mussel Mytilus edulis farms with differing hydrodynamic regimes in Quebec, Canada. For each site, model predictions were compared to observed deposition measured in situ with sediment traps. Sedimentation rates under the three mussel culture sites were ca. two to five times those observed at corresponding reference sites. Mussel biodeposits were predicted to accumulate within 30??m of the farms in the shallow depositional sites while being dispersed more than 90??m in the deeper dispersive site. At the farm site in Great-Entry Lagoon, model predictions agreed well with field data for the 0 + and 1 + mussel cohorts when the maximum biodeposit production parameter was used. At the farm site in House-Harbour Lagoon, model predictions did not agree with observed sedimentation rates, due most likely to the resuspension and advection of non farm-derived material and complex hydrodynamics. The model correctly predicted the pattern of waste dispersal at the third farm site in Cascapedia Bay, although it underestimated biodeposition. Predicted fluxes may have been underestimated at this site because biodeposits from biofouling communities were not included in the calculation of aquaculture wastes. The relationship between modelled long-term biodeposition and benthic descriptors was assessed for the three farms. Alterations to the benthic community were observed at high biodeposition rates ({\textbackslash}textgreater 15??g m- 2 d- 1). At the most disturbed site, predicted fluxes were best correlated with the Infaunal Trophic Index (ITI) (R = - 0.79, P {\textbackslash}textless 0.001), followed by AZTI's marine disturbance index (AMBI) (R = 0.64, P {\textbackslash}textless 0.001). The potential application of Shellfish-DEPOMOD in terms of the management of shellfish aquaculture sites is discussed. ?? 2008 Elsevier B.V. All rights reserved.},
	number = {3-4},
	journal = {Aquaculture},
	author = {Weise, Andrea M. and Cromey, Chris J. and Callier, Myriam D. and Archambault, Philippe and Chamberlain, Jon and McKindsey, Christopher W.},
	year = {2009},
	keywords = {Benthic impacts, Biodeposition, Macrofaunal community structure, Modelling, Mussels, Shellfish aquaculture},
	pages = {239--253}
}

@article{ferreira_management_2007,
	title = {Management of productivity , environmental effects and profitability of shellfish aquaculture — the {Farm} {Aquaculture} {Resource} {Management} ( {FARM} ) model},
	volume = {264},
	doi = {10.1016/j.aquaculture.2006.12.017},
	author = {Ferreira, J G and Hawkins, A J S and Bricker, S B},
	year = {2007},
	keywords = {eutrophication, - see front matter, 0044-8486, 2006 elsevier b, 44 20 7691 7827, all rights reserved, aquaculture, com, corresponding author, e-mail address, farm-scale management, fax, ferreira, g, hoomi, j, joao, nutrient trading, screening model, shellfish carrying capacity, v},
	pages = {160--174}
}

@article{miller_and_nodate,
	title = {{AND} {ITS} {MANAGEMENT}},
	author = {Miller, Daniel J and Hardwick, James E}
}

@article{porrello_influence_2005,
	title = {The influence of marine cages on the sediment chemistry in the {Western} {Mediterranean} {Sea}},
	volume = {249},
	issn = {00448486},
	doi = {10.1016/j.aquaculture.2005.02.042},
	abstract = {Few studies have been carried out regarding the environmental impact of marine cages in the Western Mediterranean Sea. In fact, many more have been published concerning the northern Atlantic areas. A study of the marine fish farm impact of a was carried out to improve knowledge regarding these arguments in the Western Mediterranean. A marine fish farm, with light fish biomass, was selected to evaluate the sensitivity of environmental variables and measure their efficiency over increasing distances. The following environmental parameters were used: hydrodynamic (water current speed and dominant direction in the whole water column) and geochemical (sediment water content, porosity, total volatile substance, sulfide, redox potential, total nitrogen, total and organic carbon, total phosphorous, and total sulphur). The sea current was measured, in the whole water column, with an ADCP (Acoustic Doppler Current Profiler). Four sampling campaigns were performed in January and July 2001, and in May 2002 and October 2002 according to the different reared biomass. The results showed that the most efficient, practical and sensitive parameters were organic carbon, total carbon, total sulphur, sulfide, potential redox, total phosphorus and total nitrogen. The more detectable effects, highlighted by high levels of organic enrichment, were observed in the stations just beneath the cages; moderate impact was present in the area 50 m around the cages and no disturbance was observed further away from this area. The strong but spatially limited organic enrichment found would seem to suggest that the implementation of best management practices should include fallowing and rotation of sea cages to allow sediment recovery. ?? 2005 Elsevier B.V. All rights reserved.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Porrello, Salvatore and Tomassetti, Paolo and Manzueto, Luigi and Finoia, Maria G. and Persia, Emma and Mercatali, Isabel and Stipa, Piergiorgio},
	year = {2005},
	keywords = {Organic enrichment, ADCP, Environmental impact, Geochemistry, Sea cage},
	pages = {145--158}
}

@book{noauthor_yucel-gier_nodate,
	title = {Yucel-{Gier} et al. {SEA} {BASS} {BENTHIC} {IMPACT} {ECOLOGY} {BIOGEOCHEM}.pdf}
}

@article{ferron_benthic_2009,
	title = {Benthic fl uxes in a tidal salt marsh creek affected by fi sh farm activities : {Río} {San} {Pedro} ( {Bay} of {Cádiz} , {SW} {Spain} )},
	volume = {113},
	issn = {0304-4203},
	url = {http://dx.doi.org/10.1016/j.marchem.2008.12.002},
	doi = {10.1016/j.marchem.2008.12.002},
	number = {1-2},
	journal = {Marine Chemistry},
	author = {Ferrón, S and Ortega, T and Forja, J M},
	year = {2009},
	pages = {50--62}
}

@article{risgaard-petersen_pdf_2017,
	title = {{PDF} hosted at the {Radboud} {Repository} of the {Radboud} {University} {Anaerobic} ammonium oxidation in an estuarine sediment},
	author = {Risgaard-petersen, Nils and Meyer, Rikke Louise and Schmid, Markus and Jetten, Mike S M and Enrich-prast, Alex and Rysgaard, Søren and Revsbech, Niels Peter},
	year = {2017}
}

@article{admiraal_tolerance_1977,
	title = {Tolerance of estuarine benthic diatoms to high concentrations of ammonia, nitrite ion, nitrate ion and orthophosphate},
	volume = {43},
	issn = {00253162},
	doi = {10.1007/BF00396925},
	number = {4},
	journal = {Marine Biology},
	author = {Admiraal, W.},
	year = {1977},
	pages = {307--315}
}

@article{palareti_comparison_2016,
	title = {Comparison between different {D}-{Dimer} cutoff values to assess the individual risk of recurrent venous thromboembolism: {Analysis} of results obtained in the {DULCIS} study},
	volume = {38},
	issn = {1751553X},
	doi = {10.1111/ijlh.12426},
	abstract = {Introduction: D-dimer assay, generally evaluated according to cutoff points calibrated for VTE exclusion, is used to estimate the individual risk of recurrence after a first idiopathic event of venous thromboembolism (VTE). Methods: Commercial D-dimer assays, evaluated according to predetermined cutoff levels for each assay, specific for age (lower in subjects {\textbackslash}textless70 years) and gender (lower in males), were used in the recent DULCIS study. The present analysis compared the results obtained in the DULCIS with those that might have been had using the following different cutoff criteria: traditional cutoff for VTE exclusion, higher levels in subjects aged ≥60 years, or age multiplied by 10. Results: In young subjects, the DULCIS low cutoff levels resulted in half the recurrent events that would have occurred using the other criteria. In elderly patients, the DULCIS results were similar to those calculated for the two age-adjusted criteria. The adoption of traditional VTE exclusion criteria would have led to positive results in the large majority of elderly subjects, without a significant reduction in the rate of recurrent event. Conclusion: The results confirm the usefulness of the cutoff levels used in DULCIS.},
	number = {1},
	journal = {International Journal of Laboratory Hematology},
	author = {Palareti, G. and Legnani, C. and Cosmi, B. and Antonucci, E. and Erba, N. and Poli, D. and Testa, S. and Tosetto, A.},
	year = {2016},
	pmid = {28199780},
	keywords = {Cutoff criteria, D-dimer, Recurrence, Venous thromboembolism},
	pages = {42--49}
}

