text:
demonstrated by large vertical H2S concentration gradients in the porewater (from 0 to 1,000 lM in the top 3 cm) at the most impacted site. The impact on ecosystem functions such as bioirrigation was evidenced by a decreasing TOU/DOU ratio, from 1.7 in the non-impacted sediments to 1 in the impacted zone. This trend was related to a shift in the macrofaunal assemblage and an increase in sediment bacterial population. The turnover time of the organic load of the sediment was estimated to be over 6 years.},
	number = {6},
	journal = {Aquatic Geochemistry},
	author = {Cathalot, Cécile and Lansard, Bruno and Hall, Per O J and Tengberg, Anders and Almroth-Rosell, Elin and Apler, Anna and Calder, Lois and Bell, Elanor and Rabouille, Christophe},
	year = {2012},
	keywords = {Fish farming, Sediment, Benthic chamber, Benthic mineralization, H2S, Microprofiling, Organic carbon, Oxygen, Scotland, Sea loch},
	pages = {515--541}
}

@article{holby_chemical_1994,
	title = {Chemical fluxes and mass balances in a marine fish cage farm. {III}. {Silicon}},
	volume = {120},
	issn = {00448486},
	doi = {10.1016/0044-8486(94)90087-6},
	abstract = {Fluxes and pathways of silicon in a marine rainbow trout cage farm were studied. The measured fluxes included those carried by fish food, juveniles, harvest, fish loss (death and escape), sedimentation from the cages, and benthic release measured with flux chambers in-situ. Two different types of Si mass balances for the farm were constructed. The mass balance according to the flux method was based on the measured fluxes and constructed for each of two consecutive growing seasons. The mass balance constructed according to the accumulation method was based on the total input and removal of Si to the cages of the farm since it was started, and the recovery of Si in the sediment originating from the farm. In both types of mass balances external input was the major source of Si, contributing a minimum of 55-80\% of the total biogenic silica in the material collected in sediment traps below the farm and of the material accumulated in the farm-derived sediment. The Si removed from the farm with harvest contributed a very small part, ???0.3\%, of the amount of Si supplied to the farm with fish food and juveniles. The loss of Si to the environment was 2.4 kg (1985), 2.5 kg (1986) and 2.5 kg (1980-1986) for each ton of fish produced. On a seasonal basis, about 4.5\% of the sedimented biogenic Si was returned in dissolved form from the sediment to the overlying water. This constituted about 0.3\% of the biogenic Si content in the farm-derived sediment. The flux of reactive silicate from sediment below the fish farm was enhanced about 2.5 times compared to nearby sediments unaffected by the farm. ?? 1994.},
	number = {3-4},
	journal = {Aquaculture},
	author = {Holby, Ola and Hall, Per O J},
	year = {1994},
	pages = {305--318}
}

@article{hubble_nutrient_2002,
	title = {Nutrient control of phytoplankton production in {Lake} {Naivasha} , {Kenya}},
	number = {Ci},
	author = {Hubble, David S and Harper, David M and Monitoring, Ecological and Gardens, Ainsley and So, Hampshire},
	year = {2002},
	keywords = {eutrophication, lake, nutrients, shallow, tropical},
	pages = {99--105}
}

@article{mcmahon_regulation_1999,
	title = {Regulation and monitoring of marine aquaculture in {Ireland}},
	author = {Mcmahon, By T},
	year = {1999}
}

@article{arnold_note_2001,
	title = {{NOTE} {EVIDENCE} {FOR} {METHYL} {JASMONATE}-{INDUCED} {PHLOROTANNIN} {PRODUCTION} {IN} {FUCUS} {VESICULOSUS} ({PHAEOPHYCEAE}) 1},
	volume = {37},
	abstract = {The plant growth regulators jasmonic acid and methyl jasmonate (MeJA) have recently been identi-fied in a variety of marine algae; however, their role in these organisms is currently unknown. Here we re-port that exposure to MeJA, during periods of tidal emergence causes the induction of polyphenolic chem-ical defenses (the phlorotannins) in two populations of the common rockweed Fucus vesiculosus (Linnaeus). Phlorotannin concentrations were up to 1.6 times higher in the growing apices of F. vesiculosus from both Avery Point (Connecticut, USA) and Roosevelt Inlet (Delaware, USA) within 10–14 days after a sin-gle brief exposure to airborne MeJA at concentra-tions ranging from 5.42 to 542 nM. The timing and magnitude of this induced increase in phlorotannin concentration are similar to that caused by real and simulated herbivory, raising the question of whether jasmonates, or their oxylipin relatives, are natural el-ements of antiherbivore responses in Fucus , as they are in vascular plants.},
	journal = {J. Phycol},
	author = {Arnold, Thomas M and Targett, Nancy M and Tanner, Christopher E and Hatch, Walter I and Ferrari, Kirstin E},
	year = {2001},
	keywords = {airborne cue, chemical defense, DM, dry mass, Fu-cus vesiculosus, herbivory, induction, JA, jasmonic acid, Key index words, MeJA, methyl jas-monate, methyl jasmonate, oxylipin, phlorotannins, polyphe-nolics Abbreviations},
	pages = {1026--1029}
}

