text:
impact of farm-origin parasites on the survival of wild fish populations. We mathematically coupled extensive data sets of native parasitic sea lice (Lepeophtheirus salmonis) transmission and pathogenicity on migratory wild juvenile pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon. Farm-origin lice induced 9-95\% mortality in several sympatric wild juvenile pink and chum salmon populations. The epizootics arise through a mechanism that is new to our understanding of emerging infectious diseases: fish farms undermine a functional role of host migration in protecting juvenile hosts from parasites associated with adult hosts. Although the migratory life cycles of Pacific salmon naturally separate adults from juveniles, fish farms provide L. salmonis novel access to juvenile hosts, in this case raising infection rates for at least the first approximately 2.5 months of the salmon's marine life (approximately 80 km of the migration route). Spatial segregation between juveniles and adults is common among temperate marine fishes, and as aquaculture continues its rapid growth, this disease mechanism may challenge the sustainability of coastal ecosystems and economies.},
	number = {42},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Krkosek, Martin and Lewis, Mark a and Morton, Alexandra and Frazer, L Neil and Volpe, John P},
	year = {2006},
	pmid = {17021017},
	pages = {15506--15510}
}

@article{crawford_effects_2003,
	title = {Effects of shellfish farming on the benthic environment},
	volume = {224},
	issn = {00448486},
	doi = {10.1016/S0044-8486(03)00210-2},
	abstract = {The benthic environment under and near three shellfish farms in Tasmania, Australia, which had had a relatively high level of production over many years was investigated. Benthic samples were collected along transects which ran across the farms, generally from 100 m upstream to 100 m downstream. Sediment deposition, redox values, sediment sulphide concentrations, organic carbon content and water turbidity levels near the bottom were significantly different between the farms but not between sites outside the farm, at the boundary and sites within the farm. Video recordings at one farm showed dense coverage of fine filamentous algae and patchy bacterial mats directly under some longlines and this algae is thought to have fallen off the mussel longlines. At another farm dense beds of seagrass were observed in the videos both under trays of oysters and outside the farm. The benthic infauna did not show clear signs of organic enrichment, and neither univariate nor multivariate measures of benthic infauna were significantly different between sites inside and outside the farm, although they were different between farms. It was concluded from these results that shellfish farming is having little impact, and much less than salmon farming, on the benthic environment in Tasmania. Thus extensive monitoring of shellfish farms would appear to be not necessary. ?? 2003 Elsevier Science B.V. All rights reserved.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Crawford, Christine M. and Macleod, Catriona K A and Mitchell, Iona M.},
	year = {2003},
	pmid = {15003161},
	keywords = {Environmental impact, Benthic environment, Shellfish farming},
	pages = {117--140}
}

@article{borja_assessing_2009-1,
	title = {Assessing the suitability of a range of benthic indices in the evaluation of environmental impact of fin and shellfish aquaculture located in sites across {Europe}},
	volume = {293},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/S0044848609004116},
	doi = {10.1016/j.aquaculture.2009.04.037},
	abstract = {The European Union-funded ECASA project (Ecosystem Approach for Sustainable Aquaculture) studied the impacts from aquaculture on ecosystems from northern Norway to Greece. The objectives of this investigation were to identify quantitative indicators of the effects of aquaculture on marine communities, and to assess their applicability over a range of ecosystems and aquaculture production systems. The study included 6 Mediterranean and 4 Atlantic sites, 7 of which produced finfish (seabream, seabass, tuna, salmon and cod), and 2 bivalve molluscs (oysters, mussels, and clams); one site produced both fish and bivalves. Cultivation methods included finfish cages, long-lines and trestles. Similar sampling methodologies were employed at the 10 study sites, obtaining sediment, hydrodynamic, and benthic faunal data. The horizontal impact from organic enrichment extended 50 m from the farms, with contradictory responses in several indicators (individual abundance, biomass) and a more consistent response of the Infaunal Trophic Index (ITI) and AZTI's Marine Biotic Index (AMBI). By means of Partial Redundancy Analysis, it was demonstrated that the environmental variables explained 53.2\% of the variability in the macrofaunal variables (individual abundance, species richness, diversity, AMBI and ITI), whilst the explained variance was partialled out within three groups of variables: (i) ‘hydrography' (depth, distance to farm, average current speed), which explained 11.5\% of the variance; (ii) ‘sediment' (Eh and percentages of silt and total organic matter), which explained 5.4\%; and (iii) ‘cages' (years of production and annual production), which explained 15.2\%. The shared variance explained by interactions among these groups was 21.1\%. These results, together with multiple regression analysis, provide an accurate assessment of the degree of impact from aquaculture. In conclusion, the use of several benthic indicators, in assessing farm impacts, together with the investigation of dynamics of the studied location, water depth, years of farm activity, and total annual production, must be included when interpreting the response of benthic communities to organic enrichment from aquaculture.},
	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},
	month = aug,
	year = {2009},
	keywords = {Europe, Environmental impact, Benthic indicators, Marine aquaculture, Molluscs, Atlantic, Background information, Cages, Fishes, Hydrodynamics, Mediterranean},
	pages = {231--240}
}

@article{kasih_modeling_2008,
	title = {Modeling early diagenesis of sediment in {Ago} {Bay}, {Japan}},
	volume = {215},
	issn = {03043800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380008000951},
	doi = {10.1016/j.ecolmodel.2008.02.025},
	abstract = {We modified a model of early diagenesis to study the biogeochemical processes occurring in the sediment at Ago Bay, Japan, and compared results from steady state and dynamic calculations. In the model, rate expressions describe organic matter oxidation and oxidation of reduced species formed as a product of organic matter oxidation. Organic matter oxidation is broken down into oxic respiration, denitrification, and manganese, iron, and sulfate reduction. Transport processes include advection, molecular diffusion, bioturbation and bioirrigation by benthic macrofauna. Performance of the model was evaluated against the extensive observed data available from Tategami, an area in Ago Bay. Our steady-state calculation reasonably reproduced the year-averaged vertical profile and our dynamic calculation also captured the overall trend of seasonal variation in the concentration of material in the sediment. These results illustrate the validity of our model of early diagenesis. We also found an interesting point that is a discrepancy between the steady-state solution and the year-averaged data obtained using the dynamic calculation. This difference was probably caused by the non-linear nature of the system (non-linear dependency on temperature) and suggests the suitability of dynamic analysis for the sediment in subtropical sea areas such as Ago Bay. Sensitivity analysis revealed that the calculated concentration of materials in the sediment was strongly affected by changes in following parameters: the deposition flux of organic matter and iron hydroxide, transport parameters, Q10 values, and the mineralization rate of dissolved organic matter.},
	number = {1-3},
	journal = {Ecological Modelling},
	author = {Kasih, G.A. Anggara and Chiba, S. and Yamagata, Y. and Shimizu, Y. and Haraguchi, K.},
	month = jul,
	year = {2008},
	keywords = {Sediment, Ago Bay, Dynamic calculation, Early diagenesis, Japan, Model expectations, modelling 1D steady state, Sensitivity analysis, sensitivity testing, Steady state},
	pages = {40--54}
}

@article{rysgaard_oxygen_1994,
	title = {Oxygen regulation of nitrification and denitrification in sediments},
	volume = {39},
	issn = {00243590},
	url = {http://www.jstor.org/stable/2838200%5Cnhttp://about.jstor.org/terms http://doi.wiley.com/10.4319/lo.1994.39.7.1643},
	doi = {10.4319/lo.1994.39.7.1643},
	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. is collaborating with JSTOR to digitize, preserve and extend access to Limnology and Oceanography This content downloaded from 131.193.193.128 on Thu, 28 Jul 2016 19:38:31 UTC All use subject to http://about.jstor.org/terms Abstract Oxygen regulation of nitrification and denitrification in sediments was investigated with '5N-isotope techniques. Sediment cores were incubated in a continuous flowthrough system in which the 02 concen-tration was varied in the overlying water while the NO3-concentration was kept constant. Nitrification was stimulated with increasing 02 concentrations in the overlying water from 0 to 100\% of atmospheric saturation, whereas only a slight stimulation was observed above 100\%. At 02 concentrations below 100\% of atmospheric saturation, NO3-from the overlying water was the most important source of N for denitrification, whereas above 100\% of atmospheric saturation, NO3-produced by nitrification was the main source of N for denitrification. The converse effects of the 02 levels on the source of NO3-can be explained by applying a simple one-dimensional model: 02 in the overlying water controls the diffusional distance of NO3-to the anoxic zone of denitrification and consequently the location of NO3-vertically in the sediment as well as the magnitude of the nitrification activity. Our results suggest that in aquatic environments containing low N03-concentrations in the overlying water (such as coastal waters), higher 02 conditions will stimulate denitrification, while the opposite will occur in systems containing high N03-concentrations (such as eutrophic lakes and streams).},
	number = {7},
	journal = {Limnology and Oceanography},
	author = {Rysgaard, Søren and Risgaard-Petersen, Nils and Niels Peter, Sloth and Kim, Jensen and Lars Peter, Nielsen},
	month = nov,
	year = {1994},
	pages = {1643--1652}
}

@article{cathalot_spatial_2012-1,
	title = {Spatial and {Temporal} {Variability} of {Benthic} {Respiration} in a {Scottish} {Sea} {Loch} {Impacted} by {Fish} {Farming}: {A} {Combination} of {In} {Situ} {Techniques}},
	volume = {18},
	issn = {13806165},
	doi = {10.1007/s10498-012-9181-4},
	abstract = {The effects of fish farm activities on sediment biogeochemistry were investigated in Loch Creran (Western Scotland) from March to October 2006. Sediment oxygen uptake rates (SOU) were estimated along an organic matter gradient generated from an Atlantic salmon farm using a combination of in situ techniques: microelectrodes, planar optode and benthic chamber incubations. Sulphide (H2S) and pH distributions in sediment porewater were also measured using in situ microelectrodes, and dissolved inorganic carbon (DIC) fluxes were measured in situ using benthic chambers. Relationships between benthic fluxes, vertical distribution of oxidants and reduced compounds in the sediment were examined as well as bacterial abundance and biomass. Seasonal variations in SOU were relatively low and mainly driven by seasonal temperature variations. The effect of the fish farm on sediment oxygen uptake rate was clearly identified by higher total and diffusive oxygen uptake rates (TOU and DOU, respectively) on impacted stations (TOU: 70 ± 25 mmol O2 m-2 day-1; DOU: 70 ± 32 mmol O2 m-2 day-1 recalculated at the summer temperature), compared with the reference station (TOU: 28.3 ± 5.5 mmol O2 m-2 day-1; DOU: 21.5 ± 4.5 mmol O2 m-2 day-1). At the impacted stations, planar optode images displayed high centimetre scale heterogeneity in oxygen distribution underlining the control of oxygen dynamics by small-scale processes. The organic carbon enrichment led to enhanced sulphate reduction as demonstrated by large vertical H2S concentration gradients in the porewater (from 0 to 1,000 lM in the top 3 cm) at the most impacted site. The impact on ecosystem functions such as bioirrigation was evidenced by a decreasing TOU/DOU ratio, from 1.7 in the non-impacted sediments to 1 in the impacted zone. This trend was related to a shift in the macrofaunal assemblage and an increase in sediment bacterial population. The turnover time of the organic load of the sediment was estimated to be over 6 years.},
	number = {6},
	journal = {Aquatic Geochemistry},
	author = {Cathalot, Cécile and Lansard, Bruno and Hall, Per O J and Tengberg, Anders and Almroth-Rosell, Elin and Apler, Anna and Calder, Lois and Bell, Elanor and Rabouille, Christophe},
	year = {2012},
	keywords = {Fish farming, Sediment, Benthic chamber, Benthic mineralization, H2S, Microprofiling, Organic carbon, Oxygen, Scotland, Sea loch},
	pages = {515--541}
}

@article{gruber_marine_2008,
	title = {The {Marine} {Nitrogen} {Cycle}: {Overview} and {Challenges} {BT} - {Nitrogen} in the {Marine} {Environment}},
	url = {papers3://publication/uuid/0062D8B9-1D1B-490B-B5B8-793C0D4B8D9D},
	doi = {http://dx.doi.org/10.1016/B978-0-12-372522-6.00001-3},
	abstract = {Publisher Summary This chapter serves as an introduction to rest of the book. The focus here is on providing an overview of the most important pools of nitrogen, their transformations, their distribution, and their connection to the cycling of other biogeochemically relevant elements, primarily carbon, oxygen, and phosphorus. The scale is global, as subsequent chapters cover individual ocean basins and systems. The chapter also addresses a series of nitrogen challenges, such as the question of how the marine nitrogen cycle appears to be able to maintain a relatively well-established homeostasis, that is, a balance between gains and losses of fixed nitrogen. Finally, it discusses the anthropogenic perturbation of the marine nitrogen cycle. As it examines, however, the answers to many of these questions remain elusive, reminding us how little we know about the marine nitrogen cycle, and how much still remains to be discovered. Although the marine nitrogen cycle occupies a central role within the biogeochemical cycles of the sea, scientific communities barely begin to its major processes and the factors that regulate them. This occurs at a time when human interventions in the Earth system rise to unprecedented levels, with a particularly strong impact on the global nitrogen cycle.},
	number = {1},
	journal = {Nitrogen in the Marine Environment},
	author = {Gruber, Nicolas},
	year = {2008},
	keywords = {nitrogen, marine, SEFS567},
	pages = {1--50}
}

