text:
.},
	author = {{V. A. Hartmann} and {K. Briggs} and {S. Shivarudrappa} and {K. M. Yeager} and {R. Diaz}},
	year = {2009},
	keywords = {Sediments, Bioturbation, bioturbation rates, hypoxia, Water, AD 2009 04, AD 2009 09, benthic community structure, benthic invertebrate fauna, biogenic structures, coastal bottom waters, computed tomography, Computed tomography, computerised tomography, Educational institutions, Focusing, Louisiana continental shelf, Louisiana Universities Marine Consortium, Mexico Gulf, northern Gulf of Mexico, oceanographic regions, Organisms, Photography, redox potential discontinuity, Sampling methods, Sea measurements, sediment profile imaging photography, sediments, Springs}
}

@article{reimers_oxygen_1984,
	title = {Oxygen consumption rates in pelagic sediments from the {Central} {Pacific}: {First} estimates from microelectrode profiles},
	volume = {48},
	issn = {00167037},
	doi = {10.1016/0016-7037(84)90183-2},
	abstract = {Oxygen profiles in pelagic sediments from the Manganese Nodule Program calcareous and siliceous ooze sites (MANOP sites C and S) in the central Pacific Ocean were measured with microelectrodes and are used to predict oxygen consumption rates beneath the sediment-water interface. We explain possible artifacts which occur during sample recovery and argue that minimum estimates of 0.083 and 0.025 ?? moles O2 cm2day (C and S, respectively) can be calculated from the data. These oxygen consumption rates are in good agreement with in situ respirometer measurements previously reported for comparable sediments in the north Pacific, but previous estimates based on modeling of pore water nitrate profiles at both sites are two to five times smaller than our minimum fluxes. The differences in oxygen fluxes calculated by the two methods are probably in part due to uncertainty in the assumptions inherent in the nitrate model. However, non-steady state fluctuations in particulate organic matter fluxes could also be a reason for the disparity. ?? 1984.},
	number = {5},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Reimers, Clare E. and Kalhorn, Susan and Emerson, Steven R. and Nealson, Kenneth H.},
	year = {1984},
	pages = {903--910}
}

@article{nizzoli_impact_2006,
	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{iwama_interactions_1991,
	title = {Interactions between aquaculture and the environment},
	volume = {21},
	issn = {1040-838X},
	url = {http://www.tandfonline.com/doi/abs/10.1080/10643389109388413},
	doi = {10.1080/10643389109388413},
	number = {2},
	journal = {Critical Reviews in Environmental Control},
	author = {Iwama, George K.},
	month = jan,
	year = {1991},
	pages = {177--216}
}

@article{rysgaard_nitrification_1993,
	title = {Nitrification and denitrification in lake and estuarine sediments measured by the {N} dilution technique and isotope pairing.},
	volume = {59},
	issn = {0099-2240},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16348987 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC182241},
	abstract = {The transformation of nitrogen compounds in lake and estuarine sediments incubated in the dark was analyzed in a continuous-flowthrough system. The inflowing water contained NO(3), and by determination of the isotopic composition of the N(2), NO(3), and NH(4) pools in the outflowing water, it was possible to quantify the following reactions: total NO(3) uptake, denitrification based on NO(3) from the overlying water, nitrification, coupled nitrification-denitrification, and N mineralization. In sediment cores from both lake and estuarine environments, benthic microphytes assimilated NO(3) and NH(4) for a period of 25 to 60 h after darkening. Under steady-state conditions in the dark, denitrification of NO(3) originating from the overlying water accounted for 91 to 171 mumol m h in the lake sediments and for 131 to 182 mumol m h in the estuarine sediments, corresponding to approximately 100\% of the total NO(3) uptake for both sediments. It seems that high NO(3) uptake by benthic microphytes in the initial dark period may have been misinterpreted in earlier investigations as dissimilatory reduction to ammonium. The rates of coupled nitrification-denitrification within the sediments contributed to 10\% of the total denitrification at steady state in the dark, and total nitrification was only twice as high as the coupled process.},
	number = {7},
	journal = {Applied and environmental microbiology},
	author = {Rysgaard, S and Risgaard-Petersen, N and Nielsen, Lars Peter and Revsbech, N P},
	month = jul,
	year = {1993},
	pmid = {16348987},
	pages = {2093--8}
}

@article{roberts_increased_2014,
	title = {Increased rates of dissimilatory nitrate reduction to ammonium ({DNRA}) under oxic conditions in a periodically hypoxic estuary},
	volume = {133},
	issn = {00167037},
	url = {http://www.sciencedirect.com/science/article/pii/S0016703714001525},
	doi = {10.1016/j.gca.2014.02.042},
	abstract = {The Yarra River Estuary is a salt wedge estuary prone to hypoxia in the bottom waters during low flow periods. Rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were quantified using 15N in relation to oxygen, nitrate and available reductants. Denitrification was the dominant nitrate reduction pathway under all oxygen conditions, however, DNRA increased from {\textbackslash}textless1\% under hypoxic conditions ({\textbackslash}textless50μmolL−1O2) to ∼18\% of total nitrate reduction under oxygen saturation in the water column in intact core incubations. Microprofiles of nitrate reduction pathways in intact cores using diffusive equilibrium in thin layer (DET) gels showed significant rates of DNRA only occurred under oxic conditions in the presence of Fe2+. Cores incubated anoxically, developed free sulfide within the porewater, had very low concentrations of Fe2+ and low rates of DNRA. Slurry incubations with varying concentrations of NO3− showed that denitrifying bacteria had a higher affinity than nitrate ammonifying bacteria with Km values of 49 and 86μmolL−1 for denitrification and DNRA, respectively, however, this could not explain the change in the rates of DNRA relative to denitrification observed. Further slurry incubations to investigate the relationship between DNRA and Fe2+ oxidation were inconclusive and complicated by very high backgrounds of sorbed (HCl extractable) Fe2+. Addition of Fe2+ to the slurry did not stimulate denitrification compared to a control (no Fe2+ addition), however, there was a significant decrease in the Fe2+ concentration over the period where DNRA occurred in the Fe2+ addition treatment, and no significant decrease in the control treatment. The ratio of DNRA to Fe2+ consumption was 15±6 and 7±3 for the Fe2+ and control treatments, respectively. We suggest reduced rates of DNRA under anoxic conditions can be explained by the binding of Fe2+ with free sulfides and the formation of FeS removing available Fe2+ for DNRA.},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Roberts, Keryn L. and Kessler, Adam J. and Grace, Michael R. and Cook, Perran L.M.},
	month = may,
	year = {2014},
	keywords = {DNRA, ADM, ammonium diffusion method, DET, diffusive equilibrium in thin films, dissimilatory nitrate reduction ammonium, dissolved oxygen, DO},
	pages = {313--324}
}

@article{algar_predicting_2014,
	title = {Predicting microbial nitrate reduction pathways in coastal sediments},
	volume = {71},
	issn = {0948-3055},
	url = {http://www.int-res.com/abstracts/ame/v71/n3/p223-238/},
	doi = {10.3354/ame01678},
	abstract = {We present an ecosystem model that describes the biogeochemistry of a sediment nitrate reducing microbial community. In the midel, the microbial community is represented as a distributed metabolic network. Biogeochemical pathways are controlled through the synthesis and allocation of biological structure that serves to catalyze each process. Allocation is determined by way of a thermodynamically constrained optimization according to the principle of maximum entropy production (MEP). According to the MEP principle, ecosystems will organize so as to maximize the dissipation of free energy based upon the available resources (nutrients and electron donors and acceptore). In the model, 3 nitrate reduction pathways, viz. heterotrophic denitrification, anamox, and dissimilatory nitrate reduction to ammonium, compete for electrom acceptors (nitrate and nitrite). The model predicts switches in the dominant nitrate cycling pathways based upon the ratio of carbon to nitrate supply. An advantage of this approach over a traditional organism-centric kinetic approach is that the Monod growth parameters, maximum uptake rate (vmax), and half saturation (km) constants are determined during the optimization proceture as opposed to parameters specified a priori. Such a model is therefore useful for applications where these kinetic parameters are unkown and difficult to measure, such as the marine subsurface, or when ecosystems undergo large-scale environmental perturbations resulting in shifts in the dominant organisms.},
	number = {3},
	journal = {Aquatic Microbial Ecology},
	author = {Algar, CK and Vallino, JJ},
	month = jan,
	year = {2014},
	keywords = {Denitrification, Diagenesis, Anammox, DNRA, Biogeochemistry, Ecosystem modeling, Maximum entropy production},
	pages = {223--238}
}

@article{brigolin_modelling_2009,
	title = {Modelling the impact of aquaculture on early diagenetic processes in sea loch sediments},
	volume = {388},
	issn = {0171-8630},
	url = {http://www.int-res.com/abstracts/meps/v388/p63-80/},
	doi = {10.3354/meps08072},
	journal = {Marine Ecology Progress Series},
	author = {Brigolin, D and Pastres, R and Nickell, TD and Cromey, CJ and Aguilera, DR and Regnier, P},
	month = aug,
	year = {2009},
	keywords = {Atlantic salmon, Benthic mineralization, DEPOMOD, Loch Creran, RTM, Transient simulation},
	pages = {63--80}
}

@article{sunda_ammonium_2007,
	title = {Ammonium uptake and growth limitation in marine phytoplankton},
	volume = {52},
	issn = {00243590},
	url = {http://80-www.aslo.org/lo/toc/vol_52/issue_6/2496.pdf},
	doi = {10.4319/lo.2007.52.6.2496},
	abstract = {We used continuous culture techniques and a sensitive fluorescence method to quantify relationships among ammonium (NHz species ranging in diameter from 3 to 11 mm. The growth rate of two high–nutrient-requiring coastal diatoms, Thalassiosira weissflogii and Thalassiosira pseudonana, were limited at NHz 4 ) concentration, cellular NHz while those of low-nutrient–adapted species, the oceanic coccolithophore Emiliania huxleyi, the coastal pelagophyte Aureoumbra lagunensis, and the coastal trebouxiophyte Nannochloris atomus, were limited at concentrations ,30–40 nmol L21. In the nitrogen-limited cyclostats, the residence times of dissolved ammonium were extremely short (4–12 min at chlorophyll a levels of 20–30 mgL21), and these short times had to be taken into account to obtain accurate NHz 4 uptake rates, and growth rate limitation for five marine algal 4 concentrations ,90–100 nmol L21, ocean waters (3–15 nmol L21) fall within the range that substantially limited algal growth rates in our experiments, providing evidence for nitrogen limitation in these waters. Ammonium uptake rates and associated specific growth rates were much lower for T. weissflogii (10–11 mm in diameter) than for the other smaller (3.1– 4.5 mm in diameter) species under ammonium limitation owing to the limits imposed byNHz surface. Diffusion per unit of cell volume varies with the inverse square of the cell diameter and, thus, greatly restricts growth of large-celled species under NHz in ammonium-limited ocean waters should promote rapid grazing and nutrient cycling and minimum nutrient loss via settling of intact cells and zooplankton fecal material. 4 limitation. The resultant selection of small-celled algal species},
	number = {6},
	journal = {Limnology and oceanography},
	author = {Sunda, Wg},
	year = {2007},
	pages = {2496--2506}
}

@article{song_linking_2014,
	title = {Linking {DNRA} community structure and activity in a shallow lagoonal estuarine system},
	volume = {5},
	issn = {1664-302X},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2014.00460/abstract},
	doi = {10.3389/fmicb.2014.00460},
	abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are two nitrate respiration pathways in the microbial nitrogen cycle. Diversity and abundance of denitrifying bacteria have been extensively examined in various ecosystems. However, studies on DNRA bacterial diversity are limited, and the linkage between the structure and activity of DNRA communities has yet to be discovered. We examined the composition, diversity, abundance and activities of DNRA communities at five sites along a salinity gradient in the New River Estuary, North Carolina, USA, a shallow temporal/lagoonal estuarine system. Sediment slurry incubation experiments with 15N-nitrate were conducted to measure potential DNRA rates, while the abundance of DNRA communities was calculated using quantitative PCR of nrfA genes encoding cytochrome C nitrite reductase, commonly found in DNRA bacteria. A pyrosequencing method targeting nrfA genes was developed using an Ion Torrent sequencer to examine the diversity and composition of DNRA communities within the estuarine sediment community. We found higher levels of nrfA gene abundance and DNRA activities in sediments with higher percent organic content. Pyrosequencing analysis of nrfA genes revealed spatial variation of DNRA communities along the salinity gradient of the New River Estuary. Percent abundance of dominant populations was found to have significant influence on overall activities of DNRA communities. Abundance of dominant DNRA bacteria and organic carbon availability are important regulators of DNRA activities in the eutrophic New River Estuary.},
	journal = {Frontiers in Microbiology},
	author = {Song, Bongkeun and Lisa, Jessica A. and Tobias, Craig R.},
	month = sep,
	year = {2014},
	keywords = {DNRA, diversity, nrfA, pyrosequencing, qPCR},
	pages = {460}
}