@article{fulweiler_evidence_2013,
	title = {Evidence and a conceptual model for the co-occurrence of nitrogen fixation and denitrification in heterotrophic marine sediments},
	volume = {482},
	issn = {01718630},
	doi = {10.3354/meps10240},
	abstract = {Marine waters are often nitrogen (N) limited. Denitrification, the microbial conver- sion of nitrate to dinitrogen (N2) gas, is responsible for significant N removal from the coastal ocean. In contrast, nitrogen fixation, the microbial transformation of N2 to ammonium, is typically regarded as an inconsequential N source. The imbalance between these 2 processes is responsi- ble, at least in part, for N limitation in the coastal ocean. Organic matter quality and quantity has been shown to determine rates of these critical N cycling processes. We hypothesized that the tim- ing of organic matter deposition to the benthos might also be important in determining which pro- cess dominates. We tested this hypothesis using a coupled biogeochemical-molecular approach. We report directly measured net sediment denitrification rates and corresponding expression of nirS, a gene in the denitrification pathway, with the simultaneous expression of nifH, a gene asso- ciated with nitrogen fixation. The timing of organic matter deposition determined the magnitude of the net sediment N2 fluxes. Highest rates of denitrification occurred soon after deposition, and the lowest rates occurred over 200 d after the last deposition event concomitant with increased nifH expression. Phylogenetic evidence suggests that sulfur and sulfate reducers are responsible for the nitrogen fixation. Globally, warming water temperatures, changes in light, and reduced nutrient loads through management intervention have been linked to decreases and/or altered phenology of water column productivity. Based on a conceptual model developed here, we sug- gest that in these systems, heterotrophic sediment nitrogen fixation may become an important component of the nitrogen budget.},
	journal = {Marine Ecology Progress Series},
	author = {Fulweiler, R. W. and Brown, S. M. and Nixon, S. W. and Jenkins, B. D.},
	year = {2013},
	keywords = {Denitrification, Direct sediment N2 fluxes, Heterotrophic nitrogen fixation, Marine sediments, NifH expression},
	pages = {57--68}
}

@article{beltran_rodriguez_spatio-temporal_2007,
	title = {Spatio-temporal variation in organic nitrogen and carbon in sediments associated with tropical submerged- cage aquaculture},
	author = {Beltrán Rodriguez, Diana M},
	year = {2007}
}

@article{jenkins_coupling_1984,
	title = {The coupling of nitrification and denitrification in two estuarine sediments l v2},
	volume = {29},
	issn = {0024-3590},
	number = {3},
	journal = {Limnology and Oceanography},
	author = {Jenkins, Mark C and Kemp, W Michael},
	year = {1984},
	keywords = {1984, 29, 3, 609-6 19, nol, oceanogr},
	pages = {609--619}
}

@article{furukawa_role_2000,
	title = {The role of biologically-enhanced pore water transport in early diagenesis: {An} example from carbonate sediments in the vicinity of {North} {Key} {Harbor}, {Dry} {Tortugas} {National} {Park}, {Florida}},
	volume = {58},
	issn = {00222402},
	doi = {10.1357/002224000321511124},
	abstract = {Biologically enhanced pore water irrigation affects the course of early diagenesis in shallow marine sediments, as illustrated here for the carbonate sediments from North Key Harbor, Dry Tortugas National Park, Florida. Whereas macrofaunal activity at the study site extends approximately 15 cm below the water-sediment interface, measured O-2 microprofiles only show O-2 penetration to depths of a few mm. This apparent discrepancy can be explained by considering the 3-D O-2 distribution in the burrowed sediments. Calculations based on an idealized tube model for burrow irrigation show that measureable O-2 concentrations are limited to the immediate vicinity of burrows. Given the observed burrow density (705 +/- 15 m(-2)), a randomly positioned O-2 microprofile has a high probability ({\textbackslash}textgreater90\%) to fall outside the reach of radial O-2 diffusion from burrows. Hence, the shallow penetration depths recorded at the site do not exclude a much deeper supply of O-2 in the sediment via the burrows. Other characteristic features observed in the upper 15-20 cm of the sediments, in particular, the absence of SO42- depletion and the presence of subsurface maxims in the profiles of NH4+ and TCO2, are also the result of pore water irrigation. These features are reproduced by the multicomponent reactive transport model STEADYSED1. Results of the model simulations indicate that bacterial SO42- reduction is the dominant pathway of organic carbon degradation, but that consumption of SO42- in the sediments is compensated by its enhanced transport by irrigation. Thus, depth profiles of SO42- may be poor indicators of the importance of SO42- reduction in irrigated sediments.},
	number = {3},
	journal = {Journal of Marine Research},
	author = {Furukawa, Yoko and Bentley, Samuel J. and Shiller, Alan M. and Lavoie, Dawn L. and Van Cappellen, Philippe},
	year = {2000},
	pages = {493--522}
}

@article{brigolin_ocean_2015,
	title = {Ocean \& {Coastal} {Management} {Space} allocation for coastal aquaculture in {North} {Africa} : {Data} constraints , industry requirements and conservation issues},
	volume = {116},
	issn = {0964-5691},
	url = {http://dx.doi.org/10.1016/j.ocecoaman.2015.07.010},
	doi = {10.1016/j.ocecoaman.2015.07.010},
	journal = {Ocean and Coastal Management},
	author = {Brigolin, Daniele and Lourguioui, Hichem and Amine, Mohamed and Venier, Chiara and Mangin, Antoine and Pastres, Roberto},
	year = {2015},
	pages = {89--97}
}

@book{noauthor_tomaszek_nodate,
	title = {Tomaszek and {Gruca}-{Rokosz} 2007 {RATES} {DNRA} {FACTORS}-{Determinants}.pdf}
}

@article{cury_resolving_2014,
	title = {Resolving {Hjort}'s {Dilemma}: {How} {Is} {Recruitment} {Related} to {Spawning} {Stock} {Biomass} in {Marine} {Fish}?},
	volume = {27},
	issn = {10428275},
	url = {http://tos.org/oceanography/article/resolving-hjorts-dilemma-how-is-recruitment-related-to-spawning-stock-bioma},
	doi = {10.5670/oceanog.2014.85},
	abstract = {The relationship between spawning fish abundance and the number of offspring, the so-called stock-recruitment relationship, is crucial for fisheries management and conservation measures. Using the most comprehensive data set ever assembled, we quantify this relationship for 211 fish stocks worldwide, revealing a global pattern with a pervasive asymptotic shape that shows increasing recruitment reaching an upper limit for values around half to two-thirds of parental biomass. This corroborates previous theoretical and modeling results. However, parental biomass is a predictor for only 5\% to 15\% of the variance in recruitment, demonstrating the weak predictive power of the stock-recruitment relationship in marine fish populations. Thus, there is a need to move rapidly toward models that integrate environmental conditions and species interactions in fisheries stock assessment and management, as suggested by Johan Hjort 100 years ago.},
	number = {4},
	journal = {Oceanography},
	author = {Cury, Philippe and Fromentin, Jean-Marc and Figuet, Sarah and Bonhommeau, Sylvian},
	month = dec,
	year = {2014},
	pages = {42--47}
}