@article{norkko_welcome_2012-1,
	title = {A welcome can of worms? {Hypoxia} mitigation by an invasive species},
	volume = {18},
	issn = {13541013},
	doi = {10.1111/j.1365-2486.2011.02513.x},
	abstract = {Invasive species and bottom-water hypoxia both constitute major global threats to the diversity and integrity of marine ecosystems. These stressors may interact with unexpected consequences, as invasive species that require an initial environmental disturbance to become established can subsequently become important drivers of ecological change. There is recent evidence that improved bottom-water oxygen conditions in coastal areas of the northern Baltic Sea coincide with increased abundances of the invasive polychaetes Marenzelleria spp. Using a reactive-transport model, we demonstrate that the long-term bioirrigation activities of dense Marenzelleria populations have a major impact on sedimentary phosphorus dynamics. This may facilitate the switch from a seasonally hypoxic system back to a normoxic system by reducing the potential for sediment-induced eutrophication in the upper water column. In contrast to short-term laboratory experiments, our simulations, which cover a 10-year period, show that Marenzelleria has the potential to enhance long-term phosphorus retention in muddy sediments. Over time bioirrigation leads to a substantial increase in the iron-bound phosphorus content of sediments while reducing the concentration of labile organic carbon. As surface sediments are maintained oxic, iron oxyhydroxides are able to persist and age into more refractory forms. The model illustrates mechanisms through which Marenzelleria can act as a driver of ecological change, although hypoxic disturbance or natural population declines in native species may be needed for them to initially become established. Invasive species are generally considered to have a negative impact; however, we show here that one of the main recent invaders in the Baltic Sea may provide important ecosystem services. This may be of particular importance in low-diversity systems, where disturbances may dramatically alter ecosystem services due to low functional redundancy. Thus, an environmental problem in one region may be either exacerbated or alleviated by a single species from another region, with potentially ecosystem-wide consequences.},
	number = {2},
	journal = {Global Change Biology},
	author = {Norkko, Joanna and Reed, Daniel C. and Timmermann, Karen and Norkko, Alf and Gustafsson, Bo G. and Bonsdorff, Erik and Slomp, Caroline P. and Carstensen, Jacob and Conley, Daniel J.},
	year = {2012},
	keywords = {Hypoxia, Remediation, Invasive species, Multiple stressors, Reactive-transport model, Sediment phosphorus dynamics},
	pages = {422--434}
}

@article{hargrave_towards_2008,
	title = {Towards a classification of organic enrichment in marine sediments based on biogeochemical indicators.},
	volume = {56},
	issn = {0025-326X},
	url = {http://www.sciencedirect.com/science/article/pii/S0025326X08000763},
	doi = {10.1016/j.marpolbul.2008.02.006},
	abstract = {A nomogram is developed to show that pH, redox potentials (Eh(NHE)) and measures of dissolved sulfides (H2S + HS(-) + S(2-))(total free S(2-)) can be used to classify organic enrichment impacts in marine sediments. The biogeochemical cycle of sulfur in marine sediments is described to show that changes in macrobenthic infauna community structure associated with high levels of organic matter supply result from stress due to oxygen deficiency (hypoxia and anoxia) and toxic effects of S(2-). The changes reflect enhancement of microbial sulfate reduction under conditions of high organic matter sedimentation and the progressive formation of hypoxic-anoxic conditions measured by decreased Eh NHE and increased concentrations of S(2-). The nomogram provides a basis for classification of the oxic status of marine sediments based on changes in inter-related biological and biogeochemical variables along an organic enrichment gradient.},
	number = {5},
	journal = {Marine pollution bulletin},
	author = {Hargrave, B T and Holmer, M and Newcombe, C P},
	month = may,
	year = {2008},
	pmid = {18343458},
	keywords = {Animals, Geologic Sediments, Background info, Aerobiosis, Anaerobiosis, Carbonates, Sulfur Compounds, Sulfur Compounds: analysis, Sulfur Compounds: toxicity, Sulfur cycle},
	pages = {810--24}
}

@article{papageorgiou_effects_2010,
	title = {Effects of fish farming on the biological and geochemical properties of muddy and sandy sediments in the {Mediterranean} {Sea}.},
	volume = {69},
	issn = {1879-0291},
	url = {http://www.sciencedirect.com/science/article/pii/S0141113609001731},
	doi = {10.1016/j.marenvres.2009.12.007},
	abstract = {The aim of this paper was to test how benthic fauna and biogeochemical properties of sediment will vary in response to similar levels of organic enrichment (induced by fish farming) as a function of bottom-habitat type (i.e., mud versus seagrass/coarse sediments), distance from the enrichment source and depth. Our results showed that samples from silty sediments in the vicinity of fish farms have higher TOC and TON values, higher oxygen consumption, higher PO(4) release and lower benthic diversity. In this context muddy sites are more likely to be identified as impacted/critical, than coarse sediment ones.},
	number = {5},
	journal = {Marine environmental research},
	author = {Papageorgiou, Nafsika and Kalantzi, Ioanna and Karakassis, Ioannis},
	month = jun,
	year = {2010},
	pmid = {20085847},
	keywords = {Aquaculture, Environment, Animals, Ecosystem, Geologic Sediments, Fishes, Mediterranean Sea},
	pages = {326--36}
}

@article{ferr??n_benthic_2009,
	title = {Benthic fluxes in a tidal salt marsh creek affected by fish farm activities: {R}??o {San} {Pedro} ({Bay} of {C}??diz, {SW} {Spain})},
	volume = {113},
	issn = {03044203},
	url = {http://dx.doi.org/10.1016/j.marchem.2008.12.002},
	doi = {10.1016/j.marchem.2008.12.002},
	abstract = {Benthic fluxes of dissolved inorganic carbon, total alkalinity, oxygen, nutrients, nitrous oxide and methane were measured in situ at three sites of R??o San Pedro salt marsh tidal creek (Bay of C??diz, SW Spain) during three seasons. This system is affected by the discharges of organic carbon and nutrients from the surrounding aquaculture installations. Sediment oxygen uptake rates and inorganic carbon fluxes ranged respectively from 16 to 79??mmol O2 m- 2 d- 1 and from 48 to 146??mmol C m- 2 d- 1. Benthic alkalinity fluxes were corrected for the influence of NH4+ and NO3- + NO2- fluxes, and the upper and lower limits for carbon oxidation rates were inferred by considering two possible scenarios: maximum and minimum contribution of CaCO3 dissolution to corrected alkalinity fluxes. Average Cox rates were in all cases within ?? 25\% of the upper and lower limits and ranged from 40 to 122??mmol C m- 2 d- 1. Whereas carbon mineralization did not show significant differences among the sites, Cox rates varied seasonally and were correlated with temperature (r2 = 0.72). During winter and spring denitrification was estimated to account for an average loss of 46\% and 75\%, respectively, of the potentially recyclable N, whereas during the summer no net removal was observed. A possible shift from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) during this period is argued. Dissolved CH4 and N2O fluxes ranged from 5.7 to 47????mol CH4 m- 2 d- 1 and 4.3 to 49????mol N-N2O m- 2 d- 1, respectively, and represented in all cases a small fraction of total inorganic C and N flux. Overall, about 60\% of the total particulate organic matter that is discharged into the creek by the main fish farm facility is estimated to degrade in the sediments, resulting in a significant input of nutrients to the system. ?? 2008 Elsevier B.V. All rights reserved.},
	number = {1-2},
	journal = {Marine Chemistry},
	author = {Ferr??n, S. and Ortega, T. and Forja, J. M.},
	year = {2009},
	keywords = {Aquaculture, Nutrients, Benthic fluxes, Nitrous oxide, Carbon mineralization, Dissolved inorganic carbon, Methane, Salt marsh creek},
	pages = {50--62}
}

@article{jonsson_cultured_2006,
	title = {Cultured {Atlantic} salmon in nature: a review of their ecology and interaction with wild fish},
	volume = {63},
	issn = {10543139},
	doi = {10.1016/j.icesjms.2006.03.004},
	abstract = {When cultured Atlantic salmon are released into nature, they compete with wild fish for food, space, and breeding partners. As a result of morphological, physiological, ecological, and behavioural changes that occur in hatcheries, their comp etitive ability often differs from that of wild fish. These changes are partly phenotypic and partly genetic. Cultured juveniles' faster growth rate influences age and size at smolting and maturity, reproductive output, and longevity. Fast-growing parr tend to smolt younger, produce more but smaller eggs, attain maturity earlier, and die younger. Juvenile learning influences a number of behavioural traits, and differences in early experience appear to affect feeding and spawning success, migratory behaviour, and homing ability. Genetic change in hatcheries is chiefly the result of natural selection, with differential mortality among genotypes and broodstock selection based on production traits such as high adult body mass and fast growth rate. Experimental evidence has revealed that cultured parr's greater aggression often allows them to dominate wild parr, although smaller cultured parr can be subordinated if they co-occur in fast-flowing water and if wild smolts have established prior residence. During spawning, the fitness of wild salmon is superior to that of cultured conspecifics. Cultured males are inferior to wild males in intra-sexual competition, courting, and spawning; cultured females have greater egg retention, construct fewer nests, and are less efficient at covering their eggs in the substratum than their wild counterparts. In rivers, the early survival of cultured offspring is lower than that of their wild counterparts. The lifetime reproductive success of farmed fish has been estimated at 17\% that of similar-sized wild salmon. As a result of ecological interaction and through density-dependent mechanisms, cultured fish may displace wild conspecifics to some extent, increase their mortality, and decrease their growth rate, adult size, reproductive output, biomass, and production. © 2006 International Council for the Exploration of the Sea.},
	number = {7},
	journal = {ICES Journal of Marine Science},
	author = {Jonsson, Bror and Jonsson, Nina},
	year = {2006},
	keywords = {captive, competition, cultured, density-dependence, farmed Atlantic salmon, hatchery rearing, spawning},
	pages = {1162--1181}
}

@article{pereira_recovery_2004,
	title = {Recovery of sediments after cessation of marine fish farm production},
	volume = {235},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/S0044848604000031},
	doi = {10.1016/j.aquaculture.2003.12.023},
	abstract = {Following cessation of fish production at a fish farm site in Loch Creran, Scotland, a study of the recovery of the benthic environment was undertaken. Sediment samples for macrofauna and geochemical parameters (redox potential, organic carbon, oxygen flux) were collected over a period of 15 months from three stations following a gradient of impact from the former fish farm site. The data collected were analysed by a combination of uni-and multivariate statistical methods. The macrobenthic community at the two stations furthest from the fish cage site showed signs of recovery with time in terms of indicator species, number of species and abundance, being, however, still moderately to slightly disturbed at the end of this study. At the station nearest to the former fish cage site, recovery of the macrobenthic community was also evident, but this station was still highly impacted 15 months after fish production ceased, with opportunistic species dominant. Fifteen months after fallowing, highly reduced conditions were still persistent in subsurface sediments at the stations on the periphery of the former fish cage site. Bulk sediment organic carbon, although an indicator of a spatial gradient, was not found to be a significant indicator of recovery. Combinations of different environmental parameters appear to affect different stages of benthic recovery with sediment oxygen uptake as the main observed parameter conditioning early stages of macrobenthic succession.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Pereira, Paula M.F and Black, Kenneth D and McLusky, Donald S and Nickell, Thom D},
	month = jun,
	year = {2004},
	keywords = {Fish farm, Benthos, Macrofauna, Recovery, Oxygen Flux, Sediment redox},
	pages = {315--330}
}

@article{burgin_have_2007-1,
	title = {Have we overemphasized in aquatic removal of nitrate the role ecosystems ? pathways of denitrification review},
	volume = {5},
	issn = {1540-9295},
	doi = {10.1890/1540-9295(2007)5[89:HWOTRO]2.0.CO;2},
	abstract = {The removal of nitrogen (N) in aquatic ecosystems is of great interest because excessive nitrate in groundwater and surface water is a growing problem. High nitrate loading degrades water quality and is linked to eutrophica tion and harmful algal blooms, especially in coastal marine waters. Past research on nitrate removal processes has emphasized plant or microbial uptake (assimilation) or respiratory denitrification by bacteria. The increasing application of stable isotopes and other tracer techniques to the study of nitrate removal has yielded a growing body of evidence for alternative, microbially mediated processes of nitrate transformation. These include dissim ilatory (the reduction of nitrogen into other inorganic compounds, coupled to energy producing processes) reduction of nitrate to ammonium (DNRA), chemoautotrophic denitrification via sulfur or iron oxidation, and anaerobic ammonium oxidation (anammox), as well as abiotic nitrate removal processes. Here, we review evi dence for the importance of alternative nitrate removal pathways in aquatic ecosystems and discuss how the pos sible prevalence of these pathways may alter views of N cycling and its controls. These alternative pathways are of particular importance for the management of excess N in the environment, especially in cases where nitrate is transformed to ammonium, a biologically available and less mobile N form, rather than to dinitrogen gas.},
	number = {2},
	journal = {Frontiers in Ecology and the Environment},
	author = {Burgin, Amy J and Hamilton, Stephen K},
	year = {2007},
	pmid = {21781233},
	pages = {89--96}
}

@article{an_dissimilatory_2002-1,
	title = {Dissimilatory nitrate reduction to ammonium ({DNRA}) as a nitrogen link, versus denitrification as a sink in a shallow estuary ({Laguna} {Madre}/{Baffin} {Bay}, {Texas})},
	volume = {237},
	issn = {0171-8630},
	url = {http://www.int-res.com/abstracts/meps/v237/p41-50/},
	doi = {10.3354/meps237041},
	journal = {Marine Ecology Progress Series},
	author = {An, S and Gardner, WS},
	month = jul,
	year = {2002},
	keywords = {Denitrification, DNRA, Brown tide, Dissimilatory nitrate reduction to ammonium, Laguna Madre/Baffin Bay, Nitrogen conservation},
	pages = {41--50}
}