@book{noauthor_nutrient_nodate,
	title = {Nutrient {Cycling} in {Lakes} and {Streams}: {Insights} from a {Comparative} {Analysis} on {JSTOR}},
	url = {http://www.jstor.org/stable/3658631?seq=1#page_scan_tab_contents},
	urldate = {2016-06-21}
}

@article{jorgensen_sulfide_2004,
	title = {Sulfide oxidation in marine sediments : {Geochemistry} meets microbiology},
	volume = {379},
	issn = {0072-1077},
	doi = {10.1130/0-8137-2379-5.63},
	abstract = {The main pathways of sulfide oxidation in marine sediments involve complex interactions of chemical reaction and microbial metabolism. Sulfi de becomes partly oxidized and bound by Fe(III), and the resulting iron-sulfur minerals are transport- ed toward the oxic sediment-water interface by bioturbating and irrigating fauna. Although oxygen is the main oxidant for pyrite or amorphous iron sulfi de, oxidation reactions may also take place with nitrate or manganese oxide. Intermediate oxida- tion products such as elemental sulfur or thiosulfate undergo disproportionation reactions and thereby provide shunts in the sedimentary sulfur cycle. Although of widespread occurrence, chemolithoautotrophic sulfi de oxidizing bacteria, such as Thiobacillus spp. or Thiomicrospira spp., appear to be of minor signifi cance relative to heterotrophic or mixotrophic sulfi de oxidizers of diverse phylogenetic lineages. As a unique group, the large sulfur bacteria of the genera Beggiatoa, Thioploca, and Thiomargarita have developed specialized modes of sulfi de oxidation using nitrate stored in intracellular vacuoles. By commuting between electron acceptor and donor, or by temporally bridging their occurrences in the environment through a great stor- age potential for both nitrate and elemental sulfur, these bacteria compete effi ciently with other microbial pathways of sulfi de oxidation. Dissimilatory nitrate reduction in these bacteria leads preferentially to ammonium rather than to dinitrogen, as in the denitrifying bacteria. Beggiatoa appears to be widely distributed in coastal sediments with a high organic load. In such sediments where Beggiatoa often occurs unnoticed in the anoxic, oxidized zone rather than growing as a visible mat on the sediment surface, dissimilatory nitrate reduction to ammonium may dominate over denitrification.},
	journal = {Geological Society of America Special Papers 2004},
	author = {Jørgensen, Bo Barker and Nelson, Douglas C},
	year = {2004},
	keywords = {j, 2004, and, and nelson, autotrophy, b, beggiatoa, bjoergen, c, chemo-, d, de, disproportionation, edwards, geochemistry meets microbiology, in amend, jørgensen, k, marine sediments, mpi-bremen, p, sulfate reduction, sulfi de oxidation in, sulfur bacteria, sulfur cycle},
	pages = {63--81}
}

@article{riget_baseline_1997,
	title = {Baseline {Levels} and {Natural} {Variability} of {Elements} in {Three} {Seaweed} {Species} from {West} {Greenland}},
	volume = {34},
	abstract = {Element levels in three seaweed species (Fucus vesiculo-sus, F. distichus and Ascophyllum nodosum) from different sampling sites in a West Greenland fjord system were determined during a three year period. The elements studied were Cd, Cu, Pb, Zn, Na, Ca, Sc, Cr, Fe, Co, As, Br, Rb, Sr, Cs and Ce. The variability of element concentrations showed a complicated pattern. Differences between both species and localities were found for most elements. Species differences were found to depend on the locality. In most cases where differences between seaweed species were found, concentrations were lower in A. nodosum than in F. vesiculosus which in turn were lower than in F. distichus. At the outer part of the fjord system concentrations of Na, Br and Cd were considerably higher than in the inner part while concentrations of Ca, Fe, Co, Ce, Sr, Sc and Cu were lower. Pb and Zn concentrations show no consistent geographical pattern. The results from a principal component analysis were difficult to interpret. The possible underlying factors controlling the variability of element concentrations are poorly understood. The influence of seawater on the fjord system and variations in run-off from rivers may account for a significant part of the variability seen for many elements. The concentra-tions of most of the elements, especially the heavy metals, were relatively low compared to other areas in Europe and North America.},
	number = {3},
	journal = {Marine Pollution Bulletin},
	author = {Riget, Frank and Johansen, Poul and Asmund, Gert},
	year = {1997},
	keywords = {baseline levels, brown seaweed, correla-tions, elements, variability, West Greenland},
	pages = {171--176}
}

@article{gillibrand_use_1997,
	title = {The use of simple models in the regulation of the impact of fish farms on water quality in {Scottish} sea lochs},
	volume = {159},
	author = {Gillibrand, P A},
	year = {1997},
	pages = {33--46}
}

@article{castro-gonzalez_first_2014,
	title = {The first report of a microdiverse anammox bacteria community in waters of {Colombian} {Pacific}, a transition area between prominent oxygen minimum zones of the eastern tropical {Pacific}},
	volume = {6},
	issn = {17582229},
	doi = {10.1111/1758-2229.12165},
	abstract = {Anaerobic ammonium oxidizers contribute to the removal of fixed nitrogen in oxygen-deficient marine ecosystems such as oxygen minimum zones (OMZ). Here we surveyed for the first time the occurrence and diversity of anammox bacteria in the Colombian Pacific, a transition area between the prominent South and North Pacific OMZs. Anammox bacteria were detected in the coastal and oceanic areas of the Colombian Pacific in low oxygen ({\textbackslash}textless 22 M), high nitrate (25–35 M) and low nitrite ({\textbackslash}textless 0.07 M), and ammonium ({\textbackslash}textless 1 M) waters. In these waters, anammox bacteria were rich [∼ 7 operational taxonomic units (OTUs), 98\% cut-off) and microdiverse (Shannon index H′ {\textbackslash}textless 1.24), in comparison with the observed at the prominent OMZ of the Eastern Tropical South Pacific, Arabian Sea and Black Sea. Anammox bacteria-like sequences from the Colombian Pacific were grouped together with sequences retrieved from the distinct OMZ's marine subclusters (Peru, Northern Chile and Arabian Sea) within Candidatus ‘Scalindua spp'. Moreover, some anammox bacteria OTUs shared a low similarity with environmental phylotypes (86–94\%). Our results indicated that a microdiverse anammox community inhabits the Colombian Pacific, generating new questions about the ecological and biogeochemical differences influencing its community structure.},
	number = {6},
	journal = {Environmental Microbiology Reports},
	author = {Castro-González, M. and Molina, V. and Rodríguez-Rubio, E. and Ulloa, O.},
	year = {2014},
	pmid = {25756112},
	pages = {595--604}
}

@article{kirstensen_organic_2000,
	title = {Organic matter diagenesis at the oxic/anoxic interfacein coastal marine sediments, with emphasis on the role of burrowing animals},
	number = {426},
	journal = {Hydrobiologia},
	author = {Kirstensen, E},
	year = {2000},
	keywords = {marine sediments, animala, bacteria, bioturbation, diagenesis, irrigation, oxic/anoxic interface, oxygen},
	pages = {1--24}
}

@book{noauthor_rosa_nodate,
	title = {La {Rosa} et al. 2004 {FISH} {FARM} {RECOVERY} {IMPACT} {BENTHIC}.pdf}
}

@article{nicholls_widespread_2009,
	title = {Widespread occurrence of the anammox reaction in estuarine sediments},
	volume = {55},
	doi = {10.3354/ame01285},
	number = {May},
	author = {Nicholls, Joanna C and Trimmer, Mark},
	year = {2009},
	keywords = {anammox, estuary, nitrate, organic carbon, permitted without, publisher, resale or republication not, sediment, written consent of the},
	pages = {105--113}
}

@book{noauthor_danovaro_nodate,
	title = {Danovaro et al. 2004 {MUSSEL} {CULTURE} {IMPACT} {SUSTAINABLE}.pdf}
}

@article{burkholder_complex_2006,
	title = {The {Complex} {Relationships} {Between} {Increases} in {Fertilization} of the {Earth}, {Coastal} {Eutrophication} and {Proliferation} of {Harmful} {Algal} {Blooms}},
	volume = {189},
	doi = {citeulike-article-id:7074734},
	journal = {Ecological Studies},
	author = {Burkholder, J M},
	year = {2006},
	pages = {241--254}
}