@article{middelburg_empirical_1997-1,
	title = {Empirical relationships for use in global diagenetic models},
	volume = {44},
	issn = {09670637},
	doi = {10.1016/S0967-0637(96)00101-X},
	abstract = {A database containing published rates of sediment and pore-water transport and biogeochemical transformations has been established to derive empirical predictive equations to calibrate and parameterize global diagenetic models. Rates of sediment accumulation, organic carbon burial, organic matter decomposition via aerobic and anaerobic pathways and bioturbation (in terms of bioturbation coefficients) can be predicted quite well using exponential relationships with water depth as an independent variable. The relationships are corrected for skewhess to reduce the bias inherent in the back transformation from a lognormal to an arithmetic estimate. Bioturbation is shown to be the dominant mode of sediment transport in the upper centimeters of oceanic sediments. The derived empirical relationships are combined with bathymetric maps to estimate globally integrated rates of benthic processes. Ocean margin sediments account for about 85\% of the materials accumulating in the ocean and about 80-90\% of the mineralization in marine sediments.},
	number = {2},
	journal = {Deep-Sea Research Part I: Oceanographic Research Papers},
	author = {Middelburg, Jack J. and Soetaert, Karline and Herman, Peter M J},
	year = {1997},
	pages = {327--344}
}

@article{ferron_benthic_2009-1,
	title = {Benthic fluxes in a tidal salt marsh creek affected by fish farm activities: {Río} {San} {Pedro} ({Bay} of {Cádiz}, {SW} {Spain})},
	volume = {113},
	issn = {03044203},
	url = {http://www.sciencedirect.com/science/article/pii/S030442030800203X},
	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 Río San Pedro salt marsh tidal creek (Bay of Cádiz, 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 μmol CH4 m−2 d−1 and 4.3 to 49 μmol 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.},
	number = {1-2},
	journal = {Marine Chemistry},
	author = {Ferrón, S. and Ortega, T. and Forja, J.M.},
	month = jan,
	year = {2009},
	keywords = {Aquaculture, Nutrients, Benthic fluxes, Nitrous oxide, Carbon mineralization, Dissolved inorganic carbon, Methane, Salt marsh creek},
	pages = {50--62}
}

@techreport{wilson_ecasa_2006,
	title = {{ECASA} {Study} {Site} {Report}; {Loch} {Creran}, {Scotland}},
	institution = {Scottish Association for Marine Science},
	author = {Wilson, A and Nickell, T and Cromey, C and Black, K},
	year = {2006},
	pages = {36}
}

@article{hartmann_impact_2009,
	title = {The {Impact} of {Hypoxia} on {Bioturbation} {Rates} in the {Louisianna} {Continental} {Shelf}, {Northern} {Gulf} of {Mexico} - {Storming} {Media}},
	url = {http://www.stormingmedia.us/44/4473/A447315.html},
	abstract = {Variation in the spatial and temporal extent of hypoxia in coastal bottom waters of the northern Gulf of Mexico leads to changes in benthic community structure and sediment physical properties. Past and present benthic community structure determines what types of biogenic structures are present in the sediment as well as faunal mixing rates. Therefore, hypoxia has an important effect upon bioturbation. This study focuses upon the effects of hypoxia on bioturbation specifically on the continental shelf of Louisiana, where hypoxia has become an important issue due to its seasonal reoccurrence and increasing expansion across the northern Gulf of Mexico over the past 30 years. In this project, characteristics of biogenic structures in the sediment including number, diameter, and depth are correlated with benthic communities dwelling in hypoxic, intermittently hypoxic, and normoxic conditions using non-destructive Computed Tomography (CT) imagery of sediment cores and Sediment Profile Imaging (SPI) photography. Biogenic structures are also correlated with sediment physical properties, bioturbation rates, and bioturbation behaviors (dilator or compactor) of benthic invertebrate fauna. Initial data for this project was collected during two cruises along the continental shelf of Louisiana, the first in April 2009 and the second in September 2009. Four different provinces were chosen for sampling using bottom water oxygen concentration data from the Louisiana Universities Marine Consortium (LUMCON) and archived sediment type data. These four sampling sites represent normoxic and hypoxic provinces with a consistent sediment type. The provinces consist of a normoxic site (NO) that has experienced hypoxia less than 25\% of the time and briefly hypoxic (BH), frequently hypoxic (FH) and hypoxic (HO) sites that have experienced hypoxia greater than 25\% of the time.},
	author = {Hartmann, V. and Briggs, Kevin and Shivarudrappa, S. and Yeager, Kevin M. and Diaz, Robert J.},
	year = {2009},
	keywords = {Gulf of Mexico, bioturbation, hypoxia}
}

@article{kelly-gerreyn_model_2001,
	title = {A model discriminating denitrification and dissimilatory nitrate reduction to ammonium in a temperate estuarine sediment},
	volume = {220},
	issn = {0171-8630},
	url = {http://www.int-res.com/abstracts/meps/v220/p33-46/},
	doi = {10.3354/meps220033},
	journal = {Marine Ecology Progress Series},
	author = {Kelly-Gerreyn, BA and Trimmer, M and Hydes, DJ},
	month = sep,
	year = {2001},
	keywords = {Denitrification, Dissimilatory nitrate reduction to ammonium, Diagenesis model, Temperature},
	pages = {33--46}
}

@article{kaspar_effects_1988,
	title = {Effects of sea cage salmon farming on sediment nitrification and dissimilatory nitrate reductions},
	volume = {70},
	journal = {Aquaculture},
	author = {Kaspar, H.F. and Hall, Grahame H. and Holland, A.J.},
	year = {1988},
	pages = {333--344}
}

@article{keeley_benthic_2015,
	title = {Benthic recovery and re-impact responses from salmon farm enrichment: {Implications} for farm management},
	volume = {435},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/S0044848614005158},
	doi = {10.1016/j.aquaculture.2014.10.007},
	abstract = {This paper describes a two-year study of spatial and temporal patterns and processes in the benthos in response to the removal of salmon cages from a sheltered coastal embayment, coupled with the simultaneous reintroduction of cages at an adjacent location. Significant recovery was evident at the fallowed site in the first six months; however, the macrofaunal assemblage remained impacted at the conclusion of the study. By comparison, the reintroduction of a fully operational farm overwhelmed the macrobenthic community within three months, with anoxic and near-azoic conditions developing. Both removal and reintroduction of the farms triggered alternating oscillations of geochemical and biological variables, which were attributed to effects on sediment chemistry from organic loading, ‘boom and bust' cycles of opportunistic taxa in response to food supply, and the associated variations in metabolic potential. The study also revealed interesting spatial dynamics in the benthos and some useful indicators of different stages of recovery and re-impact. It is concluded that farm reintroductions should aim to gradually increase production; allowing time for the benthos to adapt to the additional organic flux, and be maintained at a level that avoids macrofaunal collapse. The sediment's ability to cope with organic inputs from fish farming, and hence the duration of the recovery period, is contingent on the organic load in each farming cycle and the extent to which the sediment community is allowed to recover. Understanding the influence of each of these on sediment processes is important for sustainable long-term management of farming operations.},
	journal = {Aquaculture},
	author = {Keeley, Nigel B. and Forrest, Barrie M. and Macleod, Catriona K.},
	month = jan,
	year = {2015},
	keywords = {Environmental management, Fallowing, Macrofauna, New Zealand, Spatial and temporal patterns},
	pages = {412--423}
}

@article{macleod_ecological_2008,
	title = {Ecological and functional changes associated with long-term recovery from organic enrichment},
	volume = {365},
	issn = {0171-8630},
	url = {http://www.int-res.com/abstracts/meps/v365/p17-24/},
	doi = {10.3354/meps07534},
	journal = {Marine Ecology Progress Series},
	author = {Macleod, CK and Moltschaniwskyj, NA and Crawford, CM},
	month = aug,
	year = {2008},
	keywords = {Aquaculture, Organic enrichment, Macrofauna, Benthic recovery, Functional ecology, Recolonisation},
	pages = {17--24}
}

@article{volkenborn_intermittent_2012,
	title = {Intermittent bioirrigation and oxygen dynamics in permeable sediments: {An} experimental and modeling study of three tellinid bivalves},
	volume = {70},
	url = {http://openurl.ingenta.com/content/xref?genre=article&issn=0022-2402&volume=70&issue=6&spage=794},
	doi = {10.1357/002224012806770955},
	abstract = {To explore the dynamic nature of geochemical conditions in bioirrigated marine permeable sediments, we studied the hydraulic activity of three tellinacean bivalve molluscs (the Pacific species Macoma nasuta and Macomona liliana, and the northern Atlantic and Pacific species Macoma balthica). We combined porewater pressure sensing, time-lapse photography and oxygen imaging to quantify the durations and frequencies of tellinid irrigation activity and the associated oxygen dynamics in the sediment. Porewater pressure records of all tellinids were dominated by intermittent porewater pressurization, induced by periodic water injection into the sediment through their excurrent siphons, which resulted in intermittent oxygen supply to subsurface sediments. The irrigation (two–12 minutes long) and intervals between subsequent irrigation bouts (1.5–13 minutes) varied among tellinid species and individual sizes. For large M. liliana and M. nasuta, the average intervals between irrigation bouts were sufficiently long (10 minutes and four minutes, respectively) to allow complete oxygen consumption in between irrigation bouts in all tested sediment types. Irrigation patterns of smaller conspecifics and the smaller species M. balthica were characterized by significantly shorter separation of irrigation bouts, which resulted in more continuous oxygenation of the sediment. Transport-reaction modeling confirmed these species- and size-specific geochemical signatures and indicated that the geochemical character of the sediment is largely conditioned by the interplay between temporal irrigation patterns and sedimentary oxygen consumption rates. For large tellinids, model simulations indicated that oscillatory rather than stationary geochemical conditions are prevalent in a wide range of sediment types, with oxic pockets collapsing completely between periods of active irrigation. Based on the model results we developed analytical approximations that allow estimation of spatio-temporal characteristics of sediment oxygenation for a wide range of sediment types and infaunal activity patterns. Our results emphasize the need to consider the intermittent nature of bioirrigation when studying the geochemical impact of infauna in permeable sediments.},
	number = {6},
	journal = {Journal of Marine Research},
	author = {Volkenborn, Nils and Meile, Christof and Polerecky, Lubos and Pilditch, Conrad A. and Norkko, Alf and Norkko, Joanna and Hewitt, Judi E. and Thrush, Simon F. and Wethey, David S. and Woodin, Sarah A.},
	month = nov,
	year = {2012},
	keywords = {oxygen, bioirrigation, modelling, bivalves, oxygen pumping},
	pages = {794--823}
}

@article{glibert_pluses_2016,
	title = {Pluses and minuses of ammonium and nitrate uptake and assimilation by phytoplankton and implications for productivity and community composition, with emphasis on nitrogen-enriched conditions},
	volume = {61},
	issn = {19395590},
	doi = {10.1002/lno.10203},
	abstract = {Anthropogenic activities are altering total nutrient loads to many estuaries and freshwaters, resulting in high loads not only of total nitrogen (N), but in some cases, of chemically reduced forms, notably NH4+. Long thought to be the preferred form of N for phytoplankton uptake, NH4+ may actually suppress overall growth when concentrations are sufficiently high. NH4+ has been well known to be inhibitory or repressive for NO3- uptake and assimilation, but the concentrations of NH4+ that promote vs. repress NO3- uptake, assimilation, and growth in different phytoplankton groups and under different growth conditions are not well understood. Here, we review N metabolism first in a "generic" eukaryotic cell, and the contrasting metabolic pathways and regulation of NH4+ and NO3- when these substrates are provided individually under equivalent growth conditions. Then the metabolic interactions of these substrates are described when both are provided together, emphasizing the cellular challenge of balancing nutrient acquisition with photosynthetic energy balance in dynamic environments. Conditions under which dissipatory pathways such as dissimilatory NO3-/NO2- reduction to NH4+ and photorespiration that may lead to growth suppression are highlighted. While more is known about diatoms, taxon-specific differences in NH4+ and NO3- metabolism that may contribute to changes in phytoplankton community composition when the composition of the N pool changes are presented. These relationships have important implications for harmful algal blooms, development of nutrient criteria for management, and modeling of nutrient uptake by phytoplankton, particularly in conditions where eutrophication is increasing and the redox state of N loads is changing.},
	number = {1},
	journal = {Limnology and Oceanography},
	author = {Glibert, Patricia M. and Wilkerson, Frances P. and Dugdale, Richard C. and Raven, John A. and Dupont, Christopher L. and Leavitt, Peter R. and Parker, Alexander E. and Burkholder, Joann M. and Kana, Todd M.},
	year = {2016},
	pages = {165--197}
}