@article{cathalot_spatial_2012-2,
	title = {Spatial and {Temporal} {Variability} of {Benthic} {Respiration} in a {Scottish} {Sea} {Loch} {Impacted} by {Fish} {Farming}: {A} {Combination} of {In} {Situ} {Techniques}},
	volume = {18},
	issn = {13806165},
	doi = {10.1007/s10498-012-9181-4},
	abstract = {The effects of fish farm activities on sediment biogeochemistry were investigated in Loch Creran (Western Scotland) from March to October 2006. Sediment oxygen uptake rates (SOU) were estimated along an organic matter gradient generated from an Atlantic salmon farm using a combination of in situ techniques: microelectrodes, planar optode and benthic chamber incubations. Sulphide (H2S) and pH distributions in sediment porewater were also measured using in situ microelectrodes, and dissolved inorganic carbon (DIC) fluxes were measured in situ using benthic chambers. Relationships between benthic fluxes, vertical distribution of oxidants and reduced compounds in the sediment were examined as well as bacterial abundance and biomass. Seasonal variations in SOU were relatively low and mainly driven by seasonal temperature variations. The effect of the fish farm on sediment oxygen uptake rate was clearly identified by higher total and diffusive oxygen uptake rates (TOU and DOU, respectively) on impacted stations (TOU: 70 ± 25 mmol O2 m-2 day-1; DOU: 70 ± 32 mmol O2 m-2 day-1 recalculated at the summer temperature), compared with the reference station (TOU: 28.3 ± 5.5 mmol O2 m-2 day-1; DOU: 21.5 ± 4.5 mmol O2 m-2 day-1). At the impacted stations, planar optode images displayed high centimetre scale heterogeneity in oxygen distribution underlining the control of oxygen dynamics by small-scale processes. The organic carbon enrichment led to enhanced sulphate reduction as demonstrated by large vertical H2S concentration gradients in the porewater (from 0 to 1,000 lM in the top 3 cm) at the most impacted site. The impact on ecosystem functions such as bioirrigation was evidenced by a decreasing TOU/DOU ratio, from 1.7 in the non-impacted sediments to 1 in the impacted zone. This trend was related to a shift in the macrofaunal assemblage and an increase in sediment bacterial population. The turnover time of the organic load of the sediment was estimated to be over 6 years.},
	number = {6},
	journal = {Aquatic Geochemistry},
	author = {Cathalot, Cécile and Lansard, Bruno and Hall, Per O J and Tengberg, Anders and Almroth-Rosell, Elin and Apler, Anna and Calder, Lois and Bell, Elanor and Rabouille, Christophe},
	year = {2012},
	keywords = {Fish farming, Sediment, Benthic chamber, Benthic mineralization, H2S, Microprofiling, Organic carbon, Oxygen, Scotland, Sea loch},
	pages = {515--541}
}

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

@article{silvert_modelling_1996,
	title = {Modelling environmental impacts of marine finfish aquaculture},
	volume = {12},
	issn = {0175-8659},
	url = {http://doi.wiley.com/10.1111/j.1439-0426.1996.tb00066.x},
	doi = {10.1111/j.1439-0426.1996.tb00066.x},
	number = {2},
	journal = {Journal of Applied Ichthyology},
	author = {Silvert, W. and Sowles, J. W.},
	month = jul,
	year = {1996},
	keywords = {background information, overview},
	pages = {75--81}
}

@book{brooks_interactions_2003,
	title = {Interactions of {Atlantic} salmon in the {Pacific} northwest environment. {II}. {Organic} wastes},
	volume = {62},
	isbn = {0165-7836},
	abstract = {The second paper evaluating the environmental risks associated with the culture of Atlantic salmon in the Pacific Northwest addresses organic wastes released from net-pens. It begins with the minor effects caused by dissolved nutrients from organic waste in the water column, and then follows in some detail with the more significant environmental effects created by the deposition of waste onto the benthos under and adjacent to salmon farms. The information is supplemented with new data from case studies to elucidate the relationship between organic inputs from salmon farms, which cause changes in sediment chemistry resulting in predictable biological responses. The paper continues with a discussion of chemical and biological remediation of sediments near salmon farms, and ends with some conclusions on the varying degrees of risk from the presence and accumulation of organic wastes. ?? 2003 Elsevier Science B.V. All rights reserved.},
	number = {3},
	author = {Brooks, Kenneth M. and Mahnken, Conrad V W},
	year = {2003},
	doi = {10.1016/S0165-7836(03)00064-X},
	keywords = {Atlantic salmon, Environment, Sulfide, Macrofauna, Remediation, Organic wastes, Sediment chemistry}
}

@article{bonin_influence_1999,
	title = {The influence of nitrate and carbon inputs on the end products of bacterial nitrate dissimilation in marine sediment},
	volume = {73},
	issn = {02772248},
	doi = {10.1080/02772249909358848},
	abstract = {The aim of this work was to study the influence of various carbon sources (acetate, glucose, succinate) and nitrate concentration on dissimilatory nitrate reduction rates (denitrification and dissimilatory nitrate reduction to ammonium: DNRA). Without nitrate ammendement the rate ratio DNRA/denitrification was about 11. When the nitrate added was lower than 0.05 mM, the ratio increased 3.8‐fold showing that nitrate ammonifiers have high affinity for nitrate. When nitrate concentration increased up to 0.5 mM, denitrification was stimulated. When glucose, acetate or succinate were added as electron donor, denitrification rates followed the order succinate {\textbackslash}textgreater acetate {\textbackslash}textgreater glucose {\textbackslash}textgreater control, whereas the order of DNRA values was glucose {\textbackslash}textgreater succinate {\textbackslash}textgreater acetate = control. Thus, the DNRA‐to‐denitrification activity ratio is affected by the quantity of carbon and nitrate but also by the theoretical energy of the substrate.},
	number = {July},
	journal = {Toxicology and Environmental Chemistry},
	author = {Bonin, Patricia C. and Omnes, Patrick and Chalamet, Alain},
	year = {1999},
	pages = {67--79}
}

@article{chang_development_2014,
	title = {{THE} {DEVELOPMENT} {OF} {THE} {SALMON} {AQUACULTURE} {INDUSTRY} {IN} {SOUTHWESTERN} {NEW} {BRUNSWICK}, {BAY} {OF} {FUNDY}, {INCLUDING} {STEPS} {TOWARD} {INTEGRATED} {COASTAL} {ZONE} {MANAGEMENT}},
	volume = {18},
	issn = {1365-7305},
	url = {http://www.tandfonline.com/doi/abs/10.1080/13657305.2014.855952},
	doi = {10.1080/13657305.2014.855952},
	abstract = {The salmon farming industry in southwestern New Brunswick, Bay of Fundy began in 1978. There are now 92 marine finfish farm leases within a 60 × 60 km area; 45 of these leases were actively growing Atlantic salmon in floating net cages in 2012. Salmon production peaked in 2002 at 38,900 metric tons. Annual production during 2007–2012 was 21,560–30,220 metric tons, with a value of US\$140–185 million. Farm sizes have increased considerably since 1978; during this time there has also been consolidation of industry ownership. All currently operating companies are locally owned. The industry has faced numerous challenges, including fish health problems, coastal zone conflicts, environmental concerns, and economic issues. Initially, lease applications were evaluated on a site-by-site basis, and most farms were multi-year-class operations, stocking every year. Farms are now operated within a framework of Aquaculture Bay Management Areas, and all farms are single-year-class operations, stocking every three years,...},
	language = {en},
	number = {1},
	journal = {Aquaculture Economics \& Management},
	author = {Chang, B. D. and Coombs, K. A. and Page, F. H.},
	month = jan,
	year = {2014},
	keywords = {Canada, farm management, salmon},
	pages = {1--27}
}

@article{bohlen_benthic_2011,
	title = {Benthic nitrogen cycling traversing the {Peruvian} oxygen minimum zone},
	volume = {75},
	issn = {00167037},
	doi = {10.1016/j.gca.2011.08.010},
	abstract = {Benthic nitrogen (N) cycling was investigated at six stations along a transect traversing the Peruvian oxygen minimum zone (OMZ) at 11??S. An extensive dataset including porewater concentration profiles and in situ benthic fluxes of nitrate (NO3-), nitrite (NO2-) and ammonium (NH4+) was used to constrain a 1-D reaction-transport model designed to simulate and interpret the measured data at each station. Simulated rates of nitrification, denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA) by filamentous large sulfur bacteria (e.g. Beggiatoa and Thioploca) were highly variable throughout the OMZ yet clear trends were discernible. On the shelf and upper slope (80-260m water depth) where extensive areas of bacterial mats were present, DNRA dominated total N turnover (???2.9mmolNm-2d-1) and accounted for ???65\% of NO3-+NO2- uptake by the sediments from the bottom water. Nonetheless, these sediments did not represent a major sink for dissolved inorganic nitrogen (DIN=NO3-+NO2-+NH4+) since DNRA reduces NO3- and, potentially NO2-, to NH4+. Consequently, the shelf and upper slope sediments were recycling sites for DIN due to relatively low rates of denitrification and high rates of ammonium release from DNRA and ammonification of organic matter. This finding contrasts with the current opinion that sediments underlying OMZs are a strong sink for DIN. Only at greater water depths (300-1000m) did the sediments become a net sink for DIN. Here, denitrification was the major process (???2mmolNm-2d-1) and removed 55-73\% of NO3- and NO2- taken up by the sediments, with DNRA and anammox accounting for the remaining fraction. Anammox was of minor importance on the shelf and upper slope yet contributed up to 62\% to total N2 production at the 1000m station. The results indicate that the partitioning of oxidized N (NO3-, NO2-) into DNRA or denitrification is a key factor determining the role of marine sediments as DIN sinks or recycling sites. Consequently, high measured benthic uptake rates of oxidized N within OMZs do not necessarily indicate a loss of fixed N from the marine environment. ?? 2011 Elsevier Ltd.},
	number = {20},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Bohlen, L. and Dale, A. W. and Sommer, S. and Mosch, T. and Hensen, C. and Noffke, A. and Scholz, F. and Wallmann, K.},
	year = {2011},
	pages = {6094--6111}
}

@article{hulth_nitrogen_2005,
	title = {Nitrogen removal in marine environments: recent findings and future research challenges},
	volume = {94},
	issn = {03044203},
	url = {http://www.sciencedirect.com/science/article/pii/S0304420304002439},
	doi = {10.1016/j.marchem.2004.07.013},
	abstract = {Respiratory reduction of nitrate (denitrification) is recognized as the most important process converting biologically available (fixed) nitrogen to N2. In current N cycle models, a major proportion of global marine denitrification (50–70\%) is assumed to take place on the sea floor, particularly in organic rich continental margin sediments. Recent observations indicate that present conceptual views of denitrification and pathways of nitrate reduction and N2 formation are incomplete. Alternative N cycle pathways, particularly in sediments, include anaerobic ammonium oxidation to nitrite, nitrate and N2 by Mn-oxides, and anaerobic ammonium oxidation coupled to nitrite reduction and subsequent N2 mobilization. The discovery of new links and feedback mechanisms between the redox cycles of, e.g., C, N, S, Mn and Fe casts doubt on the present general understanding of the global N cycle. Recent models of the oceanic N budget indicate that total inputs are significantly smaller than estimated fixed N removal. The occurrence of alternative N reaction pathways further exacerbates the apparent imbalance as they introduce additional routes of N removal. In this contribution, we give a brief historical background of the conceptual understanding of N cycling in marine ecosystems, emphasizing pathways of aerobic and anaerobic N mineralization in marine sediments, and the implications of recently recognized metabolic pathways for N removal in marine environments.},
	number = {1-4},
	journal = {Marine Chemistry},
	author = {Hulth, Stefan and Aller, Robert C. and Canfield, Donald E. and Dalsgaard, Tage and Engström, Pia and Gilbert, Franck and Sundbäck, Kristina and Thamdrup, Bo},
	month = mar,
	year = {2005},
	keywords = {Nitrogen, background info, Marine, Removal},
	pages = {125--145}
}

@article{rossignol_nutrients_2011,
	title = {Nutrients in precipitation and the phytoplankton responses to enrichment in surface waters of the {Albemarle} {Peninsula}, {NC}, {USA} after the establishment of a large-scale chicken egg farm},
	volume = {671},
	issn = {00188158},
	doi = {10.1007/s10750-011-0715-3},
	abstract = {Nitrogen (N) and phosphorus (P) released in waste from animal feeding operations can stimulate phytoplankton biomass production in local receiving waters. Changes in weekly wet atmospheric N and P were measured from 2005 to 2008 at monitoring stations located 0.8, 7.9, and 10.3 km downwind from a new chicken egg production facility on the Albemarle Peninsula, North Carolina. After this farm began operating, there was a significant doubling in mean wet NH4 + concentrations (465–1,022 μg l−1) at 0.8 km with no change at the other sites. To measure the phytoplankton responses to nutrient enrichment, we conducted seasonal N and P enrichment bioassays from 2006 to 2008 on nearby Phelps Lake and Alligator River. These low-nutrient waters responded to nutrient additions, with the highest increases in phytoplankton primary productivity (14C uptake) and biomass (chlorophyll a) occurring in the combined N and P treatments suggesting co-limitation of N and P. Although we did not find an increased nutrient signal in precipitation at sites {\textbackslash}textgreater0.8 km from the farm, there is the potential for atmospheric deposition of N to these and other waters located N/NE of the farm given prevailing winds and distance that NH4 + aerosols can travel. Furthermore, surface runoff from the farm may impact receiving waters downstream (e.g., Pungo and Pamlico Rivers). In order to prevent excessive phytoplankton productivity and biomass both N and P inputs should be carefully assessed and potentially controlled in these nutrient-sensitive waters.},
	number = {1},
	journal = {Hydrobiologia},
	author = {Rossignol, Karen L. and Paerl, Hans W. and Fear, John M. and Braddy, Jeremy S.},
	year = {2011},
	keywords = {Nitrogen, Water quality, Albemarle, Bioassay, Phosphorus, Precipitation},
	pages = {181--191}
}