@article{schaller_bioturbation/bioirrigation_2014,
	title = {Bioturbation/bioirrigation by {Chironomus} plumosus as main factor controlling elemental remobilization from aquatic sediments?},
	volume = {107},
	issn = {18791298},
	url = {http://dx.doi.org/10.1016/j.chemosphere.2013.12.086},
	doi = {10.1016/j.chemosphere.2013.12.086},
	abstract = {Aquatic sediments represent a possibly significant sink of soluble inorganic elements/pollutants (metals, metalloids and rare earth elements) in ecosystems. Bioturbation/bioirrigation was shown to affect the remobilization of some elements where others seem to be unaffected. In view of these contrasting results, the effect of bioturbation/bioirrigation was examined using the invertebrate Chironomus plumosus in a laboratory experiment for a broad range (18) of elements. The experiments revealed an impact of invertebrate bioturbation/bioirrigation on elemental remobilization depending on chemical characteristics of the element ranging from strong influence to influence only at start when the larvae dig into the sediments. Three different types of remobilization were found: (i) element mobilization highly influenced by bioturbation/bioirrigation (DOC, N, Mg, Ca, Sr, Mo and U), (ii) strong element mobilization by bioturbation/bioirrigation at the start of the experiment when the larvae dig into the sediments and afterwards strong decrease, but to higher levels compared to values of treatments without invertebrate impact (Mn, Ni, As, Cd and Cs), and (iii) strong element mobilization by bioturbation/bioirrigation at start when the larvae dig into the sediments and afterwards strong decrease to levels found in treatments without invertebrate impact (Al, Fe, Co, Cu, Zn and Ce). During the experiment a distinct accumulation of most of the elements in C. plumosus was found, where they were not so much bound to the outer surface of C. plumosus but more within the gut system including food and feces. Hence, bioturbation/bioirrigation is certainly a main process controlling mobilization of elements from sediments. © 2014 Elsevier Ltd.},
	journal = {Chemosphere},
	author = {Schaller, Jörg},
	year = {2014},
	pmid = {24457053},
	keywords = {Nutrients, Bioaccumulation, DOC, Macrozoobenthos, Mining, Wetland},
	pages = {336--343}
}

@article{grall_marine_2002,
	title = {Marine eutrophication and benthos: {The} need for new approaches and concepts},
	volume = {8},
	issn = {13541013},
	doi = {10.1046/j.1365-2486.2002.00519.x},
	abstract = {In this review, using examples drawn from field observations or experimental studies, our goals are (i) to briefly summarize the major changes, in terms of species composition and functional structure, occurring in phyto and zoobenthic communities in relation to nutrient enrichment of the ecosystems; particular interest is given to the major abiotic and biotic factors occurring during the eutrophication process, (ii) to discuss the direct and indirect influences of benthic organisms on eutrophication and whether the latter can be controlled or favoured by benthos; most benthic species play a major role in the process of benthic nutrient regeneration, affecting primary production by supplying nutrients directly and enhancing rates of pelagic recycling; experimental studies have shown that the impact of benthic fauna on benthic-pelagic coupling and nutrient release is considerable. Thus, once the eutrophication process is engaged-that is, high organic matter sedimentation-it may be indirectly favoured by benthic organisms; benthos should always be considered in eutrophication studies, (iii) to evaluate the limits of our observations and data, highlighting the strong need for integrated studies leading to new concepts. Coastal ecosystems and benthic communities are potentially impacted by numerous human activities (demersal fishing, toxic contaminants, aquaculture...); in order to design strategies of ecosystem restoration or rehabilitation, we have to better understand coastal eutrophication and develop tools for quantifying the impacts; in order to achieve this goal, some possible directions proposed are: integrated studies leading to new concepts, model development based on these concepts and finally comparison of various ecosystems on a global scale.},
	number = {9},
	journal = {Global Change Biology},
	author = {Grall, Jacques and Chauvaud, Laurent},
	year = {2002},
	pmid = {2053},
	keywords = {Eutrophication, Benthos, Nutrients and carbon fluxes, Phytobenthos, Suspension feeders, Zoobenthos},
	pages = {813--830}
}

@article{trimmer_distribution_2011,
	title = {Distribution, activity, and ecology of anammox bacteria in acquatic environments},
	number = {ii},
	journal = {Nitrification},
	author = {Trimmer, M. and Engstrom, P},
	year = {2011},
	pages = {201--235}
}

@article{sorensen_comparison_1979,
	title = {A comparison of oxygen, nitrate, and sulfate respiration in coastal marine sediments},
	volume = {5},
	issn = {00953628},
	doi = {10.1007/BF02010501},
	abstract = {Aerobic respiration with oxygen and anaerobic respiration with nitrate (denitrification) and sulfate (sulfate reduction) were measured during winter and summer in two coastal marine sediments (Denmark). Both aerobic respiration and denitrification took place in the oxidized surface layer, whereas sulfate reduction was most significant in the deeper, reduced sediment. The low availability of nitrate apparently limited the activity of denitrification during summer to less than 0.2 mmoles NO 3 (-) m(-2) day(-1), whereas activities of 1.0-3.0 mmoles NO 3 (-) m(-2) day(-1) were measured during winter. Sulfate reduction, on the contrary, increased from 2.6-7.6 mmoles SO 4 (2-) m(-2) day(-1) during winter to 9.8-15.1 mmoles SO 4 (2-) m(-2) day(-1) during summer. The aerobic respiration was high during summer, 135-140 mmoles O2 m(-2) day(-1), as compared to estimated winter activities of about 30 mmoles O2 m(-2) day(-1). The little importance of denitrification relative to aerobic respiration and sulfate reduction is discussed in relation to the availability and distribution of oxygen, nitrate, and sulfate in the sediments and to the detritus mineralization.},
	number = {2},
	journal = {Microbial Ecology},
	author = {Sørensen, Jan and Jørgensen, Bo Barker and Revsbech, Niels Peter},
	year = {1979},
	pmid = {24232417},
	pages = {105--115}
}

@article{koutitonsky_box_2006,
	title = {A box model of carrying capacity for suspended mussel aquaculture in {Lagune} de la {Grande}-{Entr} ee ,},
	volume = {0},
	doi = {10.1016/j.ecolmodel.2006.07.026},
	author = {Koutitonsky, Vladimir and Dowd, Michael},
	year = {2006},
	pages = {193--206}
}

@article{vaquer-sunyer_sulfide_2010,
	title = {Sulfide exposure accelerates hypoxia-driven mortality},
	volume = {55},
	issn = {00243590},
	url = {http://doi.wiley.com/10.4319/lo.2010.55.3.1075},
	doi = {10.4319/lo.2010.55.3.1075},
	abstract = {The effect of the presence of sulfide on the survival of benthic organisms under hypoxia was tested using a meta-analysis of published experimental results evaluating the effects of the presence of hydrogen sulfide on the median survival time of benthic macrofauna under hypoxia. The meta-analysis confirmed that survival times under hypoxia are reduced by an average of 30\%in marine benthic communities exposed to hydrogen sulfide. The effect of sulfide on survival was higher for egg forms than for juvenile or adult stages. The aggravation of the negative effects of spreading hypoxia in the presence of sulfide suggests that the threats derived from hypoxia to marine biodiversity are greater than anticipated on the basis of the direct effects of low oxygen concentration alone.},
	number = {3},
	journal = {Limnology and Oceanography},
	author = {Vaquer-Sunyer, Raquel and Duarte, Carlos M.},
	year = {2010},
	pages = {1075--1082}
}

@book{noauthor_testa_nodate,
	title = {Testa et al. 2015 {MODEL} {OYSTER} {FLUXES}.pdf}
}

@article{love_life_1990,
	title = {Life {History} {Aspects} of 19 {Rockfish} {Species} ({Scorpaenidae}: {Sebastes}) from the {Southern} {California} {Bight}},
	abstract = {NOAA TECHNICAL REPORT NMFS \_ The major responsibilities of the National Marine Fisheries Service (NMFS) are to monitor and assess the abundance and geographic distribution of fishery resources, to understand and predict fluctuations in the quantity and distribution of these resources, and to establish levels for their optimum use. NMFS is also charged with the development and implementation of policies for managing national fishing grounds, development and enforcement of domestic fisheries regulations, surveillance of foreign fishing off United States coastal waters, and the development and enforcement of international fishery agreements and policies. NMFS also assists the fishing industry through marketing service and economic analysis programs, and mortgage insurance and vessel construction subsidies. It collects, analyzes, and publishes statistics on various phases of the industry.},
	author = {Love, Milton S and Morris, Pamela and Mccrae, Merritt and Collins, Robson},
	year = {1990}
}