@article{davies_energy_1975,
	title = {Energy flow through the benthos in a {Scottish} {Sea} {Loch}},
	volume = {31},
	issn = {00253162},
	doi = {10.1007/BF00392092},
	number = {4},
	journal = {Marine Biology},
	author = {Davies, J. M.},
	year = {1975},
	pmid = {612},
	pages = {353--362}
}

@article{donald_phytoplankton-specific_2013,
	title = {Phytoplankton-{Specific} {Response} to {Enrichment} of {Phosphorus}-{Rich} {Surface} {Waters} with {Ammonium}, {Nitrate}, and {Urea}},
	volume = {8},
	issn = {19326203},
	doi = {10.1371/journal.pone.0053277},
	abstract = {Supply of anthropogenic nitrogen (N) to the biosphere has tripled since 1960; however, little is known of how in situ response to N fertilisation differs among phytoplankton, whether species response varies with the chemical form of N, or how interpretation of N effects is influenced by the method of analysis (microscopy, pigment biomarkers). To address these issues, we conducted two 21-day in situ mesocosm (3140 L) experiments to quantify the species- and genus-specific responses of phytoplankton to fertilisation of P-rich lake waters with ammonium (NH(4)(+)), nitrate (NO(3)(-)), and urea ([NH(2)](2)CO). Phytoplankton abundance was estimated using both microscopic enumeration of cell densities and high performance liquid chromatographic (HPLC) analysis of algal pigments. We found that total algal biomass increased 200\% and 350\% following fertilisation with NO(3)(-) and chemically-reduced N (NH(4)(+), urea), respectively, although 144 individual taxa exhibited distinctive responses to N, including compound-specific stimulation (Planktothrix agardhii and NH(4)(+)), increased biomass with chemically-reduced N alone (Scenedesmus spp., Coelastrum astroideum) and no response (Aphanizomenon flos-aquae, Ceratium hirundinella). Principle components analyses (PCA) captured 53.2-69.9\% of variation in experimental assemblages irrespective of the degree of taxonomic resolution of analysis. PCA of species-level data revealed that congeneric taxa exhibited common responses to fertilisation regimes (e.g., Microcystis aeruginosa, M. flos-aquae, M. botrys), whereas genera within the same division had widely divergent responses to added N (e.g., Anabaena, Planktothrix, Microcystis). Least-squares regression analysis demonstrated that changes in phytoplankton biomass determined by microscopy were correlated significantly (p{\textbackslash}textless0.005) with variations in HPLC-derived concentrations of biomarker pigments (r(2) = 0.13-0.64) from all major algal groups, although HPLC tended to underestimate the relative abundance of cyanobacteria. Together, these findings show that while fertilisation of P-rich lakes with N can increase algal biomass, there is substantial variation in responses of genera and divisions to specific chemical forms of added N.},
	number = {1},
	journal = {PLoS ONE},
	author = {Donald, Derek B. and Bogard, Matthew J. and Finlay, Kerri and Bunting, Lynda and Leavitt, Peter R.},
	year = {2013},
	pmid = {23349705}
}

@article{callier_responses_2009,
	title = {Responses of benthic macrofauna and biogeochemical fluxes to various levels of mussel biodeposition: {An} in situ "benthocosm" experiment},
	volume = {58},
	issn = {0025326X},
	url = {http://dx.doi.org/10.1016/j.marpolbul.2009.05.010},
	doi = {10.1016/j.marpolbul.2009.05.010},
	abstract = {An in situ experiment was done to evaluate the dose-dependent response of mussel biodeposition on benthic communities and biogeochemical fluxes. Natural benthic communities were exposed to 7 different levels of mussel biodeposition (equivalent to that produced by 0-764 mussels m-2) over 50 days. Benthic communities responded as predicted from the Pearson, T.H., Rosenberg, R., 1978. Macrobenthic succession in relation to organic enrichment and pollution of the marine environment. Oceanogr. Mar. Biol. Annu. Rev. 16, 229-311 model of organic enrichment. Total abundance and species richness decreased with increasing biodeposition. The abundance and biomass of opportunistic species (Capitella spp.) increased in the mesocosms subject to the greatest biodeposition. Sensitive species Tellina agilis and Pherusa plumosa tended to decrease in abundance and biomass with increasing biodeposition. The biotic index M-AMBI responded clearly to increased biodeposition and may be a useful tool for assessing the effect of mussel biodeposition on the benthic environment. These results are important for the construction of predictive models for determining environmental carrying capacity for bivalve aquaculture. Crown Copyright ?? 2009.},
	number = {10},
	journal = {Marine Pollution Bulletin},
	author = {Callier, Myriam D. and Richard, Marion and McKindsey, Christopher W. and Archambault, Philippe and Desrosiers, Gaston},
	year = {2009},
	pmid = {19541330},
	keywords = {Organic enrichment, Biodeposition, Biogeochemical fluxes, Bivalve aquaculture, Dose-response relationship, Macrobenthic communities},
	pages = {1544--1553}
}

@article{read_management_2003,
	title = {Management of environmental impacts of marine aquaculture in {Europe}},
	volume = {226},
	doi = {10.1016/S0044-8486(03)00474-5},
	author = {Read, Paul and Fernandes, Teresa},
	year = {2003},
	pages = {139--163}
}