@article{macleod_assessment_2004,
	title = {Assessment of long term change in sediment condition after organic enrichment: defining recovery.},
	volume = {49},
	issn = {0025-326X},
	url = {http://www.sciencedirect.com/science/article/pii/S0025326X0400013X},
	doi = {10.1016/j.marpolbul.2004.01.010},
	abstract = {Sediment condition at an Atlantic salmon (Salmo salar) culture site in S.E. Tasmania, Australia was evaluated to determine the rate and extent of recovery after removal of farmed fish. By local standards the cage sediment at the start of this survey was markedly degraded but comparison with results from impact studies in Scotland, Canada and Norway suggests that the sediments were considerably less impacted than in northern temperate areas. The impact at the cages diminished rapidly with both time and distance; after only 2 months conditions were markedly improved. The macrobenthos indicated a slower recovery than chemical measures, after 36 months the benthic faunal community structure under the cages still differed from reference conditions even though other sediment measures had recovered. This study highlighted two other key issues in relation to monitoring and management of sediment recovery. First, techniques used to determine impact may not be appropriate for evaluation of recovery. Second, establishment of local baseline standards is extremely important to ensure appropriate evaluation of both impact and recovery.},
	number = {1-2},
	journal = {Marine pollution bulletin},
	author = {Macleod, Catriona K and Crawford, Christine M and Moltschaniwskyj, Natalie A},
	month = jul,
	year = {2004},
	pmid = {15234876},
	keywords = {Aquaculture, Salmo salar, Animals, Environmental Monitoring, Geologic Sediments, Geologic Sediments: chemistry, Invertebrates, Population Dynamics, Water Pollutants, Water Pollutants: analysis},
	pages = {79--88}
}

@article{mazzola_initial_1999-1,
	title = {Initial fish-farm impact on meiofaunal assemblages in coastal sediments of the {Western} {Mediterranean}},
	volume = {38},
	issn = {0025326X},
	doi = {10.1016/S0025-326X(99)00142-3},
	abstract = {We studied the initial impact of organic loads due to the biodeposition of a new fish farm in a non-impacted coastal area of the Tyrrhenian Sea (Western Mediterranean). Sediment chemistry and meiofaunal assemblages were investigated from July 1997 to February 1998 on a monthly basis at two stations: the first was located under the fish farm, while the second was at about 1 km distance, and served as control. Variations in the biochemical composition of the sedimentary organic matter and meiofaunal community structure were also related to changes in reared fish biomass. The presence of the cage-induced rapid changes in the benthic compartment: the sediments reached rapidly (i.e., after only 6 weeks) reducing conditions. A significant accumulation of biopolymeric carbon was observed beneath the cage both at the beginning of this study and 5-7 months after cage disposal and appeared to be related to the fish-farm production cycle. Sedimentary proteins and lipids resulted to be good descriptors of medium-term fish-farm impact. Changes in the sediment conditions beneath the cage determined a significant reduction of the total meiofaunal density (on average for 70\%). Most meiofaunal taxa, including nematodes, copepods and ostracods displayed a significant decrease in the farm sediments within 3 months after cage installation. Kinorhynchs appeared extremely sensitive to reducing conditions of the sediments and disappeared almost completely, whereas polychaete densities remained unvaried. After initial impact meiofaunal assemblages responded to organic enrichment recovering, at least partially, their apparent structural characteristics. These data indicate that studies carried out several months after cage deployment might underestimate the actual impact on benthic assemblages. Copyright (C) 1999 Elsevier Science Ltd.},
	number = {12},
	journal = {Marine Pollution Bulletin},
	author = {Mazzola, A and Mirto, S and Danovaro, R},
	year = {1999},
	keywords = {Carbohydrates, Fish farming impact, Lipids, Mediterranean sea, Meiofauna, Proteins},
	pages = {1126--1133}
}

@article{devol_denitrification_2015,
	title = {Denitrification, anammox, and {N}2 production in marine sediments},
	volume = {7},
	issn = {1941-1405},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/25560607},
	doi = {10.1146/annurev-marine-010213-135040},
	abstract = {Fixed nitrogen limits primary productivity in many parts of the global ocean, and it consequently plays a role in controlling the carbon dioxide content of the atmosphere. The concentration of fixed nitrogen is determined by the balance between two processes: the fixation of nitrogen gas into organic forms by diazotrophs, and the reconversion of fixed nitrogen to nitrogen gas by denitrifying organisms. However, current sedimentary denitrification rates are poorly constrained, especially in permeable sediments, which cover the majority of the continental margin. Also, anammox has recently been shown to be an additional pathway for the loss of fixed nitrogen in sediments. This article briefly reviews sedimentary fixed nitrogen loss by sedimentary denitrification and anammox, including in sediments in contact with oxygen-deficient zones. A simple extrapolation of existing rate measurements to the global sedimentary denitrification rate yields a value smaller than many existing measurement-based estimates but still larger than the rate of water column denitrification.},
	journal = {Annual Review of Marine Science},
	author = {Devol, Allan H},
	year = {2015},
	pmid = {25560607},
	keywords = {nitrogen cycle, anoxic sediment, nit, nitrogen budget, nitrogen isotope},
	pages = {403--423}
}

@article{holmer_organic_2005,
	title = {Organic enrichment from marine finfish aquaculture and effects on sediment biogeochemical processes},
	volume = {5},
	doi = {10.1007/b136010},
	abstract = {Organic enrichment of sediments underlying fish farms in temperate and trop- ical coastal zones is reviewed to identify similarities and important biogeochemical differences. Improvements in technology have allowed farms to move from depositional sites to more erosional offshore locations. However, low cost farms are still being located in sheltered areas, in particular in the tropics. Important differences in the response of sediment geochemical variables to organic enrichment are associated with finfish aqua- culture located under highly diverse hydrographic and sedimentological conditions in different coastal areas. In temperate latitudes where farms are often located over soft bottom, organic enrichment increases sediment microbial activity and may alter benthic community structure. Enhanced anaerobic activity may lead to accumulation of sulfides with adverse effects on aerobic bacteria, plants and fauna due to progressive oxygen de- pletion. In warm temperate waters, such as the Mediterranean and tropical latitudes, many farms are located in more advective areas with coarse-grained carbonate-rich sediments. Effects of organic enrichment in these areas are less well described, but studies have also shown sulfide accumulation in sediments indicative of deteriorated benthic habitats.},
	number = {July},
	journal = {Handbook of Environmental Chemistry},
	author = {Holmer, Marianne and Barry, Wildish},
	year = {2005},
	pages = {181--206}
}

@article{brigolin_modelling_2009-2,
	title = {Modelling the impact of aquaculture on early diagenetic processes in sea loch sediments},
	volume = {388},
	issn = {01718630},
	url = {http://www.int-res.com/abstracts/meps/v388/p63-80/},
	doi = {10.3354/meps08072},
	abstract = {We present a novel approach for the simulation of the impacts of finfish aquaculture on sedimentary redox dynamics, based on the coupling of a fish farm waste deposition model (DEPO- MOD) and a knowledge-based reactive transport model (RTM) of early diagenesis. The integrated model was applied to a salmon fish farm located in a Scottish fjordic sealoch. The major diagenetic processes of the reaction network were first identified on the basis of literature information and his- toric data. Next, the organic carbon (OC) flux at a pristine site near the farm was estimated by fitting the vertical profiles of pore water and solid-state chemical species measured in the field. DEPOMOD was then used to predict the fluxes of OC due to the release of uneaten feed and faeces at various dis- tances away from the farm. These fluxes were added to the background ‘natural' fluxes and used as forcing functions for the RTM. Comparison of the simulated transient profiles with data collected at an impacted site revealed that the RTM model satisfactorily predicted the transient dynamics of the system. We discuss the use of the model for cost-effective environmental impact assessments, site selection and the optimization of husbandry practices.},
	journal = {Marine Ecology Progress Series},
	author = {Brigolin, Daniele and Pastres, Roberto and Nickell, TD Thomas D. and Cromey, CJ Chris J. and Aguilera, DR David R. and Regnier, Pierre},
	month = aug,
	year = {2009},
	keywords = {Atlantic salmon, Benthic mineralization, DEPOMOD, Loch Creran, RTM, Transient simulation, Depomod, Loch creran, Rtm},
	pages = {63--80}
}

@article{howarth_nitrogen_2006,
	title = {Nitrogen as the limiting nutrient for eutrophication in coastal marine ecosystems: {Evolving} views over three decades},
	volume = {51},
	issn = {00243590},
	url = {http://doi.wiley.com/10.4319/lo.2006.51.1_part_2.0364},
	doi = {10.4319/lo.2006.51.1_part_2.0364},
	number = {1part2},
	journal = {Limnology and Oceanography},
	author = {Howarth, Robert W. and Marino, Roxanne},
	month = jan,
	year = {2006},
	pages = {364--376}
}

@article{roberts_hypoxic_2012,
	title = {Hypoxic events stimulate nitrogen recycling in a shallow salt-wedge estuary: {The} {Yarra} {River} {Estuary}, {Australia}},
	volume = {57},
	issn = {00243590},
	url = {http://doi.wiley.com/10.4319/lo.2012.57.5.1427},
	doi = {10.4319/lo.2012.57.5.1427},
	abstract = {The Yarra River estuary is a salt-wedge estuary prone to periods of\${\textbackslash}backslash\$nstratification-induced anoxia and hypoxia (O-2 {\textbackslash}textless 100 mu mol L-1) during\${\textbackslash}backslash\$nlow-flow events. Nitrate reduction pathways were examined using the N-15\${\textbackslash}backslash\$nisotope pairing technique in intact sediment cores, emulating in situ\${\textbackslash}backslash\$nconditions, to evaluate the fate of NO3- during changing oxygen\${\textbackslash}backslash\$nconditions. Water-column concentrations of dissolved inorganic carbon\${\textbackslash}backslash\$n(DIC), O-2, NH4+, and NOx (NO3- + NO2-) were also measured to examine\${\textbackslash}backslash\$nany deviation from conservative behavior (denoted Delta) in response to\${\textbackslash}backslash\$noxygen variability within the estuary. The estuary was a source of NH4+\${\textbackslash}backslash\$nin the anoxic bottom waters. Whole-system estimates using deviations\${\textbackslash}backslash\$nfrom conservative behavior and core incubations were in good agreement\${\textbackslash}backslash\$nand showed that NH4+ was regenerated more efficiently relative to DIC\${\textbackslash}backslash\$nunder hypoxic conditions. For the whole system, mean Delta DIC : Delta\${\textbackslash}backslash\$nNH4+ ratios under oxic (85 +/- 33) and hypoxic (20 +/- 3) conditions\${\textbackslash}backslash\$nwere significantly different. The more-efficient NH4+ regeneration\${\textbackslash}backslash\$nduring hypoxia was attributed to rapid mineralization rates and\${\textbackslash}backslash\$ncessation of nitrification; dissimilatory nitrate reduction to ammonium\${\textbackslash}backslash\$n(DNRA) was not a significant contributor. Unexpectedly, the\${\textbackslash}backslash\$ndenitrification : DNRA ratio was significantly higher under hypoxic\${\textbackslash}backslash\$nconditions, with denitrification contributing 99.1\% +/- 0.3\% of total\${\textbackslash}backslash\$nnitrate reduction. DNRA rates were significantly higher during oxic\${\textbackslash}backslash\$nconditions (123.5 +/- 30.7 mu mol m(-2) h(-1)) when compared with rates\${\textbackslash}backslash\$nduring hypoxia (0.6 +/- 0.1 mu mol m(-2) h(-1)). The increase in DNRA in\${\textbackslash}backslash\$nthe presence of oxygen was attributed to the alleviation of NO3-\${\textbackslash}backslash\$nlimitation during these conditions.},
	number = {5},
	journal = {Limnology and Oceanography},
	author = {Roberts, Keryn L. and Eate, Vera M. and Eyre, Bradley D. and Holland, Daryl P. and Cook, Perran L. M.},
	year = {2012},
	pages = {1427--1442}
}