@article{genkai-kato_regime_2007,
	title = {Regime shifts : catastrophic responses of ecosystems to human impacts},
	doi = {10.1007/s11284-006-0304-5},
	author = {Genkai-kato, Motomi},
	year = {2007},
	keywords = {{\textbackslash}a e, {\textbackslash}a e regime shift, ecosystem {\textbackslash}a e human impact, management {\textbackslash}a e mathematical model},
	pages = {214--219}
}

@article{anderson_harmful_2002,
	title = {Harmful algal blooms and eutrophication: {Nutrient} sources, composition, and consequences},
	volume = {25},
	issn = {01608347},
	doi = {10.1007/BF02804901},
	abstract = {Although algal blooms, including those considered toxic or harmful, can be natural phenomena, the nature of the global problenl of harnlful algal blooms (HABs) has expanded both in extent and its public perception over the last several decades. Of concern, especially for resource nlanagers, is the potential relationship between HABs and the accelerated eutrophication of coastal waters fronl hunlan activities. We address current insights into the relationships between HABs and eutrophication, focusing on sources of nutrients, known effects of nutrient loading and reduetion∼ new understanding of pathways of nutrient acquisition among HAB species∼ and relationships between nutrients and toxic algae. Through speeific∼ regional, and global examples of these various relationships, we offer both an assessment of the state of understanding∼ and the uncertainties that require future research efforts. The sources of nutrients poten- tially stimulating algal blooms include sewage, atmospheric deposition∼ groundwater flow, as well as agricultural and aquaculture runoff and discharge. On a global basis, strong correlations have been demonstrated between total phos- phorns inputs and phytoplankton production in freshwaters, and between total nitrogen input and phytoplankton pro- duction in estuarine and nlarine waters. There are also numerous examples in geographic regions ranging fronl the largest and second largest U.S. mainland estuaries (Chesapeake Bay and tile Albemarle-Panllico E.stuarine Systeln), to the Inland Sea of Japan∼ the Black Sea∼ and Chinese coastal waters, where increases in nutrient loading have been linked with the development of large biomass blooms, leading to anoxia and even toxic or harmful impacts on fisheries re- sources∼ ecosystems, and human health or recreation. Many of these regions have witnessed reductions in phytoplankton biomass (as chlorophyll a) or HAB incidence when nutrient controls were put in place. Shifts in species composition have often been attributed to changes in nutrient supply ratios∼ primarily N:P or N:Si. Recently this concept has been extended to include organic forms of nutrients, and an elevation in the ratio of dissolved organic carbon to dissolved organic nitrogen (DOC:DON) has been observed during several recent blooms. The physiological strategies by which different groups of species acquire their nutrients have become better understood, and alternate modes of nutrition such as heterotrophy and inLxotrophy are now recognized as common among HAB species. Despite our increased un- derstanding of the pathways by which nutrients are delivered to ecosystems and the pathways by which they are assimilated differentially by different groups of species∼ the relationships between nutrient delivery and the development of blooms and their potential toxicity or harmfulness remain poorly understood. Many factors such as algal species presence/ abundance, degree of flushing or water exchange∼ weather conditions∼ and presence and abundance of grazers contribute to the success of a given species at a given point in time. Similar nutrient loads do not have the same impact in different environments or in the same environment at different points in time. Eutrophication is one of several mechanisms by which harmful algae appear to be increasing in extent and duration in many locations. Although important, it is not the only explanation for blooms or toxic outbreaks. Nutrient enrichment has been strongly linked to stimulation of some harmful species, but for others it has not been an apparent contributing factor. The overall effect of nutrient over- enrichment on harmful algal species is clearly species specific.},
	number = {4},
	journal = {Estuaries},
	author = {Anderson, Donald M. and Glibert, Patricia M. and Burkholder, Joann M.},
	year = {2002},
	pmid = {18362973},
	pages = {704--726}
}

@article{smyth_assessing_2013,
	title = {Assessing {Nitrogen} {Dynamics} {Throughout} the {Estuarine} {Landscape}},
	volume = {36},
	issn = {15592723},
	doi = {10.1007/s12237-012-9554-3},
	abstract = {Assessing nitrogen dynamics in the estuarine landscape is challenging given the unique effects of individual habitats on nitrogen dynamics. We measured net N2 fluxes, sediment oxygen demand, and fluxes of ammonium and nitrate seasonally from five major estuarine habitats: salt marshes, seagrass beds (SAV), oyster reefs, and intertidal and subtidal flats. Net N2 fluxes ranged from 332 ± 116 μmol N-N2 m−2 h−1 from oyster reef sediments in the summer to −67 ± 4 μmol N-N2 m−2 h−1 from SAV in the winter. Oyster reef sediments had the highest rate of N2 production of all habitats. Dissimilatory nitrate reduction to ammonium (DNRA) was measured during the summer and winter. DNRA was low during the winter and ranged from 4.5 ± 3.0 in subtidal flats to 104 ± 34 μmol 15NH 4 + m−2 h−1 in oyster reefs during the summer. Annual denitrification, accounting for seasonal differences in inundation and light, ranged from 161.1 ± 19.2 mmol N-N2 m−2 year−1 for marsh sediments to 509.9 ± 122.7 mmol N-N2 m−2 year−1 for SAV sediments. Given the current habitat distribution in our study system, an estimated 28.3 × 106 mol of N are removed per year or 76 \% of estimated watershed nitrogen load. These results indicate that changes in the area and distribution of habitats in the estuarine landscape will impact ecosystem function and services.},
	number = {1},
	journal = {Estuaries and Coasts},
	author = {Smyth, Ashley R. and Thompson, Suzanne P. and Siporin, Kaylyn N. and Gardner, Wayne S. and McCarthy, Mark J. and Piehler, Michael F.},
	year = {2013},
	keywords = {Denitrification, Dissimilatory nitrate reduction to ammonium (DNRA), Marsh, Oyster reef, Seagrass},
	pages = {44--55}
}

@article{himmelman_foods_1971,
	title = {Foods and predators of the green sea urchin {Strongylocentrotus} droebachiensis in {Newfoundland} waters* **},
	volume = {9},
	abstract = {Gut analyses of the green sea urchin Strongylocentrotu8 droebachiensis (O. F. MUELLER) demonstrated that perennial phaeophytes, mostly fucoids and Alaria esculenta, were predo-minant in the diet. Ephemeral species, coralline algae and animals, were consumed in smaller amounts when available. Grazing by the urchins is evidently responsible for the dearth of non-coralline sublittoral algae in Newfoundland waters. Lobsters, rock crabs, purple sea stars, other urchins, and a variety of fishes and birds feed on S. droebachiensis, but pre-dation is apparently not effective in limiting the abundance of the urchin.},
	journal = {Marine Biology},
	author = {Himmelman, JH and Steele, D H},
	year = {1971},
	pages = {315--322}
}

@article{ward_processes_2011,
	title = {Processes, ecology, and ecosystems},
	journal = {Nitrification},
	author = {Ward, Bess B.},
	year = {2011},
	pages = {325--345}
}