@article{wu_hypoxia:_2002,
	title = {Hypoxia: {From} molecular responses to ecosystem responses},
	volume = {45},
	issn = {0025326X},
	doi = {10.1016/S0025-326X(02)00061-9},
	abstract = {Hypoxia affects thousands of km2 of marine waters all over the world, and has caused mass mortality of marine animals, benthic defaunation and decline in fisheries production in many places. The severity, frequency occurrence and spatial scale of hypoxia have increased in the last few decades. Due to rapid human population growth and global warming, the problem of hypoxia is likely to become worse in the coming years. Molecular responses of marine animals to hypoxia are poorly known. In many animals, a haem protein probably serves as the cellular sensor for oxygen, and reactive oxygen species are generated as signaling molecules. In mammal and fish, a heterodimeric transcription factor, hypoxia-inducible factor 1 (HIF-1) has been identified. HIF-1 receives signals from the molecular oxygen senor through redox reactions and/or phosphorylation, and in turn, regulates the transcription of a number of hypoxia-inducible genes, including genes involved in erythropoiesis, angiogenesis and glycolysis. These molecular responses then cascade into a series of biochemical and physiological adjustments, enabling the animal to survive better under hypoxic conditions. Marine animals respond to hypoxia by first attempting to maintain oxygen delivery (e.g. increases in respiration rate, number of red blood cells, or oxygen binding capacity of hemoglobin), then by conserving energy (e.g. metabolic depression, down regulation of protein synthesis and down regulation/modification of certain regulatory enzymes). Upon exposure to prolonged hypoxia, animals must eventually resort to anaerobic respiration. Hypoxia reduces growth and feeding, which may eventually affect individual fitness. Effects of hypoxia on reproduction and development of marine animals, albeit important in affecting species survival, remain almost unknown. Many fish and marine organisms can detect, and actively avoid hypoxia. Some benthos may leave their burrows and move to sediment surface during hypoxia. These behaviorial changes may render the animals more vulnerable to predation. Hypoxia may eliminate sensitive species, thereby causing major changes in species composition of benthic, fish and phytoplankton communities. Decreases in species diversity and species richness are well documented, and changes in trophodynamics and functional groups have also been reported. Under hypoxic conditions, there is a general tendency for suspended feeders to be replaced by deposit feeders; demersal fish by pelagic fish; and macrobenthos by meiobenthos. Microflagellates and nanoplankton also tend to dominate in the phytoplankton community in hypoxic environments. Existing evidence suggest that recovery of benthic communities in temperate region take two to several years. Recovery however, appears to be much quicker in subtropical environments. In natural conditions, hypoxia is often associated with increases in ammonia, hydrogen sulphide and particulate organic materials. The inability to isolate effects of hypoxia from interactions of these compounding factors makes it difficult to attribute many of the observed ecological effects to hypoxia. ?? 2002 Elsevier Science Ltd. All rights reserved.},
	number = {1-12},
	journal = {Marine Pollution Bulletin},
	author = {Wu, Rudolf S S},
	year = {2002},
	pmid = {12398365},
	pages = {35--45}
}

@article{algar_predicting_2014-1,
	title = {Predicting microbial nitrate reduction pathways in coastal sediments},
	volume = {71},
	url = {http://darchive.mblwhoilibrary.org/bitstream/handle/1912/6525/a071p223-1.pdf?sequence=1&isAllowed=y},
	doi = {10.3354/ame01678},
	abstract = {We present an ecosystem model that describes the biogeochemistry of a sediment nitrate reducing microbial community. In the model, the microbial community is represented as a distributed metabolic network. Biogeochemical pathways are controlled through the synthesis and allocation of biological structure that serves to catalyze each process. Allocation is determined by way of a thermodynamically constrained optimization according to the principle of maximum entropy production (MEP). According to the MEP principle, ecosystems will organize so as to maximize the dissipation of free energy based upon the available resources (nutrients and electron donors and acceptors). In the model, 3 nitrate reduction pathways, viz. heterotrophic denitrification, anammox, and dissimilatory nitrate reduction to ammonium, compete for electron acceptors (nitrate and nitrite). The model predicts switches in the dominant nitrate cycling pathways based upon the ratio of carbon to nitrate supply. An advantage of this approach over a traditional organism-centric kinetic approach is that the Monod growth parameters, maximum uptake rate (νmax), and half saturation (kM) constants are determined during the optimization procedure as opposed to parameters specified a priori. Such a model is therefore useful for applications where these kinetic parameters are unknown and difficult to measure, such as the marine subsurface, or when ecosystems undergo large-scale environmental perturbations resulting in shifts in the dominant organisms.},
	journal = {Aquatic Microbial Ecology},
	author = {Algar, Christopher K. and Vallino, Joseph J.},
	year = {2014},
	keywords = {Denitrification, Anammox, DNRA, diagenesis, biogeo},
	pages = {223--238}
}

@article{giblin_importance_2013,
	title = {The {Importance} of {Dissimilatory} {Nitrate} {Reduction} to {Ammonium} ({DNRA}) in the {Nitrogen} {Cycle} of {Coastal} {Ecosystems}},
	volume = {26},
	issn = {10428275},
	url = {http://darchive.mblwhoilibrary.org/handle/1912/6240},
	doi = {10.5670/oceanog.2013.54},
	abstract = {Author Posting. © The Oceanography Society, 2013. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 26, no. 3 (2013): 124–131, doi:10.5670/oceanog.2013.54.},
	language = {en\_US},
	number = {3},
	journal = {Oceanography},
	author = {Giblin, Anne and Tobias, Craig and Song, Bongkeun and Weston, Nathaniel and Banta, Gary and Rivera-Monroy, Victor},
	month = sep,
	year = {2013},
	keywords = {Article},
	pages = {124--131}
}

@article{behrendt_vertical_2013-1,
	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{canavan_modeling_2007,
	title = {Modeling nitrogen cycling in a coastal fresh water sediment},
	volume = {584},
	issn = {0018-8158},
	url = {http://link.springer.com/10.1007/s10750-007-0583-z},
	doi = {10.1007/s10750-007-0583-z},
	number = {1},
	journal = {Hydrobiologia},
	author = {Canavan, Richard W. and Laverman, Anniet M. and Slomp, Caroline P.},
	month = jun,
	year = {2007},
	pages = {27--36}
}

@article{brooks_chemical_2003,
	title = {Chemical and biological remediation of the benthos near {Atlantic} salmon farms},
	volume = {219},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/S0044848602005288},
	doi = {10.1016/S0044-8486(02)00528-8},
	abstract = {Salmon farms in British Columbia now typically produce over 2000 mt of fish during each 18- to 24-month production cycle. An 18-month study of Stolt Sea Farms' Arrow Pass farm was undertaken in 1996 to examine the spatial and temporal extents of chemical and biological benthic effects. Microbial metabolism of farm biodeposits in nearfield sediments resulted in increased sulfide concentrations and decreased redox potential. These physicochemical changes modified the macrobenthic community. Species sensitive to enrichment were quickly extinguished from the immediate vicinity of the farm and were replaced by the organic carbon tolerant opportunistic annelids Capitella capitata and Ophryotrocha cf. vivipara. These effects extended to at least 50 m from the net-pen's perimeter on the downcurrent transect. Chemical remediation, defined as a return to reference levels of organic carbon, a reduction in free sediment sulfides to {\textbackslash}textless960 μM and an increase in sediment redox potential to reference conditions, began as soon as the harvest commenced and was complete by the end of harvest. Biological remediation began during the harvest and was complete within 6 months of fallow. Annelids and crustaceans recruited first into the remediating sediments and were followed by at least two seres of mollusks. Routine quarterly monitoring of sediment-free sulfides, redox potential and total volatile solids (TVS) at four Stolt Sea Farms' tenures from 1999 through present has demonstrated that sediment sulfides increase rapidly during the early stages of production and decrease equally quickly during harvest. Fallow periods of 4–6 months appeared adequate for complete chemical remediation at the tenures examined. Elevated concentrations of zinc, which is added as a supplement to salmon feeds, have been observed in sediments. However, they are bound by sulfides and are not biologically available. Zinc concentrations declined to background during chemical remediation. No cumulative effects associated with either organic carbon or zinc were observed at any of these farms during successive production cycles.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Brooks, Kenneth M. and Stierns, Annette R. and Mahnken, Conrad V.W. and Blackburn, Dale B.},
	month = apr,
	year = {2003},
	keywords = {Aquaculture, Benthos, Review, Sulfide, Fallow, Recovery, Remediation, Salmon, Zinc},
	pages = {355--377}
}

@article{groffman_methods_2006,
	title = {Methods for measuring denitrification: {Diverse} approaches to a difficult problem},
	volume = {16},
	issn = {10510761},
	doi = {10.1890/1051-0761(2006)016[2091:MFMDDA]2.0.CO;2},
	abstract = {Denitrification, the reduction of the nitrogen (N) oxides, nitrate (NO3?) and nitrite (NO2?), to the gases nitric oxide (NO), nitrous oxide (N2O), and dinitrogen (N2), is important to primary production, water quality, and the chemistry and physics of the atmosphere at ecosystem, landscape, regional, and global scales. Unfortunately, this process is very difficult to measure, and existing methods are problematic for different reasons in different places at different times. In this paper, we review the major approaches that have been taken to measure denitrification in terrestrial and aquatic environments and discuss the strengths, weaknesses, and future prospects for the different methods. Methodological approaches covered include (1) acetylene-based methods, (2) 15N tracers, (3) direct N2 quantification, (4) N2:Ar ratio quantification, (5) mass balance approaches, (6) stoichiometric approaches, (7) methods based on stable isotopes, (8) in situ gradients with atmospheric environmental tracers, and (9) molecular approaches. Our review makes it clear that the prospects for improved quantification of denitrification vary greatly in different environments and at different scales. While current methodology allows for the production of accurate estimates of denitrification at scales relevant to water and air quality and ecosystem fertility questions in some systems (e.g., aquatic sediments, well-defined aquifers), methodology for other systems, especially upland terrestrial areas, still needs development. Comparison of mass balance and stoichiometric approaches that constrain estimates of denitrification at large scales with point measurements (made using multiple methods), in multiple systems, is likely to propel more improvement in denitrification methods over the next few years.},
	number = {6},
	journal = {Ecological Applications},
	author = {Groffman, Peter M. and Altabet, Mark A. and Boehlke, J. K. and Butterbach-Bahl, Klaus and David, Mark B. and Firestone, Mary K. and Giblin, Anne E. and Kana, Todd M. and Nielsen, Lars Peter and Voytek, Mary A.},
	year = {2006},
	pmid = {17205891},
	keywords = {Nitrate, Nitrogen, Denitrification, Water quality, Nitrous oxide, Greenhouse effect, Nitric oxide, Stable isotopes},
	pages = {2091--2122}
}

@article{mazouni_nutrient_1996,
	title = {Nutrient and oxygen exchanges at the water-sediment interface in a shellfish farming lagoon ({Thau}, {France})},
	volume = {205},
	issn = {00220981},
	doi = {10.1016/S0022-0981(96)02594-4},
	abstract = {The Etang de Thau (France) is a shallow lagoon characterised by the semi-intensive farming of oysters (Crassostrea gigas, Thunberg) cultured in suspension on frames. Analysis of the benthic fluxes of inorganic nutrients and oxygen over a period of a year has provided a basis for describing the dynamics of the water-sediment interface in the lagoon. Monthly measurements of fluxes at the water sediment interface at two stations have been compared. One station (UC) is located under a culture table, and is subject to intensive accumulation of organic matter (biodeposition); the other (OC) is located outside the area directly under the impact of the culture activities. Oxygen consumption ranged from 288.24 to 1026.85 ??mol ?? m-2 ?? h-1 according to the season and the station. Ammonium production was maximal at station UC in Summer (600 ??mol ?? m-2 ?? h-1) and minimal at station OC in the Autumn (30 ??mol ?? m-2 ?? h-1). In general, the fluxes recorded at station UC were 1.8-3 times higher than those recorded at station OC for oxygen and 1-5 times higher for ammonium. Nevertheless, the variability between stations was lower than the seasonal variability. Using a Multiple Correspondence Analysis (MCA), it was possible to point out the occurrence of an atypical event that was responsible for the disruption of the seasonal cycle. This event was a state of hypoxia known locally under the generic name of malaigue. The dystrophic crisis consists of a major perturbation of the ecosystem, responsible for a massive mortality affecting both the benthos and the reared stocks.},
	number = {1-2},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Mazouni, Nabila and Gaertner, Jean Claude and Deslous-Paoli, Jean Marc and Landrein, Sonia and Geringer D'Oedenberg, Malgorsata},
	year = {1996},
	keywords = {Sediment, Benthic fluxes, Oxygen, Bottom anoxia, Nutrient, Water},
	pages = {91--113}
}