@article{carroll_organic_2003,
	title = {Organic enrichment of sediments from salmon farming in {Norway}: {Environmental} factors, management practices, and monitoring techniques},
	volume = {226},
	issn = {00448486},
	doi = {10.1016/S0044-8486(03)00475-7},
	abstract = {Environmental impacts of salmon cage aquaculture resulting from deposition of organic-rich particulate matter to the sea bottom have been thought to be a function of the local environmental conditions and management practices. However, testing of these suppositions have been limited by (1) widely varying monitoring methods employed, and (2) lack of data comparability resulting from the absence of standardized national monitoring schemes. In order to determine the sensitivity of different monitoring methods in detecting benthic environmental effects, a comparative analysis was undertaken of four methods commonly employed in Norway that vary in cost and expertise required: (1) visual diver surveys, (2) faunal analysis, (3) sediment chemistry, and (4) Sediment Profile Imagery (SPI). Results indicate that all methods agreed in the common "impact zone" under and immediately next to the cages. However, each of the methods differed in their sensitivity in detecting more subtle effects at greater distances from the cages. Data from 168 environmental survey samples located at various distances from working Norwegian salmon cage farms collected using similar methodology between 1996 and 1998 were analyzed to determine the relationship between environmental variables, management regimes, and levels of environmental impact. Total organic carbon (TOC) levels in sediments were significantly higher immediately adjacent to cages compared to reference sites, and approximately 32\% of the samples under the cages showed significant degradation. At intermediate distances (50-100 m), influences from fish farming are not clearly detected by TOC analysis. Further, while neither depth nor current speed alone are good predictors for environmental management, the results suggest recovery of sites by periodic abandonment (or fallowing) is one of the best management tools for sustainable salmon farming in cold-water environments. © 2003 Elsevier B.V. All rights reserved.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Carroll, Michael L. and Cochrane, Sabine and Fieler, Reinhold and Velvin, Roger and White, Patrick},
	year = {2003},
	keywords = {Organic enrichment, Environmental classification, Environmental impacts, Management practices, Monitoring methods, Norway, Particulate effluent, Sediment quality},
	pages = {165--180}
}

@article{mcnichol_carbon_1988,
	title = {Carbon cycling in coastal sediments: 1. {A} quantitative estimate of the remineralization of organic carbon in the sediments of {Buzzards} {Bay}, {MA}},
	volume = {52},
	issn = {00167037},
	url = {http://www.sciencedirect.com/science/article/pii/0016703788902232 http://linkinghub.elsevier.com/retrieve/pii/0016703788902232},
	doi = {10.1016/0016-7037(88)90223-2},
	number = {6},
	journal = {Geochimica et Cosmochimica Acta},
	author = {McNichol, Ann P and Lee, Cindy and Druffel, Ellen R.M},
	month = jun,
	year = {1988},
	pages = {1531--1543}
}

@article{giles_sedimentation_2006,
	title = {Sedimentation from mussel ({Perna} canaliculus) culture in the {Firth} of {Thames}, {New} {Zealand}: {Impacts} on sediment oxygen and nutrient fluxes},
	volume = {261},
	issn = {00448486},
	doi = {10.1016/j.aquaculture.2006.06.048},
	abstract = {Shellfish aquaculture is growing worldwide and previous studies have shown a range of associated environmental impacts. In the Firth of Thames, New Zealand, there are more than 2000??ha of existing and approved farm area with applications pending for approximately another 6000??ha, however, no previous studies have examined the impacts of mussel culture in this region. To determine the impact of a mussel farm (45??ha) in the Firth of Thames we measured sedimentation rates by deploying sediment traps, sediment characteristics by collecting sediment cores and sediment oxygen and nutrient fluxes by deploying benthic chambers in four seasons. Sedimentation under the farm was increased by 106??g m- 2 d- 1 compared to the reference site. Similarly sediments under the farm had elevated organic carbon, nitrogen, chlorophyll a and phaeopigment concentrations indicative of the additional organic input due to bivalve biodeposition. Oxygen consumption was higher under the farm compared to a reference site (1.1-2.1??) but this increase was only significant (p {\textbackslash}textless 0.001) in summer when rates reached 3083????mol m- 2 h- 1 under the farm. Ammonia release rates ranged from 80 to 319????mol m- 2 h- 1 and were higher under the farm compared to the reference site in spring (1.8??, non-significant p = 0.588) and autumn (3??, significant p = 0.006) but in summer release rates at the reference site (275????mol m- 2 h- 1) were 1.4?? higher than those under the farm. Nitrate fluxes (3.1 to 21.8????mol m- 2 h- 1) were significantly (p = 0.001) higher at the farm site. Oxygen and nutrient fluxes generally demonstrated the typical response to increased organic input due to sedimentation from mussel culture. Unusually low nitrogen release rates in summer may indicate enhanced denitrification under the farm. Benthic regeneration at the reference site could supply 74\% of nitrogen required by pelagic primary producers whereas under the farm it could account for 94\%. This demonstrates the importance of benthic nutrient regeneration in this region and that mussel culture can lead to a redistribution of nutrients. The farm we studied is small and located in a high-energy environment and impacts from larger farms or in areas where biodeposit dispersal is limited are likely to be even more significant and we suggest that site-specific hydrodynamic and biogeochemical conditions have to be taken into account when planning new mussel farms to prevent excessive modifications of nutrient dynamics. ?? 2006 Elsevier B.V. All rights reserved.},
	number = {1},
	journal = {Aquaculture},
	author = {Giles, Hilke and Pilditch, Conrad A. and Bell, Dudley G.},
	year = {2006},
	keywords = {Nitrogen, Aquaculture, Benthic-pelagic coupling, Bivalve, Sediment oxygen consumption},
	pages = {125--140}
}

@article{murphy_microbial_2016-1,
	title = {Microbial nitrogen processing in hard clam ({Mercenaria} mercenaria) aquaculture sediments: the relative importance of denitrification and dissimilatory nitrate reduction to ammonium ({DNRA})},
	volume = {61},
	issn = {19395590},
	doi = {10.1002/lno.10305},
	abstract = {© 2016 Association for the Sciences of Limnology and OceanographyAs bivalve aquaculture expands worldwide, an understanding of its role in nutrient cycling is necessary to ensure ecological sustainability and determine the potential of using bivalves for nutrient mitigation. Whereas several studies, primarily of epifaunal bivalves, have assessed denitrification, few have considered nutrient regeneration processes such as dissimilatory nitrate reduction to ammonium (DNRA), which competes with denitrification for nitrate and results in nitrogen retention rather than loss. This study compares sediment nitrogen cycling including mineralization, DNRA, and denitrification within U.S. clam aquaculture sediments to nearby uncultivated sediments, seasonally. Clam aquaculture significantly increased sediment ammonium and phosphate effluxes relative to uncultivated sediments. Both DNRA and denitrification were significantly enhanced at clam beds compared to uncultivated sediments in July and November, while in May only DNRA was increased. The ratio of DNRA to denitrification was significantly higher at clam beds compared to uncultivated sediments, demonstrating that DNRA may be favored due to a ready supply of labile organic carbon relative to nitrate and perhaps sulfidic conditions. Functional gene abundances, nrfA (DNRA) and nirS (denitrification) followed similar patterns to nitrate respiration rates with highest nrfA abundances in the clam sediments and similar nirS abundances across seasons and sediment type. Ultimately clam sediments were found to be a significant source of nutrients to the water column whereas uncultivated sediments retained ammonium produced by microbial mineralization. Thus, clam cultivation may promote local eutrophication (i.e., increased primary production) by facilitating nutrient regeneration and retention of ammonium in the sediments.},
	number = {5},
	journal = {Limnology and Oceanography},
	author = {Murphy, Anna E. and Anderson, Iris C. and Smyth, Ashley R. and Song, Bongkeun and Luckenbach, Mark W.},
	year = {2016},
	pages = {1589--1604}
}

@article{caffrey_effect_1993,
	title = {Effect of organic loading on nitrification and denitrification in a marine sediment microcosm},
	volume = {12},
	issn = {01686496},
	url = {http://doi.wiley.com/10.1016/0168-6496(93)90011-U},
	doi = {10.1016/0168-6496(93)90011-U},
	number = {3},
	journal = {FEMS Microbiology Ecology},
	author = {Caffrey, J and Sloth, N.P. and Kaspar, H.F. and Blackburn, T.H.},
	year = {1993},
	keywords = {denitrification, benthic fluxes, microcosm, nitrification, organic loading},
	pages = {159--167}
}

@article{nielsen_denitrification_1992,
	title = {Denitrification in sediment deermined from nitrogen isotope pairing technique},
	volume = {86},
	issn = {03781097},
	journal = {FEMS Microbiology Letters},
	author = {Nielsen, LP},
	year = {1992},
	keywords = {sediment, denitrification, nitrification, 5n, isotopes, sno},
	pages = {357--362}
}

@article{benitez-nelson_biogeochemical_2000,
	title = {The biogeochemical cycling of phosphorus in marine systems},
	volume = {51},
	issn = {00128252},
	doi = {10.1016/S0012-8252(00)00018-0},
	abstract = {The cycling of phosphorus (P) in the ocean has long been viewed from a geological perspective that tends to focus on balancing P sources (riverine and atmospheric) and sinks (sedimentary burial) over long ({\textbackslash}textgreater 1000 years) time scales. There have been substantially fewer treatises, however, that have sought to review current understanding of the processes which effect the distribution of P between these two endpoints. In this paper, a comprehensive review of the biogeochemical cycling of P within the oceans is given, with particular attention focused on the composition and recycling rates of P within the water column. (C) 2000 Elsevier Science B.V. All rights reserved.},
	number = {1-4},
	journal = {Earth Science Reviews},
	author = {Benitez-Nelson, Claudia R.},
	year = {2000},
	keywords = {Biogeochemical cycling, Marine ecosystems, Nutrient cycling, Phosphorus, Turnover rates},
	pages = {109--135}
}

@article{kuypers_anaerobic_2006,
	title = {Anaerobic ammonium oxidation in the marine environment},
	volume = {64},
	abstract = {Oceanographers noticed already many years ago that far less ammonium accumulated in anoxic fjords and basins, than would be expected from the stoichiometry of heterotrophic denitrification. It was suggested that this 'missing' ammonium was oxidized with nitrate to free N(2). Since then several other workers have argued based on chemical profiles that ammonium is oxidized anaerobically in oxygen deficient marine sediments and waters with either nitrate or manganese oxides as electron acceptor. While there is as yet no direct evidence for the anaerobic ammonium oxidation with manganese oxides in either sediments or anoxic water columns, more and more evidence is being provided for anaerobic ammonium oxidation with nitrite/nitrate. The first direct evidence for the anaerobic oxidation of ammonium was provided in a waste water bioreactor, where so-called 'anammox' bacteria belonging to the Order Planctomycetales directly oxidize ammonium to N(2) with nitrite as the electron acceptor. Although the anammox process was generally seen as a promising process for waste water treatment. it was believed to be insignificant in the natural environment due to the extremely slow generation times (more than 2 weeks) of the anammox organisms. However, recent studies provide direct evidence for anaerobic oxidation of ammonium by nitrate and/or nitrite in marine sediments, oxygen minimum zones, anoxic fjords and basins as well as Arctic sea ice. Phylogenetic analysis of 16S ribosomal RNA sequences show that the bacteria involved are closely related to anammox bacteria from waste water bioreactors. The combined biogeochemical and microbiological data available indicates that anammox may contribute significantly to the loss of reactive nitrogen in the ocean.},
	journal = {Past and Present Water Column Anoxia},
	author = {Kuypers, M M M and Lavik, G and Thamdrup, B},
	year = {2006},
	keywords = {anammox, denitrification, anaerobic ammonium oxidation, fluidized-bed reactor, nitrogen cycle, anammox bacteria, autotrophic nitrogen-removal, benguela upwelling system, costa-rica, golfo-dulce, in-situ detection, marine, n-2 production, organic-carbon, oxidizing bacteria, review, suboxic},
	pages = {311--335}
}

@article{tiedje_denitrification:_1982,
	title = {Denitrification: ecological niches, competition and survival},
	volume = {48},
	issn = {00036072},
	doi = {10.1007/BF00399542},
	abstract = {Organisms with the denitrification capacity are widely distributed and in high density in nature. It is not well understood why they are so successful. A survey of denitrifying enzyme content of various habitats is presented which indicates a role of carbon and oxygen, but not nitrate, in affecting denitrifier populations. It is suggested that organic carbon is more important than oxygen status in determining denitrifying enzyme content of habitats. In low oxygen environments, denitrifiers compete with organisms that dissimilate nitrate to ammonium, a process which conserves nitrogen. The energetic and kinetic parameters that affect this competition are evaluated. The latter is examined using Michaelis-Menten theoretical models by varying Vmax, Km, and So (substrate concentration) for the two competing populations. The outcome predicted by these models is presented and discussed in relation to previous data on population densities and Km values for representatives of these competing groups. These models suggest the conditions required to achieve changes in partitioning between the two fates of nitrate. These considerations are important if one is to be able to evaluate and successfully "manage" the fate of nitrate in any habitat.},
	number = {6},
	journal = {Antonie van Leeuwenhoek},
	author = {Tiedje, James M. and Sexstone, Alan J. and Myrold, David D. and Robinson, Joseph A.},
	year = {1982},
	pmid = {6762848},
	pages = {569--583}
}