@article{love_severe_1998,
	title = {A {SEVERE} {DECLINE} {IN} {THE} {COMMERCIAL} {PASSENGER} {FISHING} {VESSEL} {ROCKFISH} ({SEBASTES} {SPP}.) {CATCH} {IN} {THE} {SOUTHERN} {CALIFORNIA} {BIGHT}, 1980-1996},
	volume = {39},
	abstract = {We analyzed data from the Marine Recreational Fishery Statistics Survey (MRFSS) to examine long-term trends in the Southern California Bight commercial pas-senger fishing vessel rockfish fishery. From 1980 to 1996 a total of 50 species were taken. There was a substantial decline in the overall catch per unit of effort (CPUE) during that time. For individual species we observed four general tem-poral patterns: (1) a steady decline throughout the period; (2) high CPUE from 1983 to 1986; (3) variable catches throughout the 1980s but extremely low catches from 1993 to 1996; and (4) variable catches through-out the entire period. Among the several species with particularly large declines were bocaccio (98.7\%), blue rockfish (95.2\%), and olive rockfish (83.0\%)). Three species that were abundant in 1980 were absent by 1996 (chilipepper, swordspine, and yellowtail rockfishes). The number of species caught also decreased during the course of the survey. We analyzed length frequencies for a subset of the species. O n average, mean total length declined. This decline was due mainly to the removal of the larger size classes rather than to increased catches of juveniles. An extreme example was observed for vermilion rock-fish: over the course of the survey, the fishery changed from one comprising primarily adults to almost en-tirely juveniles. We conclude that the declines in rockfish catches in the Southern California Bight between 1980 and 1996 reflect reduced populations. These population declines probably result from poor long-term juvede recruitment, caused by adverse oceanographic conditions, as well as from essentially unregulated overfishing of adults and subadults, perhaps leading to recruitment overfishing.},
	journal = {CalCOFl Rep},
	author = {Love, Milton S and Caselle, Jennifer E and Buskirk, Wade Van},
	year = {1998},
	pages = {1980--96}
}

@article{an_enhancement_2001,
	title = {Enhancement of coupled nitrification-denitrification by benthic photosynthesis in shallow estuarine sediments},
	volume = {46},
	issn = {00243590},
	doi = {10.4319/lo.2001.46.1.0062},
	abstract = {Net sediment-water interface fluxes of oxygen, dinitrogen, and dissolved inorganic carbon and nitrogen were determined in shallow, subtidal estuarine sediments (Galveston Bay, Texas) using in situ benthic chamber incubations. Diel variability in the sediment oxygen demand and in the flux of dinitrogen were attributable to the occurrence of benthic photosynthesis. Daytime denitrification rates exceeded nighttime rates. During daytime chamber incubations, small changes in dissolved oxygen concentration were observed. At night, oxygen concentrations decreased, as consumption reactions dominated the oxygen flux. Oxygen production by benthic microalgae enhanced rates of, and coupling between, nitrification and denitrification when ammonium was not limiting, resulting in significant loss of nitrogen from sediments as dinitrogen gas. A transient three box model was used to assess the effect of benthic primary production on sediment nitrogen cycling. Model results demonstrate increased rates of nitrification and denitrification in the presence of benthic photosynthesis and agree well with observed patterns of dissolved dinitrogen- and oxygen-flux data obtained during benthic chamber incubations. When no photosynthesis was permitted during the model runs, rates of nitrification and denitrification decreased significantly. Together, our results suggest that denitrification estimates for shallow estuaries could be underestimated if the influence of benthic primary production on denitrification is not considered.},
	number = {1},
	journal = {Limnology and Oceanography},
	author = {An, Soonmo and Joye, Samantha B.},
	year = {2001},
	pages = {62--74}
}

@article{macfarlane_survey_1952,
	title = {A {SURVEY} {OF} {CERTAIN} {SEAWEEDS} {OF} {COMMERCIAL} {IMPORTANCE} {IN} {SOUTHWEST} {NOVA} {SCOTIA}1},
	abstract = {Tlie No\${\textbackslash}backslash\$-a Scotia Research Foundation is making an extensive survey of sea-weeds of the Province that are of potential com∼aercial importance. 'fhe area in which the survey lmas been completed extends from Cape Sable Island, Shelburne County to Chebogue, Yarmouth County, and includes also a s∼nall part of Digby County. The survey includes both quantitative measurcnients anci biological studies of fucoicls, Lawranaria spp.. and Clzondrus, in a11 of which the region abounds. Clf 325 miles of coastline wrveyed for rockweecl, 140 miles are harvestable, bearing approximately 200,000 tons. Results obtained a t 255 stations, examined in detail, showecI the average density to be 37 lb. per sq. yd. The width of time zonc is from 2 to 300 yd., the average being 50 yd. Ascofihy.J.J.ltnr ?zodosunz fornms the greatest percentage of rockweed, Fucus ve.sicdo.sus ranking next. Fuc-us serruius is recordetl for the first time in this part of the Province. Larazinarz'a beds totalling 12,008 ac. in extent and bearing 900,000 tons wert. clnarted. Allortality among Lanzirraria sporophytes is high and the number ira a bed varies from year to year. In 1950 7,997,739 It). of Clzondrus were harvesteci. Density varies from 1 to 24 Ib. per sq. ft. Clzondrus bcds are listed and theit. ecology discussed. Recolonization of denuded areas is described and successiorl of alga1 cover noted on denuded areas and on concrete tdocks placed in Clzoudruc and Laminnricz beds. The survey region is compared with regions survc.∼,e(l in Scotinncl. A map of the survey region is included.},
	author = {MacFarlane, Constance},
	year = {1952}
}

@article{ritz_response_1989,
	title = {Response to organic enrichment of infaunal macrobenthic communities under salmonid seacages},
	volume = {103},
	issn = {00253162},
	doi = {10.1007/BF00543349},
	abstract = {The response of infaunal macrobenthic communities beneath salmonid seacages to solid organic wastes (food pellets and fish excreta) was tested by means of the ABC-method (abundance, biomass comparison method: Warwick 1986) on samples collected from the SAFCOL seafarm at Badger Cove, southeast Tasmania, from February to July 1988. The intermittent nature of the addition of organic waste allowed us to monitor decline and recovery of the macrofauna, i.e., harvesting of a cage permitted a period of recovery whilst restocking precipitated a decline. The ABC-method proved to be a sensitive indicator of community health. Under a normal feeding regime the macrofaunal community structure indicated a moderately disturbed condition. Only 7 wk after the cage was harvested, species richness had increased markedly and the community adopted an undisturbed condition. Further improvement was apparent 14 wk post-harvest. Similarly, a decline to a moderately disturbed condition was apparent 7 wk after restocking and species richness had declined. No such changes occurred under a cage which contained fish continuously over the same period.},
	number = {2},
	journal = {Marine Biology},
	author = {Ritz, D. A. and Lewis, M. E. and Shen, Ma},
	year = {1989},
	pages = {211--214}
}

@article{rajendran_spatial_2001,
	title = {Spatial and temporal variations of sediment quality in and around fish cage farms: {A} case study of aquaculture in the {Seto} {Inland} {Sea}, {Japan}},
	volume = {67},
	doi = {10.1046/j.1444-2906.2001.00298.x},
	number = {4},
	journal = {Fisheries Science},
	author = {Rajendran, Vaishali Pawar; Osamu Matsuda; Tamiji Yamamoto; Toshiya Hashimoto; Narasimmalu},
	year = {2001},
	keywords = {aquaculture, sediment, sustainability},
	pages = {619--627}
}

@book{noauthor_capone_nodate,
	title = {Capone 2001 {N} {Fixation} {COMMENTARY}.pdf}
}

@article{seitzinger_denitrification_2006,
	title = {Denitrification across landscaes and waterscapes: a synthesis},
	volume = {16},
	issn = {10510761},
	doi = {10.1890/1051-0761(2006)016[2064:DALAWA]2.0.CO;2},
	number = {6},
	journal = {Ecological Applications},
	author = {Seitzinger, S and Harrison, JA and Bohlke, JK and Bouwman, AF and Lowrance, R and Peterson, B and Tobias, C and Van Drecht, G},
	year = {2006},
	pmid = {17205890},
	keywords = {continental shelf, denitrification, estuaries, lakes, nitrogen, oxygen minimum zones, rivers},
	pages = {2064--2090}
}

@article{kepkay_p.e._glen_harrison_w._and_bugden_ecosystem_2005,
	title = {Ecosystem indicators of water quality {Part} {I}. {Oxygen} production and oxygen demand},
	volume = {5},
	doi = {10.1007/b136005},
	number = {July},
	journal = {Environmental Chemistry},
	author = {Kepkay, P.E., Glen Harrison, W., {and} Bugden, J.B.C.},
	year = {2005},
	pages = {83--97}
}

@book{noauthor_hargrave_nodate,
	title = {Hargrave et al. 1997 {Benthic} impacts {OM} enrichment marine aquaculture.pdf}
}

@article{christian_nutrient_2000,
	title = {nutrient and oxygen fluxes during a spring phyto-},
	number = {1984},
	author = {Christian, G and Cloern, James E and Hager, Stephen W and Cole, Brian E},
	year = {2000},
	keywords = {estuaries, benthic fluxes, h g, nutrient c y c, pelagic-benthic coupling, san francisco}
}