@article{boudreau_mathematics_2000,
	title = {The {Mathematics} of {Early} {Diagenesis}},
	volume = {38},
	issn = {8755-1209},
	doi = {10.1029/2000RG000081},
	number = {3},
	journal = {Reviews of Geophysics},
	author = {Boudreau, Bernard P.},
	year = {2000},
	keywords = {doi:10.102, http://dx.doi.org/10.1029/2000RG000081},
	pages = {389--416}
}

@article{cranford_indicators_2006,
	title = {Indicators and thresholds for use in assessing shellfish aquaculture impacts on fish habitat},
	abstract = {Abstract The purpose of this research document is to provide science advice needed to allow DFO Habitat Management to make and justify management decisions related to the potential harmful alteration, disruption and destruction (HADD) of fish habitat by shellfish aquaculture. The overall goal of this exercise and of our recommendations is to promote the avoidance and mitigation of a HADD. Our specific objectives were the following: identify, evaluate and make recommendations regarding a range of quantitative indicators (measures of habitat and ecosystem status) that could be used to monitor for potential shellfish aquaculture effects; and provide science-based decision support for the development of an environmental monitoring framework, based on identification of predetermined impact limits (operational thresholds) intended to trigger management actions. A wide range of ecosystem and habitat status indicators and methodological approaches were identified to support industry management and each was initially screened based on habitat impact predictions and observations. Selected indicators were classified based on associated strengths and weaknesses using predefined criteria, including: availability of operational thresholds; regulatory needs; cultured species; scales of impact addressed; cost/benefit; and the needs of responsive management. A habitat assessment framework is recommended for shellfish aquaculture that addresses the need for a consistent and transparent decision-making approach that is science-based, and reflects both fish habitat and ecosystem concerns. The highly diverse Canadian shellfish aquaculture industry (e.g. species cultured, husbandry method, and stocking density) and regional differences in environmental impact risks (related primarily to geographic and hydrodynamic factors) were identified as important considerations for our evaluation of shellfish aquaculture impact assessment options. Recommendations are made towards establishment of an environmental monitoring framework that incorporates sufficient flexibility to be of use in a wide range of environmental settings and that is both effective and practical for current aquaculture operations that range from less than 0.5 to 500 hectares. A primary recommendation of this report is that habitat assessments could be based on a tiered approach that recognizes that an increased risk to fish habitat requires an increase in monitoring effort. Various levels of monitoring could be triggered based on assessments of environmental sensitivity and risk (e.g. dispersive vs. depositional environment and presence of sensitive habitat), the nature of the operation (e.g. size, species and husbandry), and previous measurement and verification of environmental impacts. Inherent within the recommended framework is that ongoing monitoring programs could be continually adaptive to changes in our state-of-knowledge on potential environmental impacts, indicators and related methodologies. It is important to maintain an ability to add or remove indicators to monitoring programs based on sound science. The recommended multi-tiered impact assessment approach addresses the potential for benthic marine habitat impacts in the immediate vicinity of each shellfish aquaculture lease and it therefore parallels science recommendations for finfish aquaculture monitoring in Canada. Scientifically defensible thresholds are available for benthic biogeochemical indicators (sulfides and redox potential) and these could be used to define the hypotheses that need to be addressed in an operational monitoring program. Effective measures are also available for mitigating benthic organic enrichment impacts, and these can be linked to the operational thresholds incorporated in a responsive management framework. Ecosystem-level interactions with dense shellfish aquaculture populations are more complex than for finfish culture and many potential and observed effects on fish habitat cannot be assessed using only site-specific benthic habitat indicators. Measurements with selected far-field impact indicators are needed under certain conditions to compliment benthic operational monitoring. The inability to fully define quantitative operational thresholds for many valid and highly relevant indicators of habitat and ecosystem status (particularly those describing the structure and dynamics of pelagic habitat), owing to present gaps in our knowledge of ecosystem dynamics, should not preclude their potential use. Surveillance sampling programs based on water column parameters are needed under conditions where environmental impact assessments and ongoing monitoring data indicate a relatively high risk that bay-scale impacts will occur. Of particular importance is the need to assess the impacts of longline mussel culture operations on suspended particle concentrations and distribution and the pelagic food web (micro-flora and fauna) in extensively leased coastal embayments. Industry shellfish stocking information for all farms within a management area is considered fundamental to assessments of shellfish aquaculture impacts on fish habitat. The use of sound science practices is required for the design of monitoring programs (statistically valid sampling approaches) and for the analysis of habitat status indicators and data (e.g. quality assurance/quality control).},
	number = {January 2006},
	journal = {DFO Can. Sci. Advis. Sec. Res. Doc. 2006/034},
	author = {Cranford, P. J. and Anderson, R. and Archambault, P. and Balch, T. and Bates, S. S. and Bugden, G. and Callier, M. D. and Carver, C. and Comeau, L. A. and Hargrave, B. and Harrison, W. G. and Horne, E. and Kepkay, P. E. and Li, W. K. W. and Ouellette, M. and Strain, P.},
	year = {2006},
	pages = {125}
}

@book{noauthor_macleod_nodate,
	title = {Macleod et al. 2006 short term fallowing assessment.pdf}
}