@article{zhang_dissimilatory_2014,
	title = {Dissimilatory nitrate reduction to ammonium ({DNRA}) plays an important role in soil nitrogen conservation in neutral and alkaline but not acidic rice soil},
	volume = {15},
	issn = {16147480},
	doi = {10.1007/s11368-014-1037-7},
	abstract = {In the rice soils, the alternate wetting and drying conditions and the leakage of O-2 from rice roots provides a favorable environment for many N transformation processes, such as DNRA, nitrification, mineralization, and denitrification. Since nitrification is an inevitable process providing available NO3 (-) for DNRA and other NO3 (-) loss pathways, it is logical to hypothesize that a relationship exists between nitrification and DNRA. Thus, we quantified the specific gross N transformation rates occurring simultaneously to investigate the correlation among the N transformation rates in the rice soil. In this study, three rice soils with different pH values were selected. The combination of N-15 tracing experiment and numerical modeling method was performed to quantify the specific gross N transformation rates (e.g., DNRA), to analyze the correlation between DNRA and the other N transformations, and to estimate the functional role of DNRA comparing to other N transformation in the rice soil. The results showed that there were two NH4 (+) production pathways, organic N mineralization and DNRA, in the neutral (pH 6.2) and alkaline (pH 8.2) soils, while the DNRA process was negligible in acidic soil (pH 4.7). The mineralization rate in the acidic soil (2.69 mg kg(-1)d(-1)) was significantly higher than that in neutral and alkaline soils. The DNRA rate was 0.48 and 1.09 mg kg(-1)d(-1), which was almost equal to the mineralization rate, in the neutral (pH 6.2) and alkaline (pH 8.2) soils, offsetting efficiently the effect of low mineralization on N availability in ecosystems. The DNRA rate linearly increased with the increase in gross nitrification rate (p {\textbackslash}textless 0.05). This significant coupling relationship between DNRA and nitrification favors N conservation and availability for paddy growth in the rice ecosystem. DNRA plays an important role in soil N conservation and availability in neutral and alkaline but not acidic rice soil.},
	number = {3},
	journal = {Journal of Soils and Sediments},
	author = {Zhang, Jinbo and Lan, Ting and Müller, Christoph and Cai, Zucong},
	year = {2014},
	keywords = {Dissimilatory nitrate reduction to ammonium (DNRA), 15N tracing model, Nitrification, Mineralization, Rice soil, Soil nitrogen conservation},
	pages = {523--531}
}

@article{keeley_spatial_2014,
	title = {Spatial and temporal dynamics in macrobenthos during recovery from salmon farm induced organic enrichment: when is recovery complete?},
	volume = {80},
	issn = {1879-3363},
	url = {http://www.sciencedirect.com/science/article/pii/S0025326X13007418},
	doi = {10.1016/j.marpolbul.2013.12.008},
	abstract = {This study documents eight years of benthic recovery at a highly impacted salmon farm. Substantial recovery occurred in the first 2 years, and was assessed to be complete after ∼5 years. However, minor differences were still evident, along with some on-going benthic instability, attributable to medium-scale spatial movements and successional patterns of macrobenthos. Quantifying the endpoint of 'recovery' proved challenging due to: lack of a widely accepted definition, inherent variability in recovering sediments, differing trajectories of impact and reference sites, and statistical challenges. More complex biotic indices and metrics incorporating multiple variables were the most robust indicators. Statistical tests for 'parallelism' in the trajectories of Cage and Reference sites proved useful, but results were contingent upon how the method was applied, and should therefore be used in conjunction with data-visualisation methods. The study highlights the importance of a predetermined recovery endpoint, and using multiple indicators and a weight-of-evidence assessment approach.},
	number = {1-2},
	journal = {Marine pollution bulletin},
	author = {Keeley, Nigel B and Macleod, Catriona K and Hopkins, Grant A and Forrest, Barrie M},
	month = mar,
	year = {2014},
	pmid = {24503378},
	keywords = {Aquaculture, Animals, Ecosystem, Environmental Monitoring, Environmental Restoration and Remediation, Geologic Sediments, Geologic Sediments: chemistry, Invertebrates, Invertebrates: classification, Invertebrates: growth \& development, Salmon, Spatio-Temporal Analysis, Water Pollutants, Water Pollutants: analysis, Water Pollution, Water Pollution: statistics \& numerical data},
	pages = {250--62}
}

@article{devol_nitrogen_2003,
	title = {Nitrogen cycle: {Solution} to a marine mystery},
	volume = {422},
	issn = {0946-2171},
	url = {http://link.springer.com/10.1007/s00340-003-1120-z},
	doi = {10.1007/s00340-003-1120-z},
	abstract = {The anammox reaction, a microbial process that was first observed in waste-water treatment plants, looks as if it may be a key player in the nitrogen cycle in certain parts of the oceans.},
	journal = {Nature},
	author = {Devol, Allan H.},
	month = mar,
	year = {2003},
	pages = {575--576}
}

@article{braeckman_role_2010,
	title = {Role of macrofauna functional traits and density in biogeochemical fluxes and bioturbation},
	volume = {399},
	issn = {0171-8630},
	url = {http://www.int-res.com/abstracts/meps/v399/p173-186/},
	doi = {10.3354/meps08336},
	journal = {Marine Ecology Progress Series},
	author = {Braeckman, U and Provoost, P and Gribsholt, B and Van Gansbeke, D and Middelburg, JJ and Soetaert, K and Vincx, M and Vanaverbeke, J},
	month = jan,
	year = {2010},
	keywords = {Bioturbation, Abra alba, Density, Ecosystem functioning, Functional traits, Lanice conchilega, Macrobenthos, Nephtys sp., Temporal variability},
	pages = {173--186}
}

@article{sousa_subtidal_2007,
	title = {Subtidal macrobenthic structure in the lower lima estuary, {NW} of {Iberian} {Peninsula}},
	volume = {44},
	issn = {0003-455X},
	doi = {10.1002/aqc},
	abstract = {Seasonal variation of the subtidal macrobenthic community in the lower Lima estuary was investigated at twelve sites. Univariate and multivariate analyses were used to establish patterns in species distribution, abundance, and biomass; and to determine the influence of site and season on the subtidal macrobenthic community. A total of 10 1 macrobenthic taxa were identified and values of diversity were generally low indicating a high degree of dominance of few species. Average abundance and biomass per site ranged from 46.7 to 8060 ind. m(-2) and 0.56 to 28.96 g AFDW m(-2), respectively. Abra alba was most abundant and had the highest biomass. Multivariate analysis revealed four distinct groups. Each group was represented by a specific species composition and characterised by different environmental conditions, in particular, the sediment characteristics and salinity. Abundance/biomass comparison (ABC) indicated that the lower part of the estuary is under environmental stress and is dominated by opportunistic species. The subtidal macrobenthic community of the lower Lima estuary differed between sites but not between seasons of the year.},
	number = {August},
	journal = {Annales Zoologici Fennici},
	author = {Sousa, R and Dias, S and Antunes, C},
	year = {2007},
	pmid = {299},
	keywords = {amazon, atlantic forest, ecosystem services, farmers, fish ecology, fishermen, floodplain forests, local ecological knowledge},
	pages = {303--313}
}

@article{canfield_pathways_1993-1,
	title = {Pathways of organic carbon oxidation in three continental margin sediments.},
	volume = {113},
	issn = {00253227},
	doi = {10.1016/0025-3227(93)90147-N},
	abstract = {We have combined several different methodologies to quantify rates of organic carbon mineralization by the various electron acceptors in sediments from the coast of Denmark and Norway. Rates of NH4+ and Sigma CO2 liberation sediment incubations were used with O2 penetration depths to conclude that O2 respiration accounted for only between 3.6-17.4\% of the total organic carbon oxidation. Dentrification was limited to a narrow zone just below the depth of O2 penetration, and was not a major carbon oxidation pathway. The processes of Fe reduction, Mn reduction and sulfate reduction dominated organic carbon mineralization, but their relative significance varied depending on the sediment. Where high concentrations of Mn-oxide were found (3-4 wt\% Mn), only Mn reduction occurred. With lower Mn oxide concentrations more typical of coastal sediments, Fe reduction and sulfate reduction were most important and of a similar magnitude. Overall, most of the measured O2 flux into the sediment was used to oxidized reduced inorganic species and not organic carbon. We suspect that the importance of O2 respiration in many coastal sediments has been overestimated, whereas metal oxide reduction (both Fe and Mn reduction) has probably been well underestimated.},
	journal = {Marine geology},
	author = {Canfield, D E and Jorgensen, B B and Fossing, H and Glud, R and Gundersen, J and Ramsing, N B and Thamdrup, B and Hansen, J W and Nielsen, L P and Hall, P O},
	year = {1993},
	pmid = {11539842},
	keywords = {NASA Discipline Exobiology, Non-NASA Center},
	pages = {27--40}
}

@article{behrendt_vertical_2013-2,
	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{kalvelage_oxygen_2011,
	title = {Oxygen sensitivity of anammox and coupled {N}-cycle processes in oxygen minimum zones},
	volume = {6},
	issn = {19326203},
	doi = {10.1371/journal.pone.0029299},
	abstract = {Nutrient measurements indicate that 30-50\% of the total nitrogen (N) loss in the ocean occurs in oxygen minimum zones (OMZs). This pelagic N-removal takes place within only ∼0.1\% of the ocean volume, hence moderate variations in the extent of OMZs due to global warming may have a large impact on the global N-cycle. We examined the effect of oxygen (O(2)) on anammox, NH(3) oxidation and NO(3)(-) reduction in (15)N-labeling experiments with varying O(2) concentrations (0-25 µmol L(-1)) in the Namibian and Peruvian OMZs. Our results show that O(2) is a major controlling factor for anammox activity in OMZ waters. Based on our O(2) assays we estimate the upper limit for anammox to be ∼20 µmol L(-1). In contrast, NH(3) oxidation to NO(2)(-) and NO(3)(-) reduction to NO(2)(-) as the main NH(4)(+) and NO(2)(-) sources for anammox were only moderately affected by changing O(2) concentrations. Intriguingly, aerobic NH(3) oxidation was active at non-detectable concentrations of O(2), while anaerobic NO(3)(-) reduction was fully active up to at least 25 µmol L(-1) O(2). Hence, aerobic and anaerobic N-cycle pathways in OMZs can co-occur over a larger range of O(2) concentrations than previously assumed. The zone where N-loss can occur is primarily controlled by the O(2)-sensitivity of anammox itself, and not by any effects of O(2) on the tightly coupled pathways of aerobic NH(3) oxidation and NO(3)(-) reduction. With anammox bacteria in the marine environment being active at O(2) levels ∼20 times higher than those known to inhibit their cultured counterparts, the oceanic volume potentially acting as a N-sink increases tenfold. The predicted expansion of OMZs may enlarge this volume even further. Our study provides the first robust estimates of O(2) sensitivities for processes directly and indirectly connected with N-loss. These are essential to assess the effects of ocean de-oxygenation on oceanic N-cycling.},
	number = {12},
	journal = {PLoS ONE},
	author = {Kalvelage, Tim and Jensen, Marlene M. and Contreras, Sergio and Revsbech, Niels Peter and Lam, Phyllis and Günter, Marcel and LaRoche, Julie and Lavik, Gaute and Kuypers, Marcel M M},
	year = {2011},
	pmid = {22216239}
}

@article{devol_denitrification_2015-1,
	title = {Denitrification, anammox, and {N}2 production in marine sediments},
	volume = {7},
	issn = {1941-1405},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/25560607},
	doi = {10.1146/annurev-marine-010213-135040},
	abstract = {Fixed nitrogen limits primary productivity in many parts of the global ocean, and it consequently plays a role in controlling the carbon dioxide content of the atmosphere. The concentration of fixed nitrogen is determined by the balance between two processes: the fixation of nitrogen gas into organic forms by diazotrophs, and the reconversion of fixed nitrogen to nitrogen gas by denitrifying organisms. However, current sedimentary denitrification rates are poorly constrained, especially in permeable sediments, which cover the majority of the continental margin. Also, anammox has recently been shown to be an additional pathway for the loss of fixed nitrogen in sediments. This article briefly reviews sedimentary fixed nitrogen loss by sedimentary denitrification and anammox, including in sediments in contact with oxygen-deficient zones. A simple extrapolation of existing rate measurements to the global sedimentary denitrification rate yields a value smaller than many existing measurement-based estimates but still larger than the rate of water column denitrification.},
	journal = {Annual Review of Marine Science},
	author = {Devol, Allan H},
	year = {2015},
	pmid = {25560607},
	keywords = {nitrogen cycle, anoxic sediment, nit, nitrogen budget, nitrogen isotope},
	pages = {403--423}
}

@article{widdicombe_importance_2004,
	title = {Importance of bioturbators for biodiversity maintenance: indirect effects of fishing disturbance},
	volume = {275},
	url = {http://www.int-res.com/abstracts/meps/v275/p1-10/},
	doi = {10.3354/meps275001},
	abstract = {The relative impact on macrofaunal diversity of 7 naturally co-occurring bioturbators has been examined in a benthic mesocosm experiment. The bioturbators chosen were selected because of their potential vulnerability to the disturbances associated with demersal trawling. The experiment was conducted at the Solbergstrand mesocosm (Norwegian Institute for Water Research) using subtidal sediment collected from Bjørnehodebukta, a small sheltered bay in the Oslofjord. For 3 of the bioturbating species (Brissopsis lyrifera, Aphrodita aculeata and Amphiura chiajei) a positive, linear relationship was demonstrated between bioturbator abundance and measures of species richness (number of species and Margalef species richness). It was suggested that the presence of these bioturbating species increased oxygen penetration into the sediment, leading to an enhancement in the ability of benthic systems to process organic material. This had a beneficial effect on the associated fauna in terms of maintaining levels of diversity. For Nephtys caeca, highest species diversity was seen in the low abundance treatments. Predation by N. caeca on small polychaetes is proposed as a possible explanation of the lower diversity in high-density treatments. It is concluded that B. lyrifera, A. aculeata, A. chiajei and N. caeca are functionally similar with respect to setting the diversity of the associated macrobenthic community and may therefore fulfill the same role within the benthic ecosystem. The presence of Calocaris macandreae, Nuculana minuta and Astarte sulcata had no detectable effect on diversity. Trawling has been shown to reduce the abundance of bioturbating species, and the current study demonstrates important implications of this loss on the maintenance of diversity. In addition, the interactions between bioturbation, diversity and organic enrichment highlight the need for management of anthropogenic impacts within the coastal environment in a holistic way rather than by isolation.},
	journal = {Marine Ecology Progress Series},
	author = {Widdicombe, S and Austen, MC and Kendall, MA and Olsgard, F and Schaanning, MT and Dashfield, SL and Needham, HR},
	month = jul,
	year = {2004},
	keywords = {eutrophication, bioturbation, trawling, macrofauna, diversity},
	pages = {1--10}
}