@article{jensen_microscale_1993,
	title = {Microscale {Distribution} of {Nitrification} {Activity} in {Sediment} {Determined} with a {Shielded} {Microsensor} for {Nitrate}},
	volume = {59},
	number = {10},
	journal = {Applied and Environmental MicrobiologyApplied and Environmental Microbiology},
	author = {Jensen, Kim and Nielsen, Lars Peter and Revsbech, Niels Peter},
	year = {1993},
	pages = {3287--3296}
}

@article{haven_aspects_1966,
	title = {Aspects of biodeposition by oysters and other invertebrate filter feeders},
	volume = {11},
	issn = {00243590},
	doi = {10.4319/lo.1966.11.4.0487},
	abstract = {Quantities of suspended matter removed by oysters (Crassostrea virginica) and deposited as feces or pseudofeces varied seasonally, reaching maxima in September. Below 2.8C, measurable quantities were not produced. At certain seasons, levels of suspended solids influenced quantities of biodeposits. Laboratory studies indicated that the oysters on 0.405 hectare of an estuarine bottom may produce up to 981 kg of feces and pseudofeces weekly. Of the particles, 95\% were under 3 microns in diameter. All types of algal cells present in the surrounding water were represented. The deposits contained 77-91\% inorganic matter, mostly illite, chlorite, and mixed-layer clays, 4-12\% organic carbon, and 1.0 g/kg phosphorus. Biodeposits of filter feeders such as barnacles, tunicates, and other lamellibranchs were similar to those of oysters. Filter feeders may influence deposition, transport and the composition of suspended sediments in estuaries. A possible relationship between the removal from suspension and the subsequent deposition of radionuclides associated with particles of clay, silt, or planktonic algae and feces or pseudofeces is suggested.},
	number = {4},
	journal = {Limnology and Oceanography},
	author = {Haven, Dexter S. and Morales-Alamo, Reinaldo},
	year = {1966},
	pages = {487--498},
	file = {Full Text:C\:\\Users\\chand\\Zotero\\storage\\34BLCERU\\Haven and Morales-Alamo - 1966 - Aspects of biodeposition by oysters and other inve.pdf:application/pdf}
}

@article{hargreaves_nitrogen_1998,
	title = {Nitrogen biogeochemistry of aquaculture ponds},
	volume = {166},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/S0044848698002981},
	doi = {10.1016/S0044-8486(98)00298-1},
	abstract = {Nitrogen (N) biogeochemistry of aquaculture ponds is dominated by biological transformations of N added to ponds in the form of inorganic or organic fertilizers and formulated feeds. Nitrogen application in excess of pond assimilatory capacity can lead to the deterioration of water quality through the accumulation of nitrogenous compounds (e.g., ammonia and nitrite) with toxicity to fish or shrimp. Principal sources of ammonia include fish excretion and sediment flux derived from the mineralization of organic matter and molecular diffusion from reduced sediment, although cyanobacterial nitrogen fixation and atmospheric deposition are occasionally important. Principal sinks for ammonia include phytoplankton uptake and nitrification. The magnitude of losses by ammonia volatilization and ammonium fixation to cation exchange sites is minor, but unknown. Interactions between pond sediment and water are important regulators of N biogeochemistry. Sediment represents a source of ammonia and a sink for nitrite and nitrate. The large volume of reduced sediment suggests that the potential for N removal by denitrification is high, although the magnitude of N removal by this mechanism is low because nitrification and denitrification are tightly coupled in aquatic sediments and sediment nitrification is limited by the depth of sediment oxygen penetration. Nitrogen biogeochemistry of aquaculture ponds is affected by feeds and feeding practices, water exchange and circulation, aeration, pond depth and other management procedures. Opportunities for management of N biogeochemistry are limited and goals are based largely on the intensity of fish production.},
	number = {3-4},
	journal = {Aquaculture},
	author = {Hargreaves, John A.},
	month = jul,
	year = {1998},
	keywords = {Denitrification, Sediment, Nitrification, Ammonia, Background info},
	pages = {181--212}
}

@article{strain_salmon_2005-1,
	title = {Salmon {Aquaculture}, {Nutrient} {Fluxes} and {Ecosystem} {Processes} in {Southwestern} {New} {Brunswick}},
	volume = {5},
	doi = {10.1007/b136003},
	abstract = {Salmon aquaculture discharges organic wastes into the marine environment. Salmon metabolism and the waste discharges add nutrients and organic matter to and remove oxygen from both the water column and sediments. The salmon industry in Southwestern New Brunswick (SWNB) is used to illustrate how waste discharges can be estimated in the absence of detailed information on farm operations. A fish growth model and mass balance calculations are used to estimate carbon, nitrogen and phosphorus wastes at the farm scale. Feed nutrition data and environmental measurements are used to partition wastes into fractions, and to estimate the oxygen demand. The predicted demand at the time of maximum discharge is 200 times greater than the oxygen uptake measured in surface sediments at cages, suggesting that most farm wastes are dispersed over wide areas and do not accumulate directly under cages. The number of farmed fish in an inlet is then used to predict total discharges to that inlet. In SWNB, salmon aquaculture is the largest anthropogenic source of organic input to the coastal zone. The significance of the wastes on inlet scales (2–25 km) is evaluated by comparing element fluxes through salmon farms with fluxes due to natural processes: primary production, nutrient regeneration, and community respiration. In intensively farmed bays, fluxes due to salmon farms reach values of 20, 330 and 160\% of those due to natural processes for oxygen, nitrogen and carbon, respectively: significant changes to the ecosystem have occurred in these bays. Spatial scales are critical in describing such impacts: effects will be greater close to the farms, and smaller when averaged over larger areas.},
	number = {July},
	journal = {Environmental Effects of Marine Finfish Aquaculture},
	author = {Strain, P M and Hargrave, B T},
	year = {2005},
	pages = {29--57}
}

@article{levin_effects_2009-1,
	title = {Effects of natural and human-induced hypoxia on coastal benthos},
	volume = {6},
	issn = {1726-4189},
	doi = {10.5194/bg-6-2063-2009},
	abstract = {Coastal hypoxia (defined here as {\textbackslash}textless 1.42 ml L-1; 62.5 mu M; 2 mg L-1, approx. 30\% oxygen saturation) develops seasonally in many estuaries, fjords, and along open coasts as a result of natural upwelling or from anthropogenic eutrophication induced by riverine nutrient inputs. Permanent hypoxia occurs naturally in some isolated seas and marine basins as well as in open slope oxygen minimum zones. Responses of benthos to hypoxia depend on the duration, predictability, and intensity of oxygen depletion and on whether H2S is formed. Under suboxic conditions, large mats of filamentous sulfide oxidizing bacteria cover the seabed and consume sulfide. They are hypothesized to provide a detoxified microhabitat for eukaryotic benthic communities. Calcareous foraminiferans and nematodes are particularly tolerant of low oxygen concentrations and may attain high densities and dominance, often in association with microbial mats. When oxygen is sufficient to support metazoans, small, soft-bodied invertebrates (typically annelids), often with short generation times and elaborate branchial structures, predominate. Large taxa are more sensitive than small taxa to hypoxia. Crustaceans and echinoderms are typically more sensitive to hypoxia, with lower oxygen thresholds, than annelids, sipunculans, molluscs and cnidarians. Mobile fish and shellfish will migrate away from low-oxygen areas. Within a species, early life stages may be more subject to oxygen stress than older life stages. Hypoxia alters both the structure and function of benthic communities, but effects may differ with regional hypoxia history. Human-caused hypoxia is generally linked to eutrophication, and occurs adjacent to watersheds with large populations or agricultural activities. Many occurrences are seasonal, within estuaries, fjords or enclosed seas of the North Atlantic and the NW Pacific Oceans. Benthic faunal responses, elicited at oxygen levels below 2 ml L-1, typically involve avoidance or mortality of large species and elevated abundances of enrichment opportunists, sometimes prior to population crashes. Areas of low oxygen persist seasonally or continuously beneath upwelling regions, associated with the upper parts of oxygen minimum zones (SE Pacific, W Africa, N Indian Ocean). These have a distribution largely distinct from eutrophic areas and support a resident fauna that is adapted to survive and reproduce at oxygen concentrations {\textbackslash}textless 0.5 ml L-1. Under both natural and eutrophication-caused hypoxia there is loss of diversity, through attrition of intolerant species and elevated dominance, as well as reductions in body size. These shifts in species composition and diversity yield altered trophic structure, energy flow pathways, and corresponding ecosystem services such as production, organic matter cycling and organic C burial. Increasingly the influences of nature and humans interact to generate or exacerbate hypoxia. A warmer ocean is more stratified, holds less oxygen, and may experience greater advection of oxygen-poor source waters, making new regions subject to hypoxia. Future understanding of benthic responses to hypoxia must be established in the context of global climate change and other human influences such as overfishing, pollution, disease, habitat loss, and species invasions.},
	number = {10},
	journal = {Biogeosciences},
	author = {Levin, L A and Ekau, W and Gooday, A J and Jorissen, F and Middelburg, J J and Naqvi, S W A and Neira, C and Rabalais, N N and Zhang, J},
	year = {2009},
	keywords = {filamentous sulfur bacteria, fish-farm impact, gulf-of-mexico, gullmar-fjord basin, low dissolved-oxygen, lower chesapeake bay, macrobenthic community structure, northern adriatic sea, oxygen-minimum zone, yangtze-river estuary},
	pages = {2063--2098}
}

@article{na_influence_2008,
	title = {Influence of advective bio-irrigation on carbon and nitrogen cycling in sandy sediments},
	volume = {66},
	url = {http://openurl.ingenta.com/content/xref?genre=article&issn=0022-2402&volume=66&issue=5&spage=691},
	doi = {10.1357/002224008787536826},
	abstract = {In sandy sediments, the burrow ventilation activity of benthic macrofauna can generate substantial advective flows within the sediment surrounding their burrows. Here we investigated the effects of such advective bio-irrigation on carbon and nitrogen cycling in sandy sediments. To this end, we combined a range of complementary experimental and modelling approaches in a microcosm study of the lugworm Arenicola marina (Polychaeta: Annelida). Bio-irrigation rates were determined using uranine as a tracer, while benthic fluxes of oxygen (O2), total carbon dioxide (TCO2), dissolved inorganic nitrogen (NH4+, ΣNO2− + NO3−) and dinitrogen (N2) were measured in closed-core incubations containing lugworms acclimatized for a relatively short (2 d) and long (3 wk) duration. The fluxes induced by A. marina were compared to those induced by mechanical mimics that simulate the flow pattern induced by the lugworm. These mechanical mimics proved a useful tool to simulate the effect of lugworm irrigation on sediment biogeochemistry. Subsequently, reactive transport model simulations were performed to check the consistency of the measured fluxes and rates, and to construct closed mass balances for sedimentary nitrogen. This reactive transport model successfully captured the essential features of the nitrogen cycling within the sediment. Advective irrigation by both lugworm and mechanical mimics significantly stimulated the sediments O2 consumption, organic matter mineralization rate (TCO2 release), and denitrification rate (N2 production). While sedimentary O2 consumption was directly correlated to advective input of O2, increasing irrigation rates increased the importance of coupled nitrification-denitrification over the external input of nitrate from the overlying water.},
	number = {5},
	journal = {Journal of Marine Research},
	author = {Na, Taehee and Gribsholt, Britta and Galaktionov, Oleksiy S. and Lee, Tongsup and Meysman, Filip J. R.},
	month = sep,
	year = {2008},
	keywords = {bioirrigation, N-cycling, Arenicola marina, respiration},
	pages = {691--722}
}

@article{brigolin_modelling_2009-1,
	title = {Modelling the impact of aquaculture on early diagenetic processes in sea loch sediments},
	volume = {388},
	issn = {01718630},
	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, Thomas D. and Cromey, Chris J. and Aguilera, David R. and Regnier, Pierre},
	year = {2009},
	keywords = {Atlantic salmon, Benthic mineralization, Transient simulation, Depomod, Loch creran, Rtm},
	pages = {63--80}
}