@article{mills_diets_nodate,
	title = {Diets of top predators indicate pelagic juvenile rockfish ({Sebastes} spp.) abundance in the {California} {Current} {System}},
	doi = {10.1111/j.1365-2419.2006.00429.x},
	abstract = {Diets of top predators may be useful indicators to the availability of forage fish in marine ecosystems. Juvenile rockfish (young-of-the-year Sebastes spp.) compose a significant part of the diet for many pred-ators in the central California Current, including chinook salmon (Oncorhynchus tshawytscha), and sev-eral species of marine birds and mammals. Herein, we develop annual indices of juvenile rockfish relative abundance by collating time series data sets on: (i) the proportion of rockfish in the diet of three species of seabirds breeding on Southeast Farallon Island (1975– 2002); (ii) the number of rockfish in chinook salmon stomachs (1980–99); and (iii) the abundance of rockfish captured in scientific mid-water trawl net surveys (1983–2002). We used Principal Component Analysis (PCA) to combine indices, and refer to these as 'Multivariate Rockfish Indices' (MRI). Combining time series verifies the patterns shown by each alone and provides a synoptic perspective on juvenile rock-fish relative abundance. The diets of predators with the largest foraging ranges (Common Murre, Uria aalge) and chinook salmon co-varied strongly with the net samples, and appear to be the best indicators. The salmon also sampled species of Sebastes not caught in the nets. The MRI reveals interannual variability in juvenile rockfish abundance, a substantial decline in abundance in the 1990s, and a partial recovery in the early 2000s. Predator-based sampling is a cost-effective enhancement of scientific net sampling.},
	author = {Mills, K L and Laidig, T and Ralston, S and Sydeman, W J},
	keywords = {rockfish, Sebastes, California Current System, Cepphus columba, Cerorhinca monocerata, chinook salmon, climate variability, diet, ecosystem approach, indicators, Oncorhynchus tshawytscha, Principal Component Analysis, seabirds, Uria aalge}
}

@article{findlay_environmental_2017,
	title = {Environmental {Impact} of {Salmon} {Net}-{Pen} {Culture} on {Marine} {Benthic} {Communities} in {Maine} : {A} {Case} {Study} {Author} ( s ): {Robert} {H} . {Findlay} , {Les} {Watling} and {Lawrence} {M} . {Mayer} {Source} : {Estuaries} , {Vol} . 18 , {No} . 1 , {Part} {A} : {Dedicated} {Issue} : {The} {Effects} of {A}},
	volume = {18},
	number = {1},
	author = {Findlay, Robert H and Mayer, Lawrence M},
	year = {2017}
}

@article{strain_salmon_2005,
	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{canfield_pathways_1993,
	title = {Pathways of organic carbon oxidation in three continental margin sediments.},
	volume = {113},
	issn = {00253227},
	doi = {10.1016/0025-3227(93)90147-N},
	abstract = {We have combined several different methodologies to quantify rates of organic carbon mineralization by the various electron acceptors in sediments from the coast of Denmark and Norway. Rates of NH4+ and Sigma CO2 liberation sediment incubations were used with O2 penetration depths to conclude that O2 respiration accounted for only between 3.6-17.4\% of the total organic carbon oxidation. Dentrification was limited to a narrow zone just below the depth of O2 penetration, and was not a major carbon oxidation pathway. The processes of Fe reduction, Mn reduction and sulfate reduction dominated organic carbon mineralization, but their relative significance varied depending on the sediment. Where high concentrations of Mn-oxide were found (3-4 wt\% Mn), only Mn reduction occurred. With lower Mn oxide concentrations more typical of coastal sediments, Fe reduction and sulfate reduction were most important and of a similar magnitude. Overall, most of the measured O2 flux into the sediment was used to oxidized reduced inorganic species and not organic carbon. We suspect that the importance of O2 respiration in many coastal sediments has been overestimated, whereas metal oxide reduction (both Fe and Mn reduction) has probably been well underestimated.},
	journal = {Marine geology},
	author = {Canfield, D E and Jorgensen, B B and Fossing, H and Glud, R and Gundersen, J and Ramsing, N B and Thamdrup, B and Hansen, J W and Nielsen, L P and Hall, P O},
	year = {1993},
	pmid = {11539842},
	keywords = {NASA Discipline Exobiology, Non-NASA Center},
	pages = {27--40}
}

@article{gruber_elusive_2016,
	title = {Elusive marine nitrogen fixation},
	volume = {113},
	issn = {0027-8424},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1603646113},
	doi = {10.1073/pnas.1603646113},
	number = {16},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Gruber, Nicolas},
	year = {2016},
	pages = {4246--4248}
}

@article{sonthiphand_biogeography_2014,
	title = {Biogeography of anaerobic ammonia-oxidizing ( anammox ) bacteria},
	volume = {5},
	doi = {10.3389/fmicb.2014.00399},
	number = {August},
	author = {Sonthiphand, Puntipar and Hall, Michael W and Neufeld, Josh D},
	year = {2014},
	keywords = {anammox bacteria, 16S, 16s rrna gene, biogeography, brocadia, co-occurrence, planctomycetes, scalindua},
	pages = {1--14}
}

@article{esparza_impact_2014,
	title = {Impact of atypical ammonium concentrations on phytoplankton abundance and composition in fresh versus estuarine waters},
	volume = {21},
	doi = {10.3354/ab00588},
	author = {Esparza, Mary Lou and Farrell, Ann E and Craig, Douglas J and Swanson, Curt and Dhaliwal, Bhupinder S and Berg, Gry Mine},
	year = {2014},
	keywords = {ammonium, chlorophytes, diatoms, n, nh 4, no 3, p ratio, phytoplankton, ratio, san francisco estuary, suisun bay},
	pages = {191--204}
}