@article{gruber_marine_2008-1,
	title = {The {Marine} {Nitrogen} {Cycle}: {Overview} and {Challenges} {BT} - {Nitrogen} in the {Marine} {Environment}},
	url = {papers3://publication/uuid/0062D8B9-1D1B-490B-B5B8-793C0D4B8D9D},
	doi = {http://dx.doi.org/10.1016/B978-0-12-372522-6.00001-3},
	abstract = {Publisher Summary This chapter serves as an introduction to rest of the book. The focus here is on providing an overview of the most important pools of nitrogen, their transformations, their distribution, and their connection to the cycling of other biogeochemically relevant elements, primarily carbon, oxygen, and phosphorus. The scale is global, as subsequent chapters cover individual ocean basins and systems. The chapter also addresses a series of nitrogen challenges, such as the question of how the marine nitrogen cycle appears to be able to maintain a relatively well-established homeostasis, that is, a balance between gains and losses of fixed nitrogen. Finally, it discusses the anthropogenic perturbation of the marine nitrogen cycle. As it examines, however, the answers to many of these questions remain elusive, reminding us how little we know about the marine nitrogen cycle, and how much still remains to be discovered. Although the marine nitrogen cycle occupies a central role within the biogeochemical cycles of the sea, scientific communities barely begin to its major processes and the factors that regulate them. This occurs at a time when human interventions in the Earth system rise to unprecedented levels, with a particularly strong impact on the global nitrogen cycle.},
	number = {1},
	journal = {Nitrogen in the Marine Environment},
	author = {Gruber, Nicolas},
	year = {2008},
	keywords = {nitrogen, marine, SEFS567},
	pages = {1--50}
}

@article{mcghie_degradation_2000,
	title = {The degradation of fish-cage waste in sediments during fallowing},
	volume = {187},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/S0044848600003173},
	doi = {10.1016/S0044-8486(00)00317-3},
	abstract = {The composition and rate of degradation of organic waste deposited in sediment underneath and adjacent to fish cages in the Huon Estuary, Tasmania, Australia, were investigated. Sediment samples from two near-adjacent sites, but with different sediment types and depths, were analyzed for total organic matter, lipids (fatty acids and sterols), \%C, δ13C, \%N, δ15N, and redox potential during a 12-month fallowing period. Additionally, representative samples of fish food and fish faeces were analyzed. It was found that most of the accumulation of organic matter was confined to an area directly underneath the fish cages, but at 30 m from the center of the cage, indicators of fish cage waste (faeces and fish food) were still elevated compared with reference sites. As both fish food and faeces have distinctive fatty acid profiles, the relative proportion of food and/or faeces deposited on the sediment could be determined. After 12 months fallowing, fish-farm-derived organic matter in surface sediment at the center of the cage remained greater than at 30 m distance, even though redox potentials indicated that normal oxic conditions had returned.},
	number = {3-4},
	journal = {Aquaculture},
	author = {McGhie, Tony K. and Crawford, Christine M. and Mitchell, Iona M. and O'Brien, Dominic},
	month = jul,
	year = {2000},
	keywords = {Sediment, Carbon isotopes, Fallowing, Fatty acids, Fish cages, Nitrogen isotopes, Sterols},
	pages = {351--366}
}

@article{nickell_bioturbation_2003,
	title = {Bioturbation, sediment fluxes and benthic community structure around a salmon cage farm in {Loch} {Creran}, {Scotland}},
	volume = {285-286},
	issn = {00220981},
	url = {http://www.sciencedirect.com/science/article/pii/S0022098102005294},
	doi = {10.1016/S0022-0981(02)00529-4},
	abstract = {This study examined bioturbation along an organic carbon gradient away from an Atlantic salmon farm and sought to determine relationships between benthic fluxes, mixing intensity and the infaunal community structure. Macrofaunal community structure, abundance and biomass were examined at stations with varying quantities and qualities of organic matter input. In situ benthic chambers were used to determine oxygen and nutrient fluxes and mixing parameters were derived from down core profiles of chlorophyll a (chl a). Mean oxygen demand of sediments ranged between 8.8 and 467.8 mmol m-2 day-1, being highest beneath the fish farm and indicating very high rates of community respiration and organic matter diagenesis. Oxygen and nutrient fluxes followed similar trends to community abundance and biomass, declining with increasing distance from the farm. Mixing intensity increased with distance from the farm until returning, at the farthest station, to values similar to those measured beneath the farm. The differences in the community structure between sediments beneath the farm and furthest from it suggest that similar diffusive mixing coefficients are generated by different mechanisms. These results generally follow the successional model of Pearson and Rosenberg [Oceanogr. Mar. Biol. Ann. Rev. 16 (1978) 229.], with the exception of the farthest station, but suggest that the bioturbation potential of the community over short time scales is greatest at stations with intermediate qualities and quantity of organic matter. However, the methods used here to assess mixing over short time scales (i.e. diffusive mixing coefficient and the mixed layer depth) do not account for the activities of deep burrowing infaunal animals, such as Maxmuelleria lankesteri, known to be present at the farthest station. ?? 2002 Elsevier Science B.V. All rights reserved.},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Nickell, Lois A. and Black, Kenneth D. and Hughes, David J. and Overnell, Julian and Brand, Tim and Nickell, Thomas D. and Breuer, Eric and Harvey, S. Martyn and Martyn Harvey, S and Harvey, S. Martyn},
	month = feb,
	year = {2003},
	keywords = {Nutrients, Organic carbon, Oxygen, Bioturbation, Bioturbation with Aquaculture, Macrofauna, oxygen concentration},
	pages = {221--233}
}

@article{nickell_bioturbation_2003-1,
	title = {Bioturbation, sediment fluxes and benthic community structure around a salmon cage farm in {Loch} {Creran}, {Scotland}},
	volume = {285-286},
	issn = {00220981},
	doi = {10.1016/S0022-0981(02)00529-4},
	abstract = {This study examined bioturbation along an organic carbon gradient away from an Atlantic salmon farm and sought to determine relationships between benthic fluxes, mixing intensity and the infaunal community structure. Macrofaunal community structure, abundance and biomass were examined at stations with varying quantities and qualities of organic matter input. In situ benthic chambers were used to determine oxygen and nutrient fluxes and mixing parameters were derived from down core profiles of chlorophyll a (chl a). Mean oxygen demand of sediments ranged between 8.8 and 467.8 mmol m-2 day-1, being highest beneath the fish farm and indicating very high rates of community respiration and organic matter diagenesis. Oxygen and nutrient fluxes followed similar trends to community abundance and biomass, declining with increasing distance from the farm. Mixing intensity increased with distance from the farm until returning, at the farthest station, to values similar to those measured beneath the farm. The differences in the community structure between sediments beneath the farm and furthest from it suggest that similar diffusive mixing coefficients are generated by different mechanisms. These results generally follow the successional model of Pearson and Rosenberg [Oceanogr. Mar. Biol. Ann. Rev. 16 (1978) 229.], with the exception of the farthest station, but suggest that the bioturbation potential of the community over short time scales is greatest at stations with intermediate qualities and quantity of organic matter. However, the methods used here to assess mixing over short time scales (i.e. diffusive mixing coefficient and the mixed layer depth) do not account for the activities of deep burrowing infaunal animals, such as Maxmuelleria lankesteri, known to be present at the farthest station. ?? 2002 Elsevier Science B.V. All rights reserved.},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Nickell, Lois A. and Black, Kenneth D. and Hughes, David J. and Overnell, Julian and Brand, Tim and Nickell, Thomas D. and Breuer, Eric and Harvey, S. Martyn},
	year = {2003},
	keywords = {Nutrients, Organic carbon, Oxygen, Bioturbation, Macrofauna},
	pages = {221--233}
}

@article{islam_nitrogen_2005,
	title = {Nitrogen and phosphorus budget in coastal and marine cage aquaculture and impacts of effluent loading on ecosystem: {Review} and analysis towards model development},
	volume = {50},
	issn = {0025326X},
	doi = {10.1016/j.marpolbul.2004.08.008},
	abstract = {Being an essentially open system, cages are usually characterized by a high degree of interaction with environment and cage systems are highly likely to produce large bulk of wastes that are released directly into the environment. Therefore, large-scale cage aquaculture development has been put into question and concerns have been raised that cage aquaculture produces large bulk of wastes that are rich in organic matter and nutrients and are released into coastal and nearshore environment. Recent information on cage aquaculture nutrient budget is scarce and most published reports are dated. This paper reviews cage aquaculture nutrient budget and nutrient loadings and propose a model for nutrient (nitrogen, N and phosphorus, P) budget in a hypothetical cage aquaculture farm with values of feed loss, FCR (feed conversion ratio) and nutrient contents in feed and fish taken from published literature in order to calculate the amount (kg) of N and P produced and released to the environment for each ton of fish produced. The paper proposes, in addition, a critically analyzed nutrient budget based on the dry matter conversion rate instead of the usual feed conversion rate. The conceptual model shows that 132.5 kg N and 25.0 kg P are released to the environment for each ton of fish produced; these values are as high as 462.5 kg N and 80.0 kg P when calculated on the basis of dry matter conversion rate instead of usual feed conversion rate. Thus, the annual global N and P loadings from cage aquaculture (10,000 tons fish and 3000 tons dry matter) are 1325 tons N and 250 tons P and 1387.5 tons N and 240.0 tons P based on usual feed conversion rate and dry matter conversion rate respectively. The paper also proposes, by analyzing the existing data, an FCR-based regression model for predicting nutrient loadings for a given diet. Finally, attempt was made to calculate the annual global loading and release of N and P from cage aquaculture to the coastal and marine environment, the potential impacts of nutrient loading on the ecosystem were discussed and critical points to be considered for minimizing nutrient output in cage aquaculture were suggested. ?? 2004 Elsevier Ltd. All rights reserved.},
	number = {1},
	journal = {Marine Pollution Bulletin},
	author = {Islam, Md Shahidul},
	year = {2005},
	pmid = {15664033},
	keywords = {Nitrogen, Cage aquaculture, Mariculture, Phosphorus, Effluent nutrient loading, FCR, Nutrient budget},
	pages = {48--61}
}

@article{nickell_bioturbation_2003-2,
	title = {Bioturbation, sediment fluxes and benthic community structure around a salmon cage farm in {Loch} {Creran}, {Scotland}},
	volume = {285-286},
	issn = {00220981},
	url = {http://www.sciencedirect.com/science/article/pii/S0022098102005294},
	doi = {10.1016/S0022-0981(02)00529-4},
	abstract = {This study examined bioturbation along an organic carbon gradient away from an Atlantic salmon farm and sought to determine relationships between benthic fluxes, mixing intensity and the infaunal community structure. Macrofaunal community structure, abundance and biomass were examined at stations with varying quantities and qualities of organic matter input. In situ benthic chambers were used to determine oxygen and nutrient fluxes and mixing parameters were derived from down core profiles of chlorophyll a (chl a). Mean oxygen demand of sediments ranged between 8.8 and 467.8 mmol m-2 day-1, being highest beneath the fish farm and indicating very high rates of community respiration and organic matter diagenesis. Oxygen and nutrient fluxes followed similar trends to community abundance and biomass, declining with increasing distance from the farm. Mixing intensity increased with distance from the farm until returning, at the farthest station, to values similar to those measured beneath the farm. The differences in the community structure between sediments beneath the farm and furthest from it suggest that similar diffusive mixing coefficients are generated by different mechanisms. These results generally follow the successional model of Pearson and Rosenberg [Oceanogr. Mar. Biol. Ann. Rev. 16 (1978) 229.], with the exception of the farthest station, but suggest that the bioturbation potential of the community over short time scales is greatest at stations with intermediate qualities and quantity of organic matter. However, the methods used here to assess mixing over short time scales (i.e. diffusive mixing coefficient and the mixed layer depth) do not account for the activities of deep burrowing infaunal animals, such as Maxmuelleria lankesteri, known to be present at the farthest station. ?? 2002 Elsevier Science B.V. All rights reserved.},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Nickell, Lois A. and Black, Kenneth D. and Hughes, David J. and Overnell, Julian and Brand, Tim and Nickell, Thomas D. and Breuer, Eric and Martyn Harvey, S and Harvey, S. Martyn},
	month = feb,
	year = {2003},
	keywords = {Nutrients, Organic carbon, Oxygen, Bioturbation, Bioturbation with Aquaculture, Macrofauna, oxygen concentration},
	pages = {221--233}
}

@article{grant_multidisciplinary_1995,
	title = {A {Multidisciplinary} {Approach} to {Evaluating} {Impacts} of {Shellfish} {Aquaculture} on {Benthic} {Communities}},
	volume = {18},
	issn = {01608347},
	url = {http://link.springer.com/10.2307/1352288},
	doi = {10.2307/1352288},
	number = {1},
	journal = {Estuaries},
	author = {Grant, J. and Hatcher, A. and Scott, D. B. and Pocklington, P. and Schafer, C. T. and Winters, G. V.},
	month = mar,
	year = {1995},
	pages = {124}
}

@article{vanderborght_vertical_1975-1,
	title = {Vertical distribution of nitrate concentration in interstitial water of marine sediments with nitrification and denitrification},
	volume = {20},
	issn = {00243590},
	doi = {10.4319/lo.1975.20.6.0953},
	number = {6},
	journal = {Limnology \& Oceanography},
	author = {Vanderborght, Jean-Pierre and Billen, Gilles},
	year = {1975},
	pages = {953--961}
}