@article{crowe_anammox_2012,
	title = {Anammox, denitrification and fixed-nitrogen removal in sediments from the {Lower} {St}. {Lawrence} {Estuary}},
	volume = {9},
	issn = {1726-4189},
	url = {http://www.biogeosciences.net/9/4309/2012/bg-9-4309-2012.html},
	doi = {10.5194/bg-9-4309-2012},
	language = {English},
	number = {11},
	journal = {Biogeosciences},
	author = {Crowe, S. A. and Canfield, D. E. and Mucci, A. and Sundby, B. and Maranger, R.},
	month = nov,
	year = {2012},
	pages = {4309--4321}
}

@article{mccarthy_denitrification_2015-1,
	title = {Denitrification {Dominates} {Sediment} {Nitrogen} {Removal} and {Is} {Enhanced} by {Bottom}-{Water} {Hypoxia} in the {Northern} {Gulf} of {Mexico}},
	volume = {38},
	issn = {15592731},
	doi = {10.1007/s12237-015-9964-0},
	abstract = {Nutrient loads from the Mississippi River watershed are associated with seasonal development of bottom-water hypoxia in the northern Gulf of Mexico. Microbial nitrogen (N) transformations at the sediment-water interface are important in determining system productivity and the development and maintenance of hypoxia. Intact sediment cores were incubated in a continuous-flow system with stable isotope tracers to identify and quantify important N sources (e.g., N fixation), sinks (e.g., denitrification and anammox), and links (e.g., dissimilatory nitrate reduction to ammonium, DNRA). Microbial N sinks on the Louisiana-Texas continental shelf remove up to 68 \% of the total N load from the Mississippi River watershed, and up to 29 \% of this N removal (mean = 11.8 +/- 1.7 \%) may be due to anammox. The highest N-2 production rates and ammonium effluxes were observed at low bottom-water oxygen concentrations, and sediments were a significant source of ammonium to the water column at all times. DNRA and heterotrophic N fixation were not consistent pathways for total sediment N fluxes, but their potential importance to N balance and productivity in the system warrants further study and inclusion in ecosystem models. Physical disturbance from passage of two hurricanes in 2008 resulted in lower N cycling rates and sediment oxygen consumption, with sediment processes migrating into the water column. Denitrification is the dominant N sink in the northern Gulf of Mexico and provides a valuable ecosystem service by mitigating N loads from the Mississippi River watershed, particularly during seasonal bottom-water hypoxia events.},
	number = {6},
	journal = {Estuaries and Coasts},
	author = {McCarthy, Mark J. and Newell, Silvia E. and Carini, Stephen A. and Gardner, Wayne S.},
	year = {2015},
	keywords = {Denitrification, Anammox, DNRA, Gulf of Mexico, Hypoxia, N fixation},
	pages = {2279--2294}
}

@article{morata_benthic_2014,
	title = {Benthic {Recovery} after the {Cessation} of a {Gilt}-head {Seabream}, {Sparus} aurata , {Farm} in the {Mediterranean} {Sea}},
	volume = {45},
	issn = {08938849},
	url = {http://doi.wiley.com/10.1111/jwas.12128},
	doi = {10.1111/jwas.12128},
	number = {4},
	journal = {Journal of the World Aquaculture Society},
	author = {Morata, Tania and Falco, Silvia and Sospedra, Javier and Gadea, Isabel and Rodilla, Miguel},
	month = aug,
	year = {2014},
	pages = {380--391}
}

@article{queiros_can_2015,
	title = {Can benthic community structure be used to predict the process of bioturbation in real ecosystems?},
	volume = {137},
	url = {https://www.sciencedirect.com/science/article/pii/S0079661115000944#!},
	doi = {10.1016/J.POCEAN.2015.04.027},
	abstract = {Disentangling the roles of environmental change and natural environmental variability on biologically mediated ecosystem processes is paramount to predict future marine ecosystem functioning. Bioturbation, the biogenic mixing of sediments, has a regulating role in marine biogeochemical processes. However, our understanding of bioturbation as a community level process and of its environmental drivers is still limited by loose use of terminology, and a lack of consensus about what bioturbation is. To help resolve these challenges, this empirical study investigated the links between four different attributes of bioturbation (bioturbation depth, activity and distance, and biodiffusive transport); the ability of an index of bioturbation (BPc) to predict each of them; and their relation to seasonality, in a shallow coastal system – the Western Channel Observatory, UK. Bioturbation distance depended on changes in benthic community structure, while the other three attributes were more directly influenced by seasonality in food availability. In parallel, BPc successfully predicted bioturbation distance but not the other attributes of bioturbation. This study therefore highlights that community bioturbation results from this combination of processes responding to environmental variability at different time-scales. However, community level measurements of bioturbation across environmental variability are still scarce, and BPc is calculated using commonly available data on benthic community structure and the functional classification of invertebrates. Therefore, BPc could be used to support the growth of landscape scale bioturbation research, but future uses of the index need to consider which bioturbation attributes the index actually predicts. As BPc predicts bioturbation distance, estimated here using a random-walk model applicable to community settings, studies using either of the metrics should be directly comparable and contribute to a more integrated future for bioturbation research.},
	journal = {Progress in Oceanography},
	author = {Queirós, Ana M. and Stephens, Nicholas and Cook, Richard and Ravaglioli, Chiara and Nunes, Joana and Dashfield, Sarah and Harris, Carolyn and Tilstone, Gavin H. and Fishwick, James and Braeckman, Ulrike and Somerfield, Paul J.},
	month = sep,
	year = {2015},
	keywords = {community indicators, community-level bioturbation},
	pages = {559--569}
}

@article{sohm_emerging_2011,
	title = {Emerging patterns of marine nitrogen fixation.},
	volume = {9},
	issn = {1740-1526},
	doi = {10.1038/nrmicro2594},
	abstract = {Biological N(2) fixation is an important part of the marine nitrogen cycle as it provides a source of new nitrogen that can support biological carbon export and sequestration. Research in the past decade has focused on determining the patterns of distribution and abundance of diazotrophs, defining the environmental features leading to these patterns and characterizing the factors that constrain marine N(2) fixation overall. In this Review, we describe how variations in the deposition of iron from dust to different ocean basins affects the limiting nutrient for N(2) fixation and the distribution of different diazotrophic species. However, many questions remain about marine N(2) fixation, including the role of temperature, fixed nitrogen species, CO(2) and physical forcing in controlling N(2) fixation, as well as the potential for heterotrophic N(2) fixation.},
	number = {7},
	journal = {Nature reviews. Microbiology},
	author = {Sohm, Jill a and Webb, Eric a and Capone, Douglas G},
	year = {2011},
	pmid = {21677685},
	pages = {499--508}
}

@article{kalvelage_nitrogen_2013,
	title = {Nitrogen cycling driven by organic matter export in the {South} {Pacific} oxygen minimum zone},
	volume = {6},
	issn = {1752-0894},
	doi = {10.1038/ngeo1739},
	abstract = {Oxygen minimum zones are expanding globally, and at present account for around 20-40\% of oceanic nitrogen loss. Heterotrophic denitrification and anammox-anaerobic ammonium oxidation with nitrite-are responsible for most nitrogen loss in these low-oxygen waters. Anammox is particularly significant in the eastern tropical South Pacific, one of the largest oxygen minimum zones globally. However, the factors that regulate anammox-driven nitrogen loss have remained unclear. Here, we present a comprehensive nitrogen budget for the eastern tropical South Pacific oxygen minimum zone, using measurements of nutrient concentrations, experimentally determined rates of nitrogen transformation and a numerical model of export production. Anammox was the dominant mode of nitrogen loss at the time of sampling. Rates of anammox, and related nitrogen transformations, were greatest in the productive shelf waters, and tailed off with distance from the coast. Within the shelf region, anammox activity peaked in both upper and bottom waters. Overall, rates of nitrogen transformation, including anammox, were strongly correlated with the export of organic matter. We suggest that the sinking of organic matter, and thus the release of ammonium into the water column, together with benthic ammonium release, fuel nitrogen loss from oxygen minimum zones.},
	number = {3},
	journal = {Nature Geoscience},
	author = {Kalvelage, T and Lavik, G and Lam, P and Contreras, S and Arteaga, L and Loscher, C R and Oschlies, a and Paulmier, a and Stramma, L and Kuypers, M M M},
	year = {2013},
	pages = {228--234}
}

@book{brooks_seven_2004,
	title = {Seven year remediation study at the {Carrie} {Bay} {Atlantic} salmon ({Salmo} salar) farm in the {Broughton} {Archipelago}, {British} {Columbia}, {Canada}},
	volume = {239},
	isbn = {0044-8486},
	abstract = {Numerous studies describing the short-term recovery of benthic habitats impacted by organic wastes from commercial salmon farms have been published. A few of these studies have continued for up to 2 years. The Carrie Bay salmon farm in the Broughton Archipelago of British Columbia began operation in 1990 and produced four crops of Atlantic salmon. It was fallowed in 1998 after producing 2587 mt of Atlantic salmon in the preceding production cycle. Significant accumulations of organic waste were observed near the netpens in 1997 when the farm was close to maximum salmon biomass. Bottom sediments were blackened with iron sulfides and gas ebullition together with extensive Beggiatoa mats were observed to a distance of 145 m on the southern transect in 1997. Patchy Beggia remained near the netpens in 1999. Twelve benthic surveys have been completed in Carrie Bay over the last 7 years. The database reported herein describes slow, but steady, remediation of this site. Chemical remediation, including reductions in total volatile solids (TVS), free sulfides, redox potential and zinc were nearly complete at distances {\textbackslash}textgreater80 m in 2002 and rapid and significant additional chemical remediation was observed throughout the area in 2003. Sediment concentrations of zinc have declined throughout this study at all distances and were approaching background concentrations in 2002 and 2003. Macrofaunal communities at Carrie Bay's reference stations were dominated by mollusks with significantly fewer annelids and very few crustaceans. This community did not respond to organic enrichment in the classic way described by Pearson and Rosenberg [Oceanogr. Mar. Boil. Annu. Rev. 16 (1978) 229], which has accurately predicted the macrobenthic response at many intensive aquaculture facilities. None of the eight opportunistic taxa frequently found proliferating in enriched sediments near B.C. salmon farms were a large component of the Carrie Bay macrobenthos at any place or at any time. Rather, a single annelid (Nephtys cornuta) was found in moderate abundance and several bivalve mollusks that dominated local reference communities have slowly recruited into the remediating sediments. Biological remediation was nearing completion at distances ???80 m from the netpens, but was not complete under and at shorter distances in 2002 following 4 years of fallow. Based on regression analysis, it is predicted that chemical remediation (sulfides ???447 ??M) sufficient to support half of the common taxa observed at the local reference station will be complete in 2004 following approximately 65 months in fallow. Unlike four other farms in the Broughton Archipelago, where sulfide concentrations exceeded 20,000 ??M, and where chemical remediation has been complete in less than 6 months, sulfide concentrations at Carrie Bay have remained {\textbackslash}textless9410 ??M throughout this study. These relatively lower sulfide concentrations; the unique pattern of biological remediation; and the relatively long chemical and biological remediation times observed at Carrie Bay point out the need for a better understanding of the diagenesis of labile carbon compounds in sediments underlying intensive aquaculture operations. A better understanding of the underlying causes of the biochemical processes observed in this study will significantly aid farm operators and regulators in selecting benthic habitats with optimal sustainability for modern salmon farming. In addition to describing the transport of waste, computer programs designed to predict the environmental response to intensive aquaculture must incorporate modules assessing the biogeochemical and biological response to these inputs before their output can predict the unusual responses observed in Carrie Bay. ?? 2004 Elsevier B.V. All rights reserved.},
	number = {1-4},
	author = {Brooks, Kenneth M. and Stierns, Annette R. and Backman, Clare},
	year = {2004},
	doi = {10.1016/j.aquaculture.2003.12.024},
	pmid = {219},
	keywords = {Mariculture, Atlantic salmon, Benthos, British Columbia, Netpen, Remediation}
}