@article{newell_influence_2002,
	title = {Influence of simulated bivalve biodeposition and microphytobenthos on sediment nitrogen dynamics: {A} laboratory study},
	volume = {47},
	issn = {00243590},
	doi = {10.4319/lo.2002.47.5.1367},
	abstract = {Suspension-feeding eastern oysters, Crassostrea virginica, were once abundant in Chesapeake Bay and may then have exerted top-down control on phytoplankton and also reduced turbidities, thereby increasing light available to benthic plants. Alternatively, oysters may have simply recycled inorganic nutrients rapidly back to the water column, with no long-lasting reduction in phytoplankton biomass resulting from oyster feeding activity. To help distinguish between these scenarios, we explored changes in nitrogen fluxes and denitrification in laboratory incubations of sediment cores held under oxic and anoxic conditions in response to loading by pelletized phytoplankton cells, an experimental analog for oyster feces and pseudofeces. When organics were regenerated under aerobic conditions, typical of those associated with oyster habitat, coupled nitrification-denitrification was promoted, resulting in denitrification of similar to20\% of the total added nitrogen. In contrast, under anoxic conditions, typical of current summertime conditions in main-stem Chesapeake Bay where phytoplankton is microbially degraded beneath the pycnocline, nitrogen was released solely as ammonium from the added organics. We postulate that denitrification of particulate nitrogen remaining in oyster feces and pseudofeces may enhance nitrogen removal from estuaries. In aerobic incubations with sufficient light (70 mumol m(-2) s(-1)), a benthic microalgal/cyanobacterial community grew that not only absorbed the inorganic nitrogen released from the added organics but also fixed N-2. This result suggests that an ecosystem dominated by benthic primary production may develop in shallow waters when reduced turbidity associated with bivalve feeding increases light penetration to a level that can sustain benthic microalgal production.},
	number = {5},
	journal = {Limnology and Oceanography},
	author = {Newell, Roger I. E. and Cornwell, Jeffrey C. and Owens, Michael S.},
	year = {2002},
	pages = {1367--1379}
}

@article{skyring_sulfate_1987,
	title = {Sulfate reduction in coastal ecosystems},
	volume = {5},
	issn = {0149-0451},
	url = {http://www.tandfonline.com/doi/abs/10.1080/01490458709385974},
	doi = {10.1080/01490458709385974},
	abstract = {Synthesises data on sulfate reduction rates that have been determined for various coastal and other continental shelf environments, and reviews the attendant methodology. This integrated information is essential to the understanding of the basic geomicrobiological principles that are involved in the global cycling of elements, the degradation and preservation of organic matter, and the precipitation and preservation of sulfide minerals.},
	number = {3-4},
	journal = {Geomicrobiology Journal},
	author = {Skyring, G. W.},
	year = {1987},
	pages = {295--374}
}

@article{levin_effects_2009,
	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{mccain_life_nodate,
	title = {{LIFE} {HISTORY}, {GEOGRAPHICAL} {DISTRIBUTION}, {AND} {HABITAT} {ASSOCIATIONS} {OF} 82 {WEST} {COAST} {GROUNDFISH} {SPECIES}: {A} {LITERATURE} {REVIEW}},
	author = {Mccain, Bruce B and Miller, Stacey D and Waldo, W and Ii, Wakefield}
}

@article{christensen_sediment_2000,
	title = {Sediment mineralization, nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium in an estuarine fjord with sea cage trout farms},
	issn = {09483055},
	doi = {10.3354/ame021073},
	abstract = {Sediment oxygen consumption, nutrient fluxes across the sediment-water interface, den- itrification, and dissimilatory nitrate reduction to ammonium (DNRA) were measured in sediment below the cages of a rainbow trout farm in the estuary of Horsens Fjord, Denmark, and compared to that in the sediment at reference stations elsewhere in the fjord. Denitrification and DNRA were mea- sured by the isotope pairing technique and a 15N technique, respectively. The measurements are the first published data of in sjtu activities in sediment below marine fish farms. Oxygen consumption by the sediment and effluxes of NH,' and pod3- were markedly stimulated by organic matter loading from the overlying fish cages. Denitrification of nitrate from the water column (D,) was only of significance nitrate concentrations. during autumn and winter when runoff from land resulted in high water colun∼n In contrast, coupled nitrification-denitrification (D,) occurred in the sediment throughout the summer, with the rates in the sediment below the fish cages surprisingly being of the same magnitude as those at the reference stations. Competition for inorganic nitrogen from benthic microalgae probably inhib- ited the activity of both nitrifiers and denitrifiers at the reference stations, while a mat of Beggiatoa spp. on the sediment surface below the fish cages in late summer indicated the presence of sulfide in the uppermost layers of the sediment, which almost ceased D,. While DNRA was absent in sediment unaf- fected by the trout farms, it was of quantitative importance in the reduced sediment below the fish cages, DNRA activity being up to 7-fold greater than denitrification activity. The ecological conse- quence of this shift in the relative importance of the processes in response to organic matter loading was a reduced nitrogen removal by denitrification and an increased efflux of NH,' to the water column, resulting in stimulation of pelagic primary production and increased nitrogen retention by the ecosys- tem. The excess nitrogen input to the fjord from the trout farms corresponded to approximately 12 \% of the total nitrogen load from land during the summer months. Only 0.1 \% of this additional nitrogen input was removed by denitrification in the underlying sediments during the fish production season. In general, shallow estuarine ecosystems hosting fish farms may therefore face increasing eutrophication problems due to the direct supply of nutrients in the fish food and to shifts in the dominant microbial processes in the sediment below the fish cages.},
	journal = {Aquatic Microbial Ecology},
	author = {Christensen, Peter Bondo and Rysgaard, S??ren and Sloth, Niels Peter and Dalsgaard, Tage and Schw??rter, Steen},
	year = {2000},
	pmid = {19444200},
	keywords = {Denitrification, Aquaculture, DNRA, Isotope pairing technique, Benthic microalgae, Flux rates}
}