@article{nizzoli_impact_2006-1,
	title = {Impact of clam and mussel farming on benthic metabolism and nitrogen cycling, with emphasis on nitrate reduction pathways},
	volume = {315},
	issn = {01718630},
	doi = {10.3354/meps315151},
	abstract = {The influences of suspended mussel and infaunal clam cultivation on benthic metabolism and nutrient cycling were compared in Goro lagoon, Italy. Both aquaculture types stimulated benthic metabolism, with sediment oxygen demand (SOD), CO2 and ammonium effluxes of up to 14, 16 and 1.2 mmol m-2 h-1. However, whilst mussel farming preferentially stimulated anaerobic metabolism and sediment reduction, clam farming did not. The mussel ropes were also large oxygen sinks and ammonium sources, with oxygen consumption and ammonium production rates of 1.4 to 1.5 and 0.18 to 0.43 mmol kg-1 h-1. Consequently, the overall impacts of mussel farming on oxygen and nutrient dynamics were much greater than those of clam farming. There were also differences in nitrate-reduction processes and the nitrate sources that fuelled them. In winter, at high water column nitrate concentrations, highest nitrate reduction rates (∼320 mmol m-2 h-1) occurred at the mussel farm. Nitrate reduction was driven predominantly by water column nitrate and ∼30\% of nitrate reduced was recycled to ammonium via dissimilatory nitrate reduction to ammonium (DNRA). At the control and clam farm sites, nitrate reduction rates were lower (∼180 mmol m-2 h-1), nitrification supplied ∼30\% of nitrate and denitrification was dominant. In summer under low nitrate conditions, nitrate reduction was highest (∼130 mmol m-2 h-1) at the mussel farm site, but this activity was completely dependent upon water column nitrate and 95\% of nitrate was reduced via DNRA. In contrast, at the clam farm station, DNRA was unimportant and nitrification was the major nitrate source for denitrification. Consequently, whilst nitrate reduction processes eliminated fixed N from the clam farm sediments via coupled nitrification-denitrification, the dominance of DNRA at the mussel farm site resulted in a net N input to the sediment compartment. These large differences in the impacts of clam and mussel farming can be explained by the fact that infaunal clams stimulate transfer of both organic matter and oxygen to the sediment, whereas suspended mussels enhance only organic matter inputs.},
	journal = {Marine Ecology Progress Series},
	author = {Nizzoli, Daniele and Welsh, David T. and Fano, Elisa Anna and Viaroli, Pierluigi},
	year = {2006},
	keywords = {Denitrification, Biodeposition, Dissimilatory nitrate reduction to ammonium, Aquaculture impacts, Mytilus galloprovincialis, Nitrification, Nutrient cycles, Tapes philippinarum},
	pages = {151--165}
}

@article{mirto_fish-farm_2010,
	title = {Fish-farm impact on metazoan meiofauna in the {Mediterranean} {Sea}: {Analysis} of regional vs. habitat effects},
	volume = {69},
	url = {https://www.sciencedirect.com/science/article/pii/S0141113609001044?via%3Dihub},
	doi = {10.1016/J.MARENVRES.2009.07.005},
	abstract = {The worldwide exponential growth of off-shore mariculture is raising severe concerns about the impacts of this industry on marine habitats and their biodiversity. We investigated the metazoan meiofaunal response to fish-farm impact in four regions of the Mediterranean Sea. Meiofaunal assemblages were investigated in two habitats (seagrass meadows of Posidonia oceanica and non-vegetated soft bottoms) comparing sites receiving faeces and uneaten food pellets from fish farms to control sites. We report here that, consistently across different regions, the meiofaunal abundance typically responded positively to fish-farm effluents. Biodeposition caused also significant changes in assemblage structure and the reduction in the richness of higher meiofaunal taxa, but the multivariate analysis of variance revealed that the effects were region- and habitat-specific. In non-vegetated systems, three of the four regions investigated displayed significant effects of the fish farms on richness of meiofaunal taxa. In vegetated habitats, meiofauna did not respond to biodeposition (except in one region), suggesting that seagrass meadows can mask the effects of fish-farm effluents on benthic biodiversity. We conclude that different indicators of fish-farm impact are needed in vegetated and non-vegetated benthic systems.},
	number = {1},
	journal = {Marine Environmental Research},
	author = {Mirto, Simone and Bianchelli, Silvia and Gambi, Cristina and Krzelj, Maja and Pusceddu, Antonio and Scopa, Mariaspina and Holmer, Marianne and Danovaro, Roberto},
	month = feb,
	year = {2010},
	keywords = {ecology, aquaculture effects, meiofaunal community},
	pages = {38--47}
}

@article{soetaert_model_1996,
	title = {A model of early diagenetic processes from the shelf to abyssal depths},
	volume = {60},
	issn = {00167037},
	url = {http://linkinghub.elsevier.com/retrieve/pii/0016703796000130},
	doi = {10.1016/0016-7037(96)00013-0},
	abstract = {We present a numerical model of sedimentary early diagenetic processes that includes oxic and anoxic mineralization. The model belongs to the new wave of early diagenesis models that account for depth-dependent bioturbation and porosity profiles; it can be used both for calculating steady-state conditions and transient simulation. It was developed to reproduce the cycling of carbon, oxygen, and nitrogen along the ocean margin; it resolves the sediment-depth profiles of carbon, oxygen, nitrate, ammonium, and other reduced substances. Organic carbon is modeled as two degradable fractions with different first-order degradation rates and nitrogen:carbon ratios, to account for the decreasing reactivity and N/C ratio of the organic matter with depth into the sediment. The consumption of oxygen and nitrate as terminal electron acceptors is explicitly modeled, and mineralization is limited both by carbon (first order kinetics) and by oxidant availability (Michaelis-Menten type kinetics). Nitrification and oxic mineralization are decoupled, which allows the description of ammonium profiles. Mineralization processes using other oxidants (manganese oxides, iron oxides, sulphate) are lumped into one process, where degradation is only carbon limited; the terminal electron acceptors are not explicitly modeled, only the production of reduced substances is described. These substances are in part permanently removed (e.g., pyrite formation below the bioturbation zone) and partly diffuse towards the oxic layer where they react with oxygen. The values of several parameters were constrained using literature-derived relationships. The model was calibrated on a dataset obtained from the literature, which relates the magnitude of the different pathways to total organic carbon mineralization. The influence of carbon flux, bioturbation, sedimentation rate, bottomwater concentrations of oxygen, and nitrate and carbon degradability on the different mineralization pathways is examined. The relative contribution of the oxic mineralization in the model is significantly depressed under high organic flux, under low bottomwater oxygen conditions and when the bioturbation increases; higher carbon degradability has only a small positive effect, while sedimentation rate is relatively unimportant. Denitrification is mainly influenced by the nitrate concentration in the overlying bottomwater.},
	number = {6},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Soetaert, Karline and Herman, Peter M.J. and Middelburg, Jack J.},
	month = mar,
	year = {1996},
	pages = {1019--1040}
}

@article{mirto_meiofauna_2012,
	title = {Meiofauna as an indicator for assessing the impact of fish farming at an exposed marine site},
	volume = {18},
	url = {https://www.sciencedirect.com/science/article/pii/S1470160X11004171?via%3Dihub},
	doi = {10.1016/J.ECOLIND.2011.12.015},
	abstract = {This study aimed to detect the impact of organic loads due to biodeposition from a fish farm in an exposed area of the Strait of Sicily, Mediterranean Sea. Sediment chemistry and meiofaunal assemblages were investigated on a seasonal basis at four stations: two from the impacted area and two control stations. The presence of the cages induced a significant accumulation of proteins, lipids and biopolymeric carbon, resulting in a reduction in meiofaunal density at the impacted stations. Changes in community structure were also evident, as meiofauna under the cages were characterized by increased importance of polychaetes and copepods in comparison with a much lower importance of gastrotrichs and kinorynchs. Moreover, biodiversity decreased beneath the cages due to the disappearance of taxa more sensitive to organic accumulation. This finding allowed us to propose the ration of nematodes to kinorynchs as a possible, potentially interesting, indicator of fish farm biodeposition.},
	journal = {Ecological Indicators},
	author = {Mirto, Simone and Gristina, Michele and Sinopoli, Mauro and Maricchiolo, Giulia and Genovese, Lucrezia and Vizzini, Salvatrice and Mazzola, Antonio},
	month = jul,
	year = {2012},
	keywords = {aquaculture, meiofaunal communities},
	pages = {468--476}
}

@article{dunn_benthic_2013,
	title = {Benthic metabolism and nitrogen dynamics in an urbanised tidal creek: {Domination} of {DNRA} over denitrification as a nitrate reduction pathway},
	volume = {131},
	issn = {02727714},
	url = {http://dx.doi.org/10.1016/j.ecss.2013.06.027},
	doi = {10.1016/j.ecss.2013.06.027},
	abstract = {Benthic oxygen and nutrient fluxes and nitrate reduction rates were determined seasonally under light and dark conditions at three sites in a micro-tidal creek within an urbanised catchment (Saltwater Creek, Australia). It was hypothesized that stormwater inputs of organic matter and inorganic nitrogen would stimulate rates of benthic metabolism and nutrient recycling and preferentially stimulate dissimilatory nitrate reduction to ammonium (DNRA) over denitrification as a pathway for nitrate reduction. Stormwaters greatly influenced water column dissolved inorganic nitrogen (DIN) and suspended solids concentrations with values following a large rainfall event being 5-20-fold greater than during the preceding dry period. Seasonally, maximum and minimum water column total dissolved nitrogen (TDN) and DIN concentrations occurred in the summer (wet) and winter (dry) seasons. Creek sediments were highly heterotrophic throughout the year, and strong sinks for oxygen, and large sources of dissolved organic and inorganic nitrogen during both light and dark incubations, although micro-phytobenthos (MPB) significantly decreased oxygen consumption and N-effluxes during light incubations due to photosynthetic oxygen production and photoassimilation of nutrients. Benthic denitrification rates ranged from 3.5 to 17.7μmolNm2h-1, denitrification efficiencies were low ({\textbackslash}textless1-15\%) and denitrification was a minor process compared to DNRA, which accounted for ∼75\% of total nitrate reduction. Overall, due to the low denitrification efficiencies and high rates of N-regeneration, Saltwater Creek sediments would tend to increase rather than reduce dissolved nutrient loads to the downstream Gold Coast Broadwater and Moreton Bay systems. This may be especially true during wet periods when increased inputs of particulate organic nitrogen (PON) and suspended solids could respectively enhance rates of N-regeneration and decrease light availability to MPB, reducing their capacity to ameliorate N-effluxes through photoassimilation. © 2013 Elsevier Ltd.},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Dunn, Ryan J K and Robertson, David and Teasdale, Peter R. and Waltham, Nathan J. and Welsh, David T.},
	year = {2013},
	pmid = {19304834},
	keywords = {Denitrification, Dissimilatory nitrate reduction to ammonium, Benthic metabolism, Nutrient fluxes, Saltwater Creek, Stormwater impacts, Sub-tropical},
	pages = {271--281}
}

@article{kuypers_anaerobic_2006-1,
	title = {Anaerobic ammonium oxidation in the marine environment},
	volume = {64},
	abstract = {Oceanographers noticed already many years ago that far less ammonium accumulated in anoxic fjords and basins, than would be expected from the stoichiometry of heterotrophic denitrification. It was suggested that this 'missing' ammonium was oxidized with nitrate to free N(2). Since then several other workers have argued based on chemical profiles that ammonium is oxidized anaerobically in oxygen deficient marine sediments and waters with either nitrate or manganese oxides as electron acceptor. While there is as yet no direct evidence for the anaerobic ammonium oxidation with manganese oxides in either sediments or anoxic water columns, more and more evidence is being provided for anaerobic ammonium oxidation with nitrite/nitrate. The first direct evidence for the anaerobic oxidation of ammonium was provided in a waste water bioreactor, where so-called 'anammox' bacteria belonging to the Order Planctomycetales directly oxidize ammonium to N(2) with nitrite as the electron acceptor. Although the anammox process was generally seen as a promising process for waste water treatment. it was believed to be insignificant in the natural environment due to the extremely slow generation times (more than 2 weeks) of the anammox organisms. However, recent studies provide direct evidence for anaerobic oxidation of ammonium by nitrate and/or nitrite in marine sediments, oxygen minimum zones, anoxic fjords and basins as well as Arctic sea ice. Phylogenetic analysis of 16S ribosomal RNA sequences show that the bacteria involved are closely related to anammox bacteria from waste water bioreactors. The combined biogeochemical and microbiological data available indicates that anammox may contribute significantly to the loss of reactive nitrogen in the ocean.},
	journal = {Past and Present Water Column Anoxia},
	author = {Kuypers, M M M and Lavik, G and Thamdrup, B},
	year = {2006},
	keywords = {anammox, denitrification, anaerobic ammonium oxidation, fluidized-bed reactor, nitrogen cycle, anammox bacteria, autotrophic nitrogen-removal, benguela upwelling system, costa-rica, golfo-dulce, in-situ detection, marine, n-2 production, organic-carbon, oxidizing bacteria, review, suboxic},
	pages = {311--335}
}

@article{jensen_estimation_1994,
	title = {Estimation of {Nitrification} and {Denitrification} from {Microprofiles} of {Oxygen} and {Nitrate} in {Model} {Sediment} {Systems}},
	volume = {60},
	number = {6},
	author = {Jensen, Kim and Sloth, Niels P and Risgaard-petersen, Nils and Rysgaard, Sren},
	year =