@article{rich_anaerobic_2008,
	title = {Anaerobic ammonium oxidation (anammox) in {Chesapeake} {Bay} sediments},
	volume = {55},
	issn = {00953628},
	url = {http://link.springer.com/10.1007/s00248-007-9277-3},
	doi = {10.1007/s00248-007-9277-3},
	abstract = {Anaerobic ammonium oxidation (anammox) has recently been recognized as a pathway for the removal of fixed N from aquatic ecosystems. However, the quantitative significance of anammox in estuarine sediments is variable, and measurements have been limited to a few estuaries. We measured anammox and conventional denitrification activities in sediments along salinity gradients in the Chesapeake Bay and two of its sub-estuaries, the Choptank River and Patuxent River. Homogenized sediments were incubated with (14/15)N amendments of NH4+, NO3-, and NO2- to determine relative activities of anammox and denitrification. The percent of N2 production due to anammox (ra\%) ranged from 0 to 22\% in the Chesapeake system, with the highest ra\% in the freshwater portion of the main stem of upper Chesapeake Bay, where water column NO3- concentrations are consistently high. Intermediate levels of relative anammox (10\%) were detected at locations corresponding to tidal freshwater and mesohaline locations in the Choptank River, whereas anammox was not detected in the tidal freshwater location in the Patuxent River. Anammox activity was also not detected in the seaward end of Chesapeake Bay, where water column No3- concentrations are consistently low. The ra\% did not correlate with NH4+ accumulation rate in anoxic sediment incubations, but ra\% was related to water column NO3- concentrations and salinity. Anammox bacterial communities were also examined by amplifying DNA extracted from the upper Chesapeake Bay sediment with polymerase chain reaction (PCR) primers that are specific for 16S rRNA genes of anammox organisms. A total of 35 anammox-like sequences were detected, and phylogenetic analysis grouped the sequences in two distinct clusters belonging to the Candidatus "Scalindua" genus.},
	number = {2},
	journal = {Microbial Ecology},
	author = {Rich, Jeremy J and Dale, Olivia R and Song, Bongkeun and Ward, Bess B},
	month = feb,
	year = {2008},
	pmid = {17619213},
	pages = {311--320}
}

@incollection{kristensen_organic_2000,
	address = {Dordrecht},
	title = {Organic matter diagenesis at the oxic/anoxic interface in coastal marine sediments, with emphasis on the role of burrowing animals},
	url = {http://www.springerlink.com/index/10.1007/978-94-011-4148-2_1},
	booktitle = {Life at {Interfaces} and {Under} {Extreme} {Conditions}},
	publisher = {Springer Netherlands},
	author = {Kristensen, Erik},
	year = {2000},
	doi = {10.1007/978-94-011-4148-2_1},
	pages = {1--24}
}

@article{mente_effect_2006,
	title = {Effect of feed and feeding in the culture of salmonids on the marine aquatic environment: {A} synthesis for {European} aquaculture},
	volume = {14},
	issn = {09676120},
	doi = {10.1007/s10499-006-9051-4},
	abstract = {While marine aquaculture has grown rapidly, so have concerns regarding the environmental impacts caused by the industry. In particular, increasing discharges of solid and dissolved fish excretions, nutrients and therapeutic chemicals have coincided with greater public awareness of the possibility of environmental damage. This has stimulated a number of criticisms, drawn from a wide spectrum of interests, ranging from the use of natural fish stocks to produce fish meal for aqua feeds to the effects of enhanced nutrient input on the coastal marine environment. The present study reviews available information on the environmental effects of feeding practices in salmonid aquaculture in Europe. Accumulation of waste food and fish faecal material results in changes in the sediment under fish cages, characterized by a low redox potential, high content of organic material and accumulation of nitrogenous and phosphorous compounds. Although significant environmental impacts have been reported in the literature at distances of up to 100 m from the cages, in general such impacts are reported to be localized to within 20 - 50 m around the cages. For farmed salmon and trout, mass balance models have been developed for nitrogen and phosphorus, indicating that 50\% of the nitrogen and 28\% of the phosphorus supplied with the food is wasted in dissolved form. The maximum nutrient release can be estimated from the hydrographic conditions in the immediate vicinity of the farm, such as water volume, tidal water exchange and currents. At present production levels, improvements in the feeding efficiency and feed quality of aquafeeds could reduce waste and consequent environmental impacts.},
	number = {5},
	journal = {Aquaculture International},
	author = {Mente, Eleni and Pierce, Graham J. and Santos, Maria Begoña and Neofitou, Christos},
	year = {2006},
	keywords = {Aquaculture, Environment, Feeding, Feeds, Fish meal},
	pages = {499--522}
}

@article{cromey_depomod-modelling_2002,
	title = {{DEPOMOD}-modelling the deposition and biological effects of waste solids from marine cage farms},
	volume = {214},
	issn = {00448486},
	doi = {10.1016/S0044-8486(02)00368-X},
	abstract = {To enable better predictive capability of the impact from large marine cage fish farms on the benthos and improved objectivity in the regulatory decision-making process, a computer particle tracking model DEPOMOD was developed. DEPOMOD predicts the solids accumulation on the seabed arising from a fish farm and associated changes in the benthic faunal community. The grid generation module allows the user to set up a grid containing information on depth, cage and sampling station positions for the area of interest. Given the information on wastage rates of fish food and faeces and hydrodynamics of the area, the initial deposition of particles on the seabed can then be predicted with the particle tracking model. The resuspension model then redistributes particles according to near-bed current flow fields to predict the net solids accumulated on the seabed within the grid area. From quantitative relationships between benthic community descriptors and solids accumulation, predictions of the level of benthic community impact can then be made. The particle tracking model was validated using sediment trap studies. Model predictions of flux (g/m2/day) generally agreed well with field data with an accuracy of ?? 20\% and ?? 13\% for a dispersive and depositional site, respectively. Using parameters from the validated resuspension model (rare among models in this field), semi-empirical quantitative relationships between predicted solids accumulation (g/m2/year) and observed Infaunal Trophic Index (ITI) and total individual abundance were established using data from numerous Scottish marine fish farms. A submodel was also validated for predicting feed input throughout a growing cycle for planning purposes. DEPOMOD may be used for assessing the potential impact of a farm throughout a growing cycle, or if the biomass consent is increased. It may also be used in the site selection process of a new farm to investigate the proposed farm position and biomass levels. Prediction of the dispersion of particulates during use of in-feed medicines may also be undertaken. ?? 2002 Elsevier Science B.V. All rights reserved.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Cromey, Chris J. and Nickell, Thomas D. and Black, Kenneth D.},
	year = {2002},
	keywords = {Modelling, Benthos, Aquaculture impact, Husbandry, Infaunal Trophic Index, Particle tracking, Resuspension},
	pages = {211--239}
}

@article{norkko_welcome_2012,
	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{herbert_nitrogen_1999-1,
	title = {Nitrogen cycling in coastal marine ecosystems},
	volume = {23},
	issn = {1574-6976},
	url = {http://femsre.oxfordjournals.org/content/23/5/563.abstract},
	doi = {10.1111/j.1574-6976.1999.tb00414.x},
	abstract = {It is generally considered that nitrogen availability is one of the major factors regulating primary production in temperate coastal marine environments. Coastal regions often receive large anthropogenic inputs of nitrogen that cause eutrophication. The impact of these nitrogen additions has a profound effect in estuaries and coastal lagoons where water exchange is limited. Such increased nutrient loading promotes the growth of phytoplankton and fast growing pelagic macroalgae while rooted plants (sea-grasses) and benthic are suppressed due to reduced light availability. This shift from benthic to pelagic primary production introduces large diurnal variations in oxygen concentrations in the water column. In addition oxygen consumption in the surface sediments increases due to the deposition of readily degradable biomass. In this review the physico-chemical and biological factors regulating nitrogen cycling in coastal marine ecosystems are considered in relation to developing effective management programmes to rehabilitate seagrass communities in lagoons currently dominated by pelagic macroalgae and/or cyanobacteria.},
	number = {5},
	journal = {FEMS Microbiology Reviews},
	author = {Herbert, R.A.},
	year = {1999},
	pmid = {10525167},
	keywords = {Bacteria, Bacteria: metabolism, Cyanobacteria, Cyanobacteria: metabolism, Nitrogen Fixation, Nitrogen Fixation: physiology, Seawater, Soil Microbiology},
	pages = {563--590}
}

@article{thamdrup_production_2002,
	title = {Production of {N} 2 through {Anaerobic} {Ammonium} {Oxidation} {Coupled} to {Nitrate} {Reduction} in {Marine} {Sediments} {Production} of {N} 2 through {Anaerobic} {Ammonium} {Oxidation} {Coupled} to {Nitrate} {Reduction} in {Marine} {Sediments}},
	volume = {68},
	issn = {0099-2240},
	doi = {10.1128/AEM.68.3.1312},
	abstract = {In the global nitrogen cycle, bacterial denitrification is recognized as the only quantitatively important process that converts fixed nitrogen to atmospheric nitrogen gas, N2 , thereby influencing many aspects of ecosystem function and global biogeochemistry. However, we have found that a process novel to the marine nitrogen cycle, anaerobic oxidation of ammonium coupled to nitrate reduction, contributes substantially to N2 production in marine sediments. Incubations with 15 N-labeled nitrate or ammonium demonstrated that during this process, N2 is formed through one-to-one pairing of nitrogen from nitrate and ammonium, which clearly separates the process from denitrification. Nitrite, which accumulated transiently, was likely the oxidant for ammonium, and the process is thus similar to the anammox process known from wastewater bioreactors. Anaerobic ammonium oxidation accounted for 24 and 67\% of the total N2 production at two typical continental shelf sites, whereas it was detectable but insignificant relative to denitrification in a eutrophic coastal bay. However, rates of anaerobic ammonium oxidation were higher in the coastal sediment than at the deepest site and the variability in the relative contribution to N2 production between sites was related to large differences in rates of denitrification. Thus, the relative importance of anaerobic ammonium oxidation and denitrification in N2 production appears to be regulated by the availability of their reduced substrates. By shunting nitrogen directly from ammonium to N2 , anaerobic ammonium oxidation promotes the removal of fixed nitrogen in the oceans. The process can explain ammonium deficiencies in anoxic waters and sediments, and it may contribute significantly to oceanic nitrogen budgets. The},
	number = {3},
	journal = {Applied and Environmental Microbiology},
	author = {Thamdrup, Bo and Dalsgaard, Tage},
	year = {2002},
	pmid = {11872482},
	pages = {1312--1318}
}

@book{middelburg_denitrification_1996,
	title = {Denitrification in marine sediments: {A} model study},
	volume = {10},
	isbn = {0886-6236},
	abstract = {The rate and factors controlling denitrification in marine sediments have been investigated using a prognostic diagenetic model. The model is forced with observed carbon fluxes, bioturbation and sedimentation rates, and bottom water conditions. It can reproduce rates of aerobic mineralization, denitrification, and fluxes of oxygen, nitrate, and ammonium. The globally integrated rate of denitrification is estimated by this model to be about 230-285 Tg N yr", with about 100 Tg N yr' occurring in shelf sediments. This estimate is significantly higher than literature estimates (12-89 Tg N yr"), mainly because of a proposed upward revision of denitrification rates in slope and deep-sea sediments. Higher sedimentary denitrification estimates require a revision of the marine nitrogen budget and lowering of the oceanic residence time of nitrogen down to about 2 xl 03 years and are consistent with reported low NIP remineralization ratios between 1000 and 3000 m. Rates of benthic denitrification are most sensitive to the flux of labile organic carbon arriving at the sediment-water interface and bottom water concentrations of nitrate and oxygen. Denitrification always increases when bottom water nitrate increases but may increase or decrease if oxygen in the bottom water increases. Nitrification is by far the most important source of nitrate for denitrification, except for organic- rich sediments underlying oxygen-poor and nitrate-rich water.},
	number = {4},
	author = {Middelburg, Jack J. and Soetaert, Karline and Herman, Peter M J and Heip, Carlo H R},
	year = {1996},
	doi = {10.1029/96GB02562}
}

@article{hargrave_traffic_2002,
	title = {A traffic light decision system for marine finfish aquaculture siting},
	volume = {45},
	issn = {09645691},
	doi = {10.1016/S0964-5691(02)00056-X},
	abstract = {A decision support system (DSS) is described to assess far- and near-field variables potentially affected by marine finfish aquaculture. The DSS consists of 20 questions that produce positive to negative scores for ecosystem-level (far-field) and site-specific (near-field) variables based on pre-determined or proposed qualitative criteria and known or proposed threshold values for variables. A Traffic Light Method indicates scores above (A; dark green), intermediate to (B+; light green or B−; orange) or below (C; red) criteria for acceptability. Some variables are pre-emptive if scored C. Cumulative ecosystem and site indices are calculated and assessed in a conventional three-color Traffic Light scheme as acceptable (green), provisionally acceptable (caution required) (yellow) or unacceptable (red) using a decision matrix of all possible color combinations. The DSS is flexible since new questions can be added, scores for selected variables can be weighted, and revised thresholds can be incorporated to reflect additional scientific information, changes in aquaculture licensing regulations or specific jurisdictional requirements. Data from salmon farm license applications in eastern Canada are tested using the DSS.},
	number = {4},
	journal = {Ocean \& Coastal Management},
	author = {Hargrave, B.T},
	year = {2002},
	pages = {215--235}
}