@article{hansen_seasonal_1981,
	title = {Seasonal distribution of nitrifying bacteria and rates of nitrification in coastal marine sediments},
	volume = {7},
	issn = {00953628},
	doi = {10.1007/BF02341424},
	abstract = {The distribution of nitrification potential (NP) with depth in sediment and season was investigated in a shallow sandy sediment (0.5 m water) and a deeper muddy sediment (17m water). In both sediments, nitrifying bacteria were present in the anoxic strata (oxygen penetration was 5 mm below the surface). The NP at 6-8 cm depth in the sediment was 50\% and 10\% of the surface NP at the sandy and muddy sediment, respectively. It is suggested that bioturbation and physical disturbance of the sediment were the most likely reasons for this distribution. The NP increased as sediment temperature decreased. This effect was less marked in the muddy sediment. It is concluded that during the summer, the numbers or specific activity of nitrifying bacteria diminished for the following reasons: There was decreased O2 penetration into the sediment and increased competition for O2 by heterotrophs; there was increased competition for NH4 (+) and there was inhibition by H2S. These effects counteracted the potentially higher growth rates and increased rates of NH4 (+) production at the elevated summer temperatures. The potential nitrification rates in the upper 1 cm, which were measured at 22°C, were converted to calculated rates at the in situ temperature (Q10=2.5) and in situ oxygen penetration. These calculated rates were shown to closely resemble the measured in situ rates of nitrification. The relationship between the in situ rates of nitrification and the nitrification potential is discussed.},
	number = {4},
	journal = {Microbial Ecology},
	author = {Hansen, Jette I. and Henriksen, Kaj and Blackburn, T. Henry},
	year = {1981},
	pmid = {24227545},
	pages = {297--304}
}

@article{borja_assessing_2009,
	title = {Assessing the suitability of a range of benthic indices in the evaluation of environmental impact of fi n and shell fi sh aquaculture located in sites across {Europe}},
	volume = {293},
	issn = {0044-8486},
	url = {http://dx.doi.org/10.1016/j.aquaculture.2009.04.037},
	doi = {10.1016/j.aquaculture.2009.04.037},
	number = {3-4},
	journal = {Aquaculture},
	author = {Borja, Ángel and Rodríguez, J Germán and Black, Kenny and Bodoy, Alain and Emblow, Chris and Fernandes, Teresa F and Forte, Janez and Karakassis, Ioannis and Muxika, Iñigo and Nickell, Thom D and Papageorgiou, Nafsika and Pranovi, Fabio and Sevastou, Katerina and Tomassetti, Paolo and Angel, Dror},
	year = {2009},
	pages = {231--240}
}

@article{trimmer_biphasic_2005,
	title = {Biphasic {Behavior} of {Anammox} {Regulated} by {Nitrite} and {Nitrate} in an {Estuarine} {Sediment} {Biphasic} {Behavior} of {Anammox} {Regulated} by {Nitrite} and {Nitrate} in an {Estuarine} {Sediment}},
	volume = {71},
	doi = {10.1128/AEM.71.4.1923},
	number = {4},
	journal = {Society},
	author = {Trimmer, Mark and Nicholls, Joanna C and Morley, Nicholas and Davies, Christian a and Aldridge, John},
	year = {2005},
	pages = {1923--1930}
}

@book{noauthor_perreira_nodate,
	title = {Perreira et al. 2004 {LOCH} {CRERAN} {RECOVERY}.pdf}
}

@article{brandes_new_2007-1,
	title = {New developments in the marine nitrogen cycle},
	volume = {107},
	issn = {00092665},
	doi = {10.1021/cr050377t},
	abstract = {ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.},
	number = {2},
	journal = {Chemical Reviews},
	author = {Brandes, Jay A. and Devol, Allan H. and Deutsch, Curtis},
	year = {2007},
	pmid = {17300141},
	pages = {577--589}
}

@article{cornwell_denitrification_1999,
	title = {Denitrification in coastal ecosystems: {Methods}, environmental controls, and ecosystem level controls, a review},
	volume = {33},
	issn = {13862588},
	doi = {10.1023/A:1009921414151},
	abstract = {In this review of sediment denitrification in estuaries and coastal ecosystems, we examine current denitrification measurement methodologies and the dominant biogeochemical controls on denitrification rates in coastal sedi- ments. Integrated estimates of denitrification in coastal ecosystems are confounded bymethodological difficulties, a lack of systematic understanding of the effects of changing environmental conditions, and inadequate attention to spatial and temporal variability to provide both seasonal and annual rates. Recent improvements in measurement techniques involving 15N techniques and direct N2 concentration changes appear to provide realistic rates of sed- iment denitrification. Controlling factors in coastal systems include concentrations of water column NO− 3 , overall rates of sediment carbon metabolism, overlying water oxygen concentrations, the depth of oxygen penetration, and the presence/absence of aquatic vegetation and macrofauna. In systems experiencing environmental change, either degradation or improvement, the importance of denitrification can change. With the eutrophication of the Chesapeake Bay, the overall rates of denitrification relative to N loading terms have decreased, with factors such as loss of benthic habitat via anoxia and loss of submerged aquatic vegetation driving such effects.},
	number = {1},
	journal = {Aquatic Ecology},
	author = {Cornwell, Jeffrey C. and Kemp, W. Michael and Kana, Todd M.},
	year = {1999},
	pmid = {1284},
	keywords = {Nitrogen, Denitrification, Eutrophication, Estuary, Sediment-water exchange},
	pages = {41--54}
}

@book{noauthor_wang_nodate,
	title = {Wang et al. 2009 {PHYTOPLANKTON} {AQUACULTURE} {COMM}.pdf}
}

@article{banchuen_microcosm-based_2002,
	title = {A {Microcosm}-{Based} {Investigation} into {Oxidized} {Nitrogen} {Removal} in the {Hypolimnetic} {Waters} of the {Occoquan} {Reservoir} of {Northern} {Virginia}},
	issn = {1098-6596},
	doi = {10.1017/CBO9781107415324.004},
	abstract = {Oxidation-reduction reactions are very important in natural water systems. In fact, all aquatic organisms obtain their energy for metabolic processes from redox reactions. Photosynthetic organisms catalytically reduce carbon dioxide to reduced organic matter by trapping light energy, while nonphotosynthetic organisms catalytically decompose the organic products of photosynthesis through energy-yielding redox reactions. Nitrogen, which is one of the major elements in the terrestrial and aquatic environments, circulates by many microbially catalyzed redox reactions. In fact, the only non-redox process in the entire nitrogen cycle is ammonia integration with and liberation from nitrogen-containing organic matter. The movements of many other elements also involve redox reactions, such as carbon, iron, and sulfur (Snoeyink, 1996). Redox potentials (E), like free energy (G), are not absolute. The former are measured with reference to the reduction of hydrogen ions to hydrogen gas at standard state conditions: 25 degrees Celsius (°C), 1 atmospheric pressure, and one unit activity for all species. The potential of this reaction, by convention, is taken as zero. Furthermore, redox potentials are comprised of two parts: the oxidation potential, and the reduction potential. The potential of the overall reaction at the standard state can be shown by the following equation (Snoeyink, 1996): E o = E o ox + E o red Eq. 2-1 where E o ox and E o red are oxidation half reaction and reduction half reaction, respectively. For nonstandard states, the redox potential (E) may be related to standard potential by the Nernst equation (Snoeyink, 1996): E = E o – RT/nF ln Q Eq. 2-2 where R = gas constant T = absolute temperature, o K n = number of electrons involved in the reaction F = the Faraday number Q = the reaction quotient 2 -10},
	journal = {Virginia Tech's Electronic Theses and Dissertations},
	author = {Banchuen, T},
	year = {2002},
	pmid = {25246403},
	pages = {10--36}
}