@article{howarth_howarth_2006,
	title = {Howarth, {Robert} {W}., and {Roxanne} {Marino}. {Nitrogen} as the limiting nutrient for eutrophication in coastal marine ecosystems: {Evolving} views over three decades. {Limnol}. {Oceanogr}., 51(1, part 2), 2006, 364–376},
	volume = {51},
	issn = {00243590},
	doi = {10.4319/lo.2006.51.1_part_2.0364},
	abstract = {The first special volume of Limnology and Oceanography, published in 1972, focused on whether phosphorus (P) or carbon (C) is the major agent causing eutrophication in aquatic ecosystems. Only slight mention was made that estuaries may behave differently from lakes and that nitrogen (N) may cause eutrophication in estuaries. In the following decade, an understanding of eutrophication in estuaries proceeded in relative isolation from the community of scientists studying lakes. National water quality policy in the United States was directed almost solely toward P control for both lakes and estuaries, and similarly, European nations tended to focus on P control in lakes. Although bioassay data indicated N control of eutrophication in estuaries as early as the 1970s, this body of knowledge was treated with skepticism by many freshwater scientists and water-quality managers, because bioassay data in lakes often did not properly indicate the importance of P relative to C in those ecosystems. Hence, the bioassay data in estuaries had little influence on water-quality management. Over the past two decades, a strong consensus has evolved among the scientific community that N is the primary cause of eutrophication in many coastal ecosystems. The development of this consensus was based in part on data from whole-ecosystem studies and on a growing body of evidence that presented convincing mechanistic reasons why the controls of eutrophication in lakes and coastal marine ecosystems may differ. Even though N is probably the major cause of eutrophication in most coastal systems in the temperate zone, optimal management of coastal eutrophication suggests controlling both N and P, in part because P can limit primary production in some systems. In addition, excess P in estuaries can interact with the availability of N and silica (Si) to adversely affect ecological structure. Reduction of P to upstream freshwater ecosystems can also benefit coastal marine ecosystems through mechanisms such as increased Si fluxes. Nitrogen (N) pollution has increased remarkably over the past several decades as a result of increased creation of re-active N for fertilizer use and, inadvertently, from combus-tion of fossil fuels (Galloway et al. 2004). Both a ”white-paper panel” of the Ecological Society of America (Vitousek et al. 1997) and the Coastal Marine Team of the National Climate Change Assessment (Boesch et al. 2000; Scavia et al. 2002) concluded that N pollution is one of the greatest consequences of human-accelerated global change on the coastal oceans of the world. The global distribution of re-active N is far from uniform, and N pollution in coastal waters is greatest where agricultural activity and urbaniza-tion are greatest. In some regions, such as the North Sea and Yellow Sea, human activity probably has increased N fluxes to the coast by a 10-to 15-fold measure or greater, while in other areas, such as Hudson's Bay and Labrador, human ac-tivity probably has had little effect on N fluxes (Howarth 2003). On average for the United States, human activity probably has increased N fluxes to the coast by an estimated sixfold measure (Howarth et al. 2002; Howarth 2003), and some two thirds of the nation's coastal waters are moderately},
	number = {2},
	journal = {Limnol. Oceanogr},
	author = {Howarth, Robert W and Marino, Roxanne},
	year = {2006},
	pmid = {6673659},
	pages = {364--376}
}

@article{kristensen_what_2012,
	title = {What is bioturbation? {The} need for a precise definition for fauna in aquatic sciences},
	volume = {446},
	issn = {0171-8630},
	url = {http://www.int-res.com/abstracts/meps/v446/p285-302/},
	doi = {10.3354/meps09506},
	journal = {Marine Ecology Progress Series},
	author = {Kristensen, E and Penha-Lopes, G and Delefosse, M and Valdemarsen, T and Quintana, CO and Banta, GT},
	month = feb,
	year = {2012},
	keywords = {Sediment, Review, Bioirrigation, Biomixing, Bioturbation definition, Burrow ventilation, Ecosystem engineering, Particle reworking},
	pages = {285--302}
}

@article{de_smet_predator_2016,
	title = {Predator effects on the feeding and bioirrigation activity of ecosystem-engineered {Lanice} conchilega reefs},
	volume = {475},
	url = {https://www.sciencedirect.com/science/article/pii/S0022098115300551},
	doi = {10.1016/J.JEMBE.2015.11.005},
	abstract = {Ecosystem engineers can considerably affect the community composition, abundance and species richness of their environment. This study investigates the existence of positive or negative feedbacks of species that compose the community in intertidal biogenic reefs constructed by the ecosystem engineer Lanice conchilega. This tubeworm creates attractive nursery and feeding grounds for the predatory brown shrimp Crangon crangon, while at the same time is preyed upon by C. crangon. The effect of the predation pressure exerted by C. crangon on the bioirrigation and feeding activity of the tubeworm is up until now unknown and it is hypothesised that these activities are affected by the high densities of C. crangon in the reefs. A mesocosm experiment was set up to investigate the effects of predation pressure on the bioirrigation and feeding activity of L. conchilega in the i) absence; ii) restricted presence; and iii) unrestricted presence of C. crangon. Bioirrigation was quantified by the decrease of an artificially introduced bromide (Br−) tracer, while feeding activity was measured from the incorporation of 13C via stable isotope analysis. The bioirrigation rate of the L. conchilega reef equalled about 30L·m−2·d−1 and was not affected by the presence of the predator. The food uptake of the tubeworm was however about three times lower in the unrestricted presence of C. crangon, presumably due to the retraction of the worm's body and tentacles in its tube induced by physical contact with the predator. Notwithstanding the impacted food uptake of L. conchilega, the tubeworm maintains its functional role in the presence of predators in soft-bottom intertidal areas.},
	journal = {Journal of Experimental Marine Biology and Ecology},
	author = {De Smet, Bart and Braeckman, Ulrike and Soetaert, Karline and Vincx, Magda and Vanaverbeke, Jan},
	month = feb,
	year = {2016},
	keywords = {bioirrigation, bioirrigation rate, ecology, function, predator effects},
	pages = {31--37}
}