@article{morse_non-steady_2007,
	title = {A non-steady state diagenetic model for changes in sediment biogeochemistry in response to seasonally hypoxic/anoxic conditions in the "dead zone" of the {Louisiana} shelf},
	volume = {106},
	issn = {03044203},
	doi = {10.1016/j.marchem.2006.02.003},
	abstract = {Biogeochemical processes occurring near the sediment-water interface can play an important role in the establishment and persistence of hypoxic-to-anoxic conditions in areas of moderate-to-shallow water depth. Results are given in this paper for diagenetic modeling of two sites from the area on the Louisiana shelf west of the Mississippi River Delta known as the "dead zone". This is one of the largest and most studied regions where seasonal coastal hypoxia occurs. The diagenetic model was capable of generating good matches with depth profiles at both sites in the upper 8??cm. Moderate differences between predicted and observed concentrations below this depth are most likely due to the highly non-steady state conditions in this region. The model was also able to predict extremely low dissolved sulfide concentrations and bacterial sulfate reduction rates that were in good agreement with independent direct observations. A sensitivity analysis of the model to input parameters showed that the model was much more sensitive to changes in values under hypoxic conditions than norm-oxic or anoxic conditions in the overlying water. Simulations were carried out to first determine how the profiles of sediment porewater parameters and interfacial fluxes would change under differing quasi-steady state conditions where overlying dissolved oxygen concentrations and the rate of bioirrigation were varied. Next a non-steady state simulation was run to investigate how sediment biogeochemistry would change between these conditions during a hypothetical annual cycle. Results demonstrated a clear need to better understand the dynamic relationship among overlying water oxygen concentrations, the behavior of the benthic faunal community responsible for bioirrigation and sediment biogeochemistry. ?? 2006 Elsevier B.V. All rights reserved.},
	number = {1-2 SPEC. ISS.},
	journal = {Marine Chemistry},
	author = {Morse, John W. and Eldridge, Peter M.},
	year = {2007},
	keywords = {Hypoxia, Diagenetic model, Louisiana shelf},
	pages = {239--255}
}

@article{kaspar_effects_1985,
	title = {Effects of mussel aquaculture on the nitrogen cycle and benthic communities in {Kenepuru} {Sound}, {Marlborough} {Sounds}, {New} {Zealand}},
	volume = {85},
	issn = {00253162},
	doi = {10.1007/BF00397431},
	abstract = {Nitrogen pools and transformations and benthic com-munities at a Perna canaIiculus farm and a nearby reference site without direct influence of marine farming in Kenepuru Sound, New Zealand, were compared on four dates be-tween September 1982 and May 1983. The organic nitro-gen pool in the top 12 cm sediment was 7.4 to 10.8 mol m -2 at the mussel farm and 6.1 to 8.9molm -2 at the reference site. The nitrate and nitrite pools were similar in both sediments, but the ammonium pool in the mussel farm sediment was about twice as high as in the reference sediment. In January, the sediment ammonium concentra-tions ranged from 418 mnolcm -3 (surface) to 149nmol cm -3 (12 cm depth) at the mussel farm and from 86 to 112 nmol cm -3 at the reference site. The molar C:N ratio of the sediment organic matter was 6.2 to 7.2 at the mussel farm and 7.9 to 10.0 at the reference site. The molar N:P ratio of the sediment organic matter was 4.3 to 7.2 and 3.3 to 6.1 at mussel farm and reference site, respectively. The total nitrogen mineralisation rate in the top 12 cm sedi-ment ranged from 21.7 to 37.1 mmol m -2 d -1 at the mussel farm and from 8.5 to 25.0 mmol m -2 d -I at the reference site. Ammonium excretion by mussels was about 4.7\% (January) and 7.4\% (May) of the combined nitrogen mineralisation by mussels and sediment. The sediment-denitrification rate was 0.7 to 6.1 mmol m -2 d -1 at the mussel farm and 0.1 to 0.9 mmol m -2 d -1 at the reference site. In January, 76 and 93\% of the nitrate reduced in the sediments were denitrified at the mussel farm and reference site, respectively. The denitrification rate on the mussel lines (determined on detritus-covered mussels) was twice the mussel farm sediment-denitrification rate and 10 times the reference sediment-denitrification rate. Total denitrification at the mussel farm was 21\% higher than at the reference site. The loss of nitrogen through mussel harvest and denitrification was 68\% higher at the mussel farm. The surface layers of both sediments contained about 75 mg m -2 chlorophyll a. Sediment phaeophytin levels were 52 mg m -2 at the reference site and 137 mg m -2 at the mussel farm. While the benthic infauna of the mussel-farm sediment consisted only ofpolychaete worms, the reference sediment contained also bivalve molluscs, brittle stars and crustaceans.},
	number = {2},
	journal = {Marine Biology},
	author = {Kaspar, H. F. and Gillespie, P. A. and Boyer, I. C. and MacKenzie, A. L.},
	year = {1985},
	pmid = {21817026},
	pages = {127--136}
}

@article{ljungqvist_effects_nodate,
	title = {Effects of {Long}-line {Mussel} {Farming} on {Sediment} {Nitrogen} {Mineralisation} ; {Reaction} {Rates} and {Pathways} {Effects} of {Long}-line {Mussel} {Farming} on {Sediment} {Nitrogen} {Mineralisation} ; {Reaction} {Rates} and},
	number = {October 2016},
	author = {Ljungqvist, Lars}
}

@article{fernandez_nitrogen_2011,
	title = {Nitrogen fixation in denitrified marine waters},
	volume = {6},
	issn = {19326203},
	doi = {10.1371/journal.pone.0020539},
	abstract = {Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by approximately 30 fold between cruises (7.5+/-4.6 versus 190+/-82.3 micromol m(-2) d(-1)). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was approximately 5 times higher (574+/-294 micromol m(-2) d(-1)) than the oxic euphotic layer (48+/-68 micromol m(-2) d(-1)). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions.},
	number = {6},
	journal = {PLoS ONE},
	author = {Fernandez, Camila and Farías, Laura and Ulloa, Osvaldo},
	year = {2011},
	pmid = {21687726}
}

@article{hardison_influence_2015,
	title = {Influence of organic carbon and nitrate loading on partitioning between dissimilatory nitrate reduction to ammonium ({DNRA}) and {N}2 production},
	volume = {164},
	issn = {00167037},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S001670371500263X},
	doi = {10.1016/j.gca.2015.04.049},
	abstract = {Biologically available nitrogen is removed from ecosystems through the microbial processes of anaerobic ammonium oxidation (anammox) or denitrification, while dissimilatory nitrate reduction to ammonium (DNRA) retains it. A mechanistic understanding of controls on partitioning among these pathways is currently lacking. The objective of this study was to conduct a manipulative experiment to determine the influence of organic C and NO3− loading on partitioning. Sediment was collected from a location on the southern New England shelf (78 m water depth) and sieved. Half of the sediment was mixed with freeze-dried phytoplankton and the other half was not. Sediment was then spread into 1.5 mm, “thin discs” closed at the bottom and placed in large aquarium tanks with filtered, N2/CO2 sparged seawater to maintain O2 limited conditions. Half of the discs received high NO3− loading, while the other half received low NO3− loading, resulting in a multifactorial design with four treatments: no C addition, low NO3− (−C−N); C addition, low NO3− (+C−N); no C addition, high NO3− (−C+N); and C addition, high NO3− (+C+N). Sediment discs were incubated in the tanks for 7 weeks, during which time inorganic N (NH4+, NO3−, and NO2−) was monitored, and sediment discs were periodically removed from the tanks to conduct 15N isotope labeling experiments in vials to measure potential rates of anammox, denitrification, and DNRA. Temporal dynamics of inorganic N concentrations in the tanks were indicative of anoxic N metabolism, with strong response of the build up or consumption of the intermediate NO2−, depending on treatments. Vial incubation experiments with added 15NO2− + 14NH4+ indicated significant denitrification and DNRA activity in sediment thin discs, but incubations with added 15NH4+ + 14NO2− indicated anammox was not at all significant. Inorganic N concentrations in the tanks were fit to a reactive transport model assuming different N transformations. Organic C decomposition rates were inferred based on modeled rates as well as stoichiometric conversions of NH4+ production in pre-incubated vials. Based on model results, partitioning between DNRA and N2 production was positively linearly related to the ratio of C decomposition to NO3− reduction rates (C/NO3−) but not C decomposition alone. Based on vial results, partitioning was significantly related to C decomposition. Overall, this study supports the hypothesis that high organic C loading is a prerequisite for DNRA to be favored over denitrification but that N2 production may still be significant when organic C is high depending on NO3− availability.},
	journal = {Geochimica et Cosmochimica Acta},
	author = {Hardison, Amber K. and Algar, Chris K. and Giblin, Anne E. and Rich, Jeremy J.},
	year = {2015},
	pages = {146--160}
}

@article{bernard_dissimilatory_2015-2,
	title = {Dissimilatory nitrate reduction to ammonium ({DNRA}) seasonally dominates {NO}{\textbackslash}textlessinf{\textbackslash}textgreater3{\textbackslash}textless/inf{\textbackslash}textgreater {\textbackslash}textlesssup{\textbackslash}textgreater???{\textbackslash}textless/sup{\textbackslash}textgreater reduction pathways in an anthropogenically impacted sub-tropical coastal lagoon},
	volume = {125},
	issn = {1573515X},
	url = {http://littlelagoon.org/inc/files/Bernard et al 15 Nitrogen Little Lagoon.pdf},
	doi = {10.1007/s10533-015-0111-6},
	abstract = {Sediments have an important role in nutrient dynamics by providing sites for denitrification, which, in conjunction with nitrogen (N) fixation and other processes such as dissimilatory nitrate reduction to ammonium (DNRA), can regulate ecosystem N availability. Little Lagoon, Alabama, USA, is affected by anthropogenic perturbations and has N inputs from nitrate (NO3 −)-contaminated submarine groundwater discharge. N cycle pathways (N-fixation, denitrification, anammox, and DNRA) and benthic fluxes were measured at three sites over a year to investigate the hypothesis that DNRA, by producing ammonium (NH4 +) as a dissimilatory end product of NO3 − reduction, was a significant process retaining bioavailable fixed N in Little Lagoon. DNRA was found to be an important NO3 − reduction pathway, especially in the summer months (study average: 52.1 μmol N m−2 h−1) compared to denitrification (study average 7.7 μmol N m−2 h−1). Sulfidic sediments during the majority of the year interfere with denitrification and result in decreased N loss through denitrification. The conversion of NO3 − to the more biologically preferred form of N, NH4 + via DNRA, means that NO3 − reduction has considerable nourishing potential and likely will affect both ecosystem function and services. These results indicate that NO3 − reduction may contribute to, rather than counteract, eutrophication during warm summers in estuaries receiving high N inputs. As estuarine sediments provide a key ecosystem function of N removal, excess anthropogenic N input jeopardizes their ability to effectively remove reactive N in Little Lagoon and likely in other impacted ecosystems.},
	number = {1},
	journal = {Biogeochemistry},
	author = {Bernard, Rebecca J. and Mortazavi, Behzad and Kleinhuizen, Alice A.},
	year = {2015},
	keywords = {Denitrification, Anammox, DNRA, Sediment oxygen demand, Denitriﬁcation, Nitrogen cycling, S},
	pages = {47--64}
}

@article{cabello_heavy_2006,
	title = {Heavy use of prophylactic antibiotics in aquaculture: {A} growing problem for human and animal health and for the environment},
	volume = {8},
	issn = {14622912},
	doi = {10.1111/j.1462-2920.2006.01054.x},
	abstract = {The accelerated growth of finfish aquaculture has resulted in a series of developments detrimental to the environment and human health. The latter is illustrated by the widespread and unrestricted use of prophylactic antibiotics in this industry, especially in developing countries, to forestall bacterial infections resulting from sanitary shortcomings in fish rearing. The use of a wide variety of antibiotics in large amounts, including non-biodegradable antibiotics useful in human medicine, ensures that they remain in the aquatic environment, exerting their selective pressure for long periods of time. This process has resulted in the emergence of antibiotic-resistant bacteria in aquaculture environments, in the increase of antibiotic resistance in fish pathogens, in the transfer of these resistance determinants to bacteria of land animals and to human pathogens, and in alterations of the bacterial flora both in sediments and in the water column. The use of large amounts of antibiotics that have to be mixed with fish food also creates problems for industrial health and increases the opportunities for the presence of residual antibiotics in fish meat and fish products. Thus, it appears that global efforts are needed to promote more judicious use of prophylactic antibiotics in aquaculture as accumulating evidence indicates that unrestricted use is detrimental to fish, terrestrial animals, and human health and the environment.},
	number = {7},
	journal = {Environmental Microbiology},
	author = {Cabello, Felipe C.},
	year = {2006},
	pmid = {16817922},
	pages = {1137--1144}
}