@article{hargrave_assessing_2005,
	title = {Assessing and {Managing} {Environmental} {Risks} {Associated} with {Marine} {Finfish} {Aquaculture}},
	volume = {5M},
	url = {http://dx.doi.org/10.1007/b136021},
	doi = {10.1007/b136021},
	abstract = {Environmental Risk Analysis (ERA) consisting of risk assessment, management and communication can be applied to assess ecological and environmental changes associated with industrial-scale marine finfish aquaculture development. Physical, chemical, and biological variables are identified that may be used to detect thresholds for changes in ecosystem structure and function in order to apply ERA. Changes due to predictable or unpredictable effects may be local or far field. Predictable effects such as reduced dissolved oxygen, increased nutrients and organic matter, or lower diversity of benthic fauna in the vicinity of net-pens can be modeled to quantify local impacts on water column and sediment variables. Far-field and long-term risks such as interactions of escapees with natural stocks and effects of fishing to obtain food for cultured fish are more difficult to predict and quantify. Despite this, scoring methods using single or multiple indicators may be applied to determine the degree of risk associated with all identified potentially negative effects. ERA should be part of an integrated planning approach where aquaculture development occurs within a broad framework to include all development and user groups within the coastal zone. Environmental observations and models can then be combined with effective aquaculture husbandry practices to manage environmental risks from all sources.},
	number = {July},
	journal = {Environmental Effects of Marine Finfish Aquaculture},
	author = {Hargrave, Barry and Silvert, William and Keizer, Paul},
	year = {2005},
	keywords = {Earth and Environmental Science},
	pages = {433--461}
}

@article{page_dissolved_2005,
	title = {Dissolved {Oxygen} and {Salmon} {Cage} {Culture} in the {Southwestern} {New} {Brunswick} {Portion} of the {Bay} of {Fundy}},
	volume = {5},
	doi = {10.1007/b136002},
	abstract = {Information on the spatial and temporal characteristics of ambient dissolved oxygen in the southwestern New Brunswick area of the Bay of Fundy is presented to help develop an understanding of dynamics of oxygen and salmon cage culture in the region. Some modelling efforts focussed on dissolved oxygen issues associated with fish farming in the area are also presented. A description and application of a simple oxy-gen depletion index is proposed to help identify the influence of salmon cage culture on the regional and farm-scale dissolved oxygen concentrations. The chapter concludes with a brief summary and discussion of observations and model development required to enhance the understanding of oxygen dynamics in the farms and bays of southwestern New Brunswick. The knowledge can be used by industry in their farm management prac-tices and by environmental regulators in their efforts to define and sustain water quality standards.},
	number = {July},
	journal = {Hdb Env Chem},
	author = {Page, F H and Losier, · R and Mccurdy, · P and Greenberg, · D and Chaffey, · J and Chang, · B},
	year = {2005},
	pages = {1--28}
}

@article{herbert_nitrogen_1999,
	title = {Nitrogen cycling in coastal marine ecosystems},
	volume = {23},
	issn = {1574-6976},
	url = {http://femsre.oxfordjournals.org/content/23/5/563.abstract},
	doi = {10.1111/j.1574-6976.1999.tb00414.x},
	abstract = {It is generally considered that nitrogen availability is one of the major factors regulating primary production in temperate coastal marine environments. Coastal regions often receive large anthropogenic inputs of nitrogen that cause eutrophication. The impact of these nitrogen additions has a profound effect in estuaries and coastal lagoons where water exchange is limited. Such increased nutrient loading promotes the growth of phytoplankton and fast growing pelagic macroalgae while rooted plants (sea-grasses) and benthic are suppressed due to reduced light availability. This shift from benthic to pelagic primary production introduces large diurnal variations in oxygen concentrations in the water column. In addition oxygen consumption in the surface sediments increases due to the deposition of readily degradable biomass. In this review the physico-chemical and biological factors regulating nitrogen cycling in coastal marine ecosystems are considered in relation to developing effective management programmes to rehabilitate seagrass communities in lagoons currently dominated by pelagic macroalgae and/or cyanobacteria.},
	number = {5},
	journal = {FEMS Microbiology Reviews},
	author = {Herbert, R.A.},
	year = {1999},
	pmid = {10525167},
	keywords = {Bacteria, Bacteria: metabolism, Cyanobacteria, Cyanobacteria: metabolism, Nitrogen Fixation, Nitrogen Fixation: physiology, Seawater, Soil Microbiology},
	pages = {563--590}
}

@article{jensen_denitrification_1988,
	title = {Denitrification in coastal bay sediment: regional and seasonal variation in {Aarhus} {Bight}, {Denmark}},
	volume = {48},
	issn = {0171-8630},
	doi = {10.3354/meps048155},
	abstract = {The seasonal pattern of denitnfication achmty was studied in sediment from 3 stalons in the Aarhus Bight, Denmark At all 3 stations, a dramahc increase In den∼trificat∼on activity was found in early spnng coincident wlth sedimentation of the spring phytoplankton bloom The maximum of activity was followed by decllnlng rates in the early summer and low and relatively constant rates throughout the rest of the year For the 3 sedlments the total range of denltrlfication actlvity was {\textbackslash}textless0 05 to 0 5, 0 05 to 0 7 and 0 2 to 1 0 mm01 N m-' d-', respectively, and the total annual activity 35 70 and 180 mm01 N yr stations, throughout the year highest activlt∼es were observed in the most organic-nch sediment and lowest were observed in the relatively organic-poor sediment Results ∼ndicate that annual denitnflca- bon may increase in response to hlgher nutnent load and primary ploduction in the coastal sea '},
	number = {May},
	journal = {Marine Ecology Progress Series},
	author = {Jensen, Mh and Andersen, Tk and Sørensen, J},
	year = {1988},
	pages = {155--162}
}

@article{sorensen_capacity_1978,
	title = {Capacity for denitrificaiton and reduction of nitrate to {Ammonia} in a coastal marine sediment.},
	volume = {35},
	number = {2},
	journal = {Appl. Environ. Micriobiol.},
	author = {Sorensen, J},
	year = {1978},
	pages = {301--305}
}

@article{jones_society_1996,
	title = {Society for {American} {Archaeology} {Mortars}, {Pestles}, and {Division} of {Labor} in {Prehistoric} {California}: {A} {View} from {Big} {Sur}},
	volume = {61},
	url = {http://www.jstor.org http://www.jstor.org/stable/282420 http://www.jstor.org/page/},
	abstract = {JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org. This content downloaded from 129.173.72.87 on Mon, 18 Jan 2016 23:47:22 UTC All use subject to JSTOR Terms and Conditions},
	number = {2},
	journal = {Source: American Antiquity},
	author = {Jones, Terry L},
	year = {1996},
	pages = {243--264}
}

@book{noauthor_stucchi_nodate,
	title = {Stucchi et al. 2005 {SALMON} {WASTE} {DEPOSITION} {MODEL}.pdf}
}

@article{kiemer_effects_1995,
	title = {The effects of chronic and acute exposure to hydrogen sulphide on {Atlantic} salmon ({Salmo} salar {L}.)},
	volume = {135},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/0044848695010254},
	doi = {10.1016/0044-8486(95)01025-4},
	abstract = {In separate experiments, Atlantic salmon smolts (Salmo salar L.) were exposed to two different regimes of hydrogen sulphide. In the first experiment, fish were exposed to chronic, periodic but sublethal levels of hydrogen sulphide (maximally 7.8 μM) over a period of 18 weeks. Regular gill and liver samples were taken and growth determined relative to a control group. The difference in growth rate between treated and control fish was small. Gill damage (clubbing, thickening of the secondary lamellae) peaked between 6 and 8 weeks after initial exposure. Subsequently there was evidence of an adaptive response such that after 16 weeks, gill tissues from exposed fish appeared healthy and normal. Liver damage was progressive. By Week 10 more than 50\% of livers examined showed diffuse hepatic necrosis and diffuse vacuolar degeneration which increased to 80\% by Week 18. In the second experiment, salmon were exposed to one, single, acute but sub-lethal dose (22 μM or 29 μM) of hydrogen sulphide over 20 min. The effect on gills, livers and lactate dehydrogenase (LDH) activity was monitored over 14 days. For both concentrations, three salmon were sampled immediately, 1, 2, 3, 4, 6, 8, 10, 12 and 14 days after treatment. Gill tissues showed fusion of the secondary lamellae and thickening of the primary lamellae. Liver damage became evident 3 days after exposure. LDH activity was elevated compared to control for 4 days after exposure.},
	number = {4},
	journal = {Aquaculture},
	author = {Kiemer, Marius C.B. and Black, Kenneth D. and Lussot, David and Bullock, Alistair M. and Ezzi, Ivan},
	year = {1995},
	keywords = {Gill, Hydrogen sulphide, Liver, Salmo salar},
	pages = {311--327}
}

@article{lehrter_sediment-water_2012,
	title = {Sediment-water fluxes of dissolved inorganic carbon, {O} 2, nutrients, and {N} 2 from the hypoxic region of the {Louisiana} continental shelf},
	volume = {109},
	issn = {01682563},
	doi = {10.1007/s10533-011-9623-x},
	abstract = {Globally, hypoxic areas ({\textbackslash}textless63 mmol O 2 m -3) in coastal waters are increasing in number and spatial extent. One of the largest coastal hypoxic regions has been observed during the summer in the bottom-water of the Louisiana continental shelf. The shelf receives the sediments, organic matter, and nutrients exported from the Mississippi River watershed, and much of this material is ultimately deposited to the sea floor. Hence, quantifying the rates of sediment-water dissolved inorganic carbon (DIC), oxygen (O 2), and nutrient fluxes is important for understanding how these processes relate to the development and maintenance of hypoxia. In this study, the sediment-water fluxes of DIC, O 2, nutrients, and N 2 (denitrification) were measured on the Louisiana shelf during six cruises from 2005 to 2007. On each cruise, three to four sites were occupied in or directly adjacent to the region of the shelf that experiences hypoxia. DIC fluxes, a proxy for total sediment respiration, ranged from 7.9 to 21.4 mmol m -2 day -1 but did not vary significantly either spatially or as a function of bottom-water O 2 concentration. Overall, sediment respiration and nutrient flux rates were small in comparison to water-column respiration and phytoplankton nutrient demand. Nitrate fluxes were correlated with bottom-water O 2 concentrations (r = 0.69), and there was evidence that decreasing O 2 concentrations inhibited coupled nitrification-denitrification. Denitrification rates averaged 1.4 mmol N m -2 day -1. Scaled to the area of the shelf, the denitrification sink represented approximately 39\% of the N load from the Mississippi River watershed. The sediment-water fluxes reported from this study add substantial information on the spatial and temporal patterns in carbon, O 2, and nutrient cycling available for the Louisiana continental shelf and, thus, improve the understanding of this system. © 2011 Society of Wetland Scientists (outside the USA).},
	number = {1-3},
	journal = {Biogeochemistry},
	author = {Lehrter, John C. and Beddick, David L. and Devereux, Richard and Yates, Diane F. and Murrell, Michael C.},
	year = {2012},
	keywords = {Denitrification, Hypoxia, LOUISIANA shelf, O 2 and nutrient flux, Sediment-water DIC},
	pages = {233--252}
}

@article{amirkolaie_reduction_2011,
	title = {Reduction in the environmental impact of waste discharged by fish farms through feed and feeding},
	volume = {3},
	issn = {17535123},
	doi = {10.1111/j.1753-5131.2010.01040.x},
	abstract = {The discharge of waste from aquaculture operations can lead to eutrophication and destruction of natural ecosystem in receiving water body. A controlled waste production strategy is necessary to maintain sustainable aquaculture growth into the future. As feed is the major source of waste in aquaculture, the management of aquaculture waste should be approached through diet formulation or feeding strategies. Highly digestible diets have been introduced as a solution to reduce solid waste excretion. Further reductions in solid waste can be achieved through careful selection of feed ingredients and feed processing to improve nutrient availability. An increase in faeces consistency by diet manipulation can improve solid removal efficiency. This condition can reduce the proportion of solids in discharged water in the effluent and also improve farm water quality. A reduction in dissolved nitrogen waste can be achieved by ensuring a balance between protein and energy causing fish to use non-protein sources as energy. Phosphorous waste can be decreased through careful ingredient selection and proper processing to improve digestibility. A proper feed ration and feeding method for each species should be adopted because feed waste constitutes a large part of waste production. © 2011 Blackwell Publishing Asia Pty Ltd. Source: scopus},
	number = {1},
	journal = {Reviews in Aquaculture},
	author = {Amirkolaie, Abdolsamad K.},
	year = {2011},
	keywords = {Aquaculture, Dissolved waste, Environment, Feeding method, Solid waste},
	pages = {19--26}
}

@article{thamdrup_new_2012,
	title = {New {Pathways} and {Processes} in the {Global} {Nitrogen} {Cycle}},
	volume = {43},
	issn = {1543-592X},
	doi = {10.1146/annurev-ecolsys-102710-145048},
	abstract = {Our understanding of the players and pathways of the global nitrogen cycle has advanced substantially over recent years with discoveries of several new groups of organisms and new types of metabolism. This review focuses on recently discovered processes that add new functionality to the nitrogen cycle and on the organisms that perform these functions. The processes include denitrification and other dissimilatory nitrogen transformations in eukaryotes, anaerobic ammonium oxidation, and anaerobic methane oxidation with nitrite. Of these, anaerobic ammonium oxidation coupled to nitrite reduction by anammox bacteria has been well documented in natural environments and constitutes an important sink for fixed nitrogen. Benthic foraminifera also contribute substantially to denitrification in some sediments, in what potentially represents an ancestral eukaryotic metabolism. The ecophysiology of the novel organisms and their interactions with classical types of nitrogen metabolism are important for understanding the nitrogen cycle and its tight links to the cycling of carbon today, in the past, and in the future.},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	author = {Thamdrup, B},
	year = {2012},
	pmid = {16890280},
	keywords = {bacteria, anammox, nitrate, denitrification, ammonium oxidation, anaerobic ammonium oxidation, eukaryotes, fluidized-bed reactor, fresh-water lake, fungus, fusarium-oxysporum, marine-sediments, methane oxidation, nitrite reductase, nitrogen loss, oceanic fixed nitrogen, oxygen minimum zone, reduction},
	pages = {407--428}
}

@article{howarth_coupled_2011,
	title = {Coupled biogeochemical cycles: {Eutrophication} and hypoxia in temperate estuaries and coastal marine ecosystems},
	volume = {9},
	issn = {15409295},
	doi = {10.1890/100008},
	abstract = {Nutrient fluxes to coastal areas have risen in recent decades, leading to widespread hypoxia and other ecological damage, particularly from nitrogen (N). Several factors make N more limiting in estuaries and coastal waters than in lakes: desorption (release) of phosphorus (P) bound to clay as salinity increases, lack of planktonic N fixation in most coastal ecosystems, and flux of relatively P-rich, N-poor waters from coastal oceans into estuaries. During eutrophication, biogeochemical feedbacks further increase the supply of N and P, but decrease availability of silica - conditions that can favor the formation and persistence of harmful algal blooms. Given sufficient N inputs, estuaries and coastal marine ecosystems can be driven to P limitation. This switch contributes to greater far-field N pollution; that is, the N moves further and contributes to eutrophication at greater distances. The physical oceanography (extent of stratification, residence time, and so forth) of coastal systems determines their sensitivity to hypoxia, and recent changes in physics have made some ecosystems more sensitive to hypoxia. Coastal hypoxia contributes to ocean acidification, which harms calcifying organisms such as mollusks and some crustaceans.},
	number = {1},
	journal = {Frontiers in Ecology and the Environment},
	author = {Howarth, Robert and Chan, Francis and Conley, Daniel J. and Garnier, Josette and Doney, Scott C. and Marino, Roxanne and Billen, Gilles},
	year = {2011},
	pages = {18--26}
}

@article{directorate_self-pollution_1989,
	title = {Self-pollution by {Scottish} {Salmon} {Farms} ?},
	volume = {20},
	number = {8},
	author = {Directorate, Chief Scientist and Council, Nature Conservancy and House, Northminster},
	year = {1989},
	pages = {375--379}
}

@article{voss_nitrogen_2011,
	title = {Nitrogen processes in coastal and marine ecosystems, {The} {European} {Nitrogen} {Assessment}},
	doi = {10.1017/CBO9780511976988},
	journal = {The European Nitrogen Assessment},
	author = {Voss, M. and Bakker, A. and Conley, D. and Cornell, S. and Deatsch, B. and Engel, A. and Ganeshram, R. and Garnier, J. and Heiskanen, A. and Jickells, T. and Lancelot, C. and McQuatters-Gollop, A. and Middelburg, J. and Schiedek, D. and Slomp, C. P. and Conley, D. P.},
	year = {2011},
	p