@article{lin_partial_2008,
	title = {Partial recovery of infaunal communities during a fallow period at an open-ocean aquaculture},
	volume = {371},
	issn = {0171-8630},
	url = {http://www.int-res.com/abstracts/meps/v371/p65-72/},
	doi = {10.3354/meps07675},
	journal = {Marine Ecology Progress Series},
	author = {Lin, DT and Bailey-Brock, JH},
	month = nov,
	year = {2008},
	keywords = {Aquaculture, Organic enrichment, Fallow, Recovery, Hawai‘i, Indicator species, Offshore, Polychaete},
	pages = {65--72}
}

@article{mazzola_fish-farming_2000,
	title = {Fish-farming effects on benthic community structure in coastal sediments: analysis of meiofaunal recovery},
	volume = {57},
	issn = {10543139},
	url = {http://icesjms.oxfordjournals.org/content/57/5/1454.short},
	doi = {10.1006/jmsc.2000.0904},
	abstract = {To study the impact of organic enrichment and high biodeposition caused by intensive fish farming in coastal sediments, meiofaunal samples were collected on a monthly basis between March and October 1997 at two stations of the Gaeta Gulf: one under the Farmocean cage (2000 m3), while the other (the control) was located at about 1 km from an area not impacted by fish farming. The fish farm contained about 120 000 Dicentrarchus labrax (density 18 kg m-3). The most evident changes in the benthic habitat under the cage were a large accumulation of primary organic material (phytopigment concentrations up to 44 \{micro\}g g-1), changes in sedimentary organic matter composition (increased lipid levels related to the composition of the fish diet), and a strong reduction of redox potential values, which resulted in a significant reduction of meiofaunal penetration depth into the sediments. Organic loads had a clear impact on meiofaunal densities, which were 50\% lower under the cage than at the control site (1112\{+/-\}118 and 2160\{+/-\}339 ind. 10 cm-2, respectively). Compared with the control, farm sediments also showed an increased importance of copepods, which dominated the meiofauna together with nematodes (both 39\% of the total density) and polychaetes (17\%). The removal of the fish farm from the site on July 1997 allowed an analysis to be made of the initial short and medium-term recovery of the assemblages. After two months, meiofaunal densities were closer to the control (about 30\% recovery). Community structure recovered only partially to the characteristics typical of the study area, with increased importance of nematodes (about 70\% of total density) and reduced copepod contribution, but it was still characterized by a lower number of taxa after four months. These data suggest that meiofaunal recovery after fish farm disturbance is rapid, but far from complete after four months.},
	number = {5},
	journal = {ICES Journal of Marine Science},
	author = {Mazzola, A},
	month = oct,
	year = {2000},
	pages = {1454--1461}
}

@article{christensen_impacts_2003,
	title = {Impacts of longline mussel farming on oxygen and nitrogen dynamics and biological communities of coastal sediments},
	volume = {218},
	issn = {00448486},
	url = {http://www.sciencedirect.com/science/article/pii/S0044848602005872},
	doi = {10.1016/S0044-8486(02)00587-2},
	abstract = {Benthic communities and benthic mineralization were studied in two shallow coastal regions of New Zealand: Tasman Bay, a possible future site for mussel farm development, and Beatrix Bay, which already hosts several longline mussel farms. In Tasman Bay, microphytobenthic (MPB) production added significantly to the total primary production of the bay. The activity of benthic microalgae had a pronounced effect on oxic conditions, solute exchange and denitrification rates. Benthic mineralization, quantified as the dark oxygen uptake, was in the range of 675±11 μmol m−2 h−1. Denitrification rates were high and fueled entirely by nitrate produced by the nitrifying community within the sediment. Competition for inorganic nitrogen between benthic microalgae and nitrifiers/denitrifiers resulted in diel variation in nitrogen cycling and reduced the inorganic nitrogen efflux and denitrification activity in the light. Calculated in electron equivalents, denitrification accounted for 11–20\% of the total carbon mineralization—one of the highest numbers reported for coastal sediments. Reduced sediments, containing low MPB biomass and few subsurface macroinvertebrate species, were observed below a mussel farm in Beatrix Bay, presumably due to the intensified sedimentation of organic matter. Oxygen consumption increased in the organic-rich sediments, and ammonium effluxes were up to 14 times higher than those of unaffected sediments 250 m away from the farm. Denitrification rates below the farm were low as the coupled nitrification–denitrification was inhibited by the presence of sulfide. The dissimilative reduction of nitrate to ammonium (DRNA) was, however, stimulated in the reduced sediment. The enhanced benthic mineralization was associated with sulfidic sediments and a lower nitrogen removal rate due to impeded benthic photosynthesis and denitrification activity. The described local conditions associated with mussel farming should be taken into account when new areas are considered for development.},
	number = {1-4},
	journal = {Aquaculture},
	author = {Christensen, Peter Bondo and Glud, Ronnie N and Dalsgaard, Tage and Gillespie, Paul},
	month = mar,
	year = {2003},
	keywords = {Benthic mineralization, Greenshell™ mussel, Macroinvertebrates, Microphytobenthic production, Nutrient fluxes and denitrification},
	pages = {567--588}
}

@article{burgin_have_2007,
	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{thornton_effect_1999,
	title = {Effect of illumination and emersion period on the exchange of ammonium across the estuarine sediment-water interface},
	volume = {184},
	issn = {01718630},
	doi = {10.3354/meps184011},
	abstract = {ABSTRACT: The metabolic activity of the microphytobenthos may effect inorganic nutrient exchange across the sediment-water interface. Ammonium exchange across the sediment-water interface was investigated in intact sediment cores and microphytobenthos isolated using lens tissue. Ammonium uptake rates of lens tissue extracts in darkness were 11.4 ± 5 µmol (mg chl a)-1 h-1 (mean ± SE). Uptake by lens tissue extracts was 2 to 5 times greater in the light than dark; however, uptake under illumination was not correlated with photosynthetically available radiation (PAR) intensity. Emersion under illumination and in the dark affected ammonium exchange after immersion in sediment cores. In dark-emersed cores there was net ammonium efflux from the sediment into the overlying water after immersion. An illuminated emersion period reduced the flux of ammonium to the overlying water or affected uptake after immersion. There was a significant positive relationship between the length of the period of emersion under illumination (and therefore photosynthesis) and the subsequent ammonium demand of the sediment after immersion. Porewater profiles revealed low ammonium concentrations in illuminated-emersed cores compared to dark-emersed and dark-immersed cores. Ammonium demand in illuminated-emersed cores was a result of direct and indirect effects by the microphytobenthos. As well as direct ammonium uptake in the light, the production of oxygen probably stimulated oxic bacterial processes such as nitrification (NH4+ to NO3-) in the surface of the sediment. These data show that the effect of the illumination and emersion period should be considered when nutrient budgets are calculated for intertidal, cohesive sediments dominated by microphytobenthos.},
	journal = {Marine Ecology Progress Series},
	author = {Thornton, Daniel C O and Underwood, Graham J C and Nedwell, David B.},
	year = {1999},
	keywords = {Ammonium, Ammonium uptake, Diatom, Emersion period, Estuarine, Microphytobenthos, Nutrient exchange},
	pages = {11--20}
}

@article{heilskov_benthic_2006,
	title = {Benthic fauna bio-irrigation effects on nutrient regeneration in fish farm sediments},
	volume = {339},
	url = {https://www.sciencedirect.com/science/article/pii/S0022098106004412},
	doi = {10.1016/J.JEMBE.2006.08.003},
	abstract = {Impacts of organic enrichment and a modified benthic fauna community (caused by fish farming) on benthic mineralization rates and nutrient cycling were studied in sediments at one Danish and one Cypriote fish farm. Sediment organic matter concentration and macrofauna community composition were manipulated in microcosms and changes in total benthic metabolism (oxygen consumption, TCO2 production), anaerobic metabolism (sulfate reduction rates), nutrient fluxes and sediment parameters were followed for a period of 3 weeks. Mineralization rates were found to be highly correlated with irrigation velocities and largest fauna effects were found in the Danish sediments with the large and active irrigating climax species (Nereis diversicolor and Macoma balthica). Eastern Mediterranean climax species (Glycera rouxii and Naineris laevigata) also stimulated mineralization rates but to a smaller extent due to lower irrigation, whereas the opportunistic species (Capitella in Danish sediment and Hermodice carunculata in Cypriote sediment) showed less effect on mineralization. Ammonium and phosphate release increased with increasing irrigation velocities, but much less in Cyprus indicating higher nutrient retention at the ultra-oligotrophic location compared to eutrophic Danish site. Irrigation velocities, and thus mineralization rates, increased by organic matter loading, indicating larger fauna-induced oxidation in enriched environments. The result implies that a change in fauna structure in fish farm sediment towards smaller opportunistic polychaete species with lower irrigation will result in slower mineralization rates and potentially increase accumulation of organic waste products.},
	number = {2},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {Heilskov, Anna C. and Alperin, Marc and Holmer, Marianne},
	month = dec,
	year = {2006},
	keywords = {aquaculture, remineralization},
	pages = {204--225}
}

@article{d.m._official_2011,
	title = {{THE} {OffICIAl} {MAGAzINE} {Of} {THE} {OCEANOGRAPHY} {SOCIETY}},
	volume = {24},
	issn = {10428275},
	url = {http://dx.doi.org/10.5670/oceanog.2011.80.},
	doi = {10.5670/oceanog.2011.65},
	abstract = {Sea ice extent in the Arctic Ocean diminished significantly during the first decade of the 2000s, most particularly in the Canada Basin where the loss of both multiyear and first-year ice was greater than in the other three subbasins. Using data collected during basin -wide ...},
	number = {3},
	journal = {Oceanography},
	author = {D.M., Anderson and Reguera, B. and Pitcher, G.C. and Enevoldsen, H.O.},
	year = {2011},
	pmid = {1000287730},
	pages = {162--173}
}

@article{trimmer_nitrogen_1998,
	title = {Nitrogen fluxes through the lower estuary of the river {Great} {Ouse}, {England}: {The} role of the bottom sediments},
	volume = {163},
	issn = {01718630},
	doi = {10.3354/meps163109},
	abstract = {ABSTRACT: Sediment-water nutrient exchange, oxygen uptake, denitrification (acetylene blockage) and pore water nutnent concentration profiles were measured at intertidal sediment (predominantly silWclays) sites in the lower estuary of the nver Great Ouse, England. Sedments were consistent sinks for No3- (310 pm01 m-2 h-', mean sites 4 to 9) and O2 (2800 pm01 m-2 h-', mean sites 4 to 7), sources of NH,' (270 pol m-2 h-', mean sites 4 to 9) but neutral with respect to NOz- and urea Oxygen uptake was significantly correlated (p c 0.05) 14th seasonal temperature. Nitrate exchange became saturated at No3- concentrations {\textbackslash}textgreater 400 pM, at a rate of about 400 pm01 NO3- m-' h-'. Denitrification accounted annually for 46\% of the NO,- exchanged into the sediments and approached asymptotic rates during spnng and summer at NO3- concentrations {\textbackslash}textgreater 400 yM. Of the total N flux through the sediments, NH,' efflux accounted for 51 \%, whist 49\% was converted to gases, compared to {\textbackslash}textgreater90\% in the upper estuary Freshwater flushlng tunes were calculated for a defined area of the estuary and ranged from 20.5 d in June to 3.25 d in November. Attenuation of the riverine total oxidlsed nitrogen (NO,- + NO2-) load to the estuary ranged from 1 \% in the middle of winter to 56'::) at the height of summer and annually the sehments denitrified 38.4 Mm01 N. Recycling of nitrogen in the sedirnents, via NO3 arnmonification (calculated by difference) and organic ammonification, generated an annual NH,' efflux of 128 Mm01 N, equivalent to 22\% of the primary production N requirement in the Wash. KEY},
	journal = {Marine Ecology Progress Series},
	author = {Trimmer, M. and Nedwell, D. B. and Sivyer, D. B. and Malcolm, S. J.},
	year = {1998},
	keywords = {Denitrification, Bottom sediments, Freshwater flushing, Nutrient attenuation},
	pages = {109--124}
}

@article{krkosek_epizootics_2006,
	title = {Epizootics of wild fish induced by farm fish},
	volume = {103},
	issn = {0027-8424},
	doi = {10.1073/pnas.0603525103},
	abstract = {The continuing decline of ocean fisheries and rise of global fish consumption has driven aquaculture growth by 10\% annually over the last decade. The association of fish farms with disease emergence in sympatric wild fish stocks remains one of the most controversial and unresolved threats aquaculture poses to coastal ecosystems and fisheries. We report a comprehensive analysis of the spread and

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branch_name: refs/heads/master

extension: bib