@article{remaili_impact_2016,
	title = {The impact of sediment bioturbation by secondary organisms on metal bioavailability, bioaccumulation and toxicity to target organisms in benthic bioassays: {Implications} for sediment quality assessment},
	volume = {208},
	url = {https://www.sciencedirect.com/science/article/pii/S0269749115301342},
	doi = {10.1016/J.ENVPOL.2015.10.033},
	abstract = {Bioturbation alters the properties of sediments and modifies contaminant bioavailability to benthic organisms. These naturally occurring disturbances are seldom considered during the assessment of sediment quality. We investigated how the presence (High bioturbation) and absence (Low bioturbation) of a strongly bioturbating amphipod within three different sediments influenced metal bioavailability, survival and bioaccumulation of metals to the bivalve Tellina deltoidalis. The concentrations of dissolved copper decreased and manganese increased with increased bioturbation. For copper a strong correlation was observed between increased bivalve survival (53–100\%) and dissolved concentrations in the overlying water. Increased bioturbation intensity resulted in greater tissue concentrations for chromium and zinc in some test sediments. Overall, the results highlight the strong influence that the natural bioturbation activities from one organism may have on the risk contaminants pose to other organisms within the local environment. The characterisation of field-based exposure conditions concerning the biotic or abiotic resuspension of sediments and the rate of attenuation of released contaminants through dilution or readsorption may enable laboratory-based bioassay designs to be adapted to better match those of the assessed environment.},
	journal = {Environmental Pollution},
	author = {Remaili, Timothy M. and Simpson, Stuart L. and Amato, Elvio D. and Spadaro, David A. and Jarolimek, Chad V. and Jolley, Dianne F.},
	month = jan,
	year = {2016},
	keywords = {bioturbation, copper, heavy metal flux, heavy metals},
	pages = {590--599}
}

@article{de_juan_functional_2007,
	title = {Functional changes as indicators of trawling disturbance on a benthic community located in a fishing ground ({NW} {Mediterranean} {Sea})},
	volume = {334},
	url = {http://www.int-res.com/abstracts/meps/v334/p117-129/},
	doi = {10.3354/meps334117},
	journal = {Marine Ecology Progress Series},
	author = {de Juan, D and Thrush, SF and Demestre, M},
	month = mar,
	year = {2007},
	keywords = {ecology, community ecology, ecological impacts, trawling},
	pages = {117--129}
}

@article{banks_influence_2013,
	title = {Influence of a burrowing, metal-tolerant polychaete on benthic metabolism, denitrification and nitrogen regeneration in contaminated estuarine sediments},
	volume = {68},
	url = {https://www.sciencedirect.com/science/article/pii/S0025326X13000039},
	doi = {10.1016/J.MARPOLBUL.2013.01.002},
	abstract = {We investigated the effects of the burrowing cirratulid polychaete Cirriformia filigera (Delle Chiaje, 1828) on benthic respiration and nitrogen regeneration in metal-contaminated estuarine sediments using laboratory mesocosms. C. filigera is a dominant component of assemblages in the most severely contaminated sediments within the Derwent estuary, southern Australia. In the presence of C. filigera sediment O2 consumption doubled, with approximately 55\% of this increase due to their respiration and the remaining 45\% attributable to oxidation reactions and increased microbial respiration associated with burrow walls. Combined NO3 and NO2 fluxes were unaffected. The addition of labile organic matter did not affect benthic fluxes, in the presence or absence of C. filigera, presumably due to the short timeframe of the experiment and naturally enriched test sediments. The results suggest that a combination of tolerance and burrowing activity enables this species to provide an ecosystem service in the removal of N from contaminated sites.},
	number = {1-2},
	journal = {Marine Pollution Bulletin},
	author = {Banks, Joanne L. and Ross, D. Jeff and Keough, Michael J. and Macleod, Catriona K. and Keane, John and Eyre, Bradley D.},
	month = mar,
	year = {2013},
	keywords = {bioturbation, ecology, DNF-NF, polychaeta},
	pages = {30--37}
}

@article{shull_infaunal_2009,
	title = {Infaunal burrow ventilation and pore-water transport in muddy sediments},
	volume = {83},
	url = {https://www.sciencedirect.com/science/article/pii/S0272771409001802},
	doi = {10.1016/J.ECSS.2009.04.005},
	abstract = {The ventilation of burrows by tube-dwelling benthos is understood to be important in determining rates of exchange of solutes between the sediment and overlying water. However, few models have attempted to link the burrow ventilation behavior of tube-dwelling organisms with their geochemical consequences. The classic cylinder model of bioirrigation in muddy sediments (Aller, R.C., 1980. Quantifying solute distributions in the bioturbated zone of marine sediments by defining an average microenvironment. Geochimica et Cosmochimica Acta 44, 1955–1965) links pore-water processes and burrow sizes and distributions in the sediment by assuming that burrows are fully flushed. The equivalence between the cylinder model and the more commonly used one-dimensional non-local exchange model depends upon this assumption. However, this assumption has seldom been tested in the field. We have extended the cylinder model of bioirrigation to include burrow ventilation activities of organisms. Burrow ventilation is modeled as a simple non-local exchange of burrow water with overlying water. Model simulations indicate that burrow ventilation has a large effect on vertical profiles and fluxes of solute tracers. We collected data on burrow geometry in the field by CT-scanning freshly collected sediment cores. At the same study sites, we measured activity profiles of 222Rn, a naturally occurring radionuclide tracer of pore-water transport. With model geometry independently constrained, we tested the model by comparing our model-predicted profiles with measured profiles. Our results demonstrate that burrows in the field are not fully flushed. Our estimated burrow ventilation rates compare favorably with previous laboratory measurements. The inclusion of realistic burrow ventilation in this pore-water transport model strongly affects modeled solute profiles and fluxes. We demonstrate how model parameters can be determined from field samples and present a model that more realistically simulates pore-water transport processes in muddy sediments.},
	number = {3},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Shull, D.H. and Benoit, J.M. and Wojcik, C. and Senning, J.R.},
	month = jul,
	year = {2009},
	keywords = {bioturbation, bioirrigation, mechanistic, modelling, tube-dwelling},
	pages = {277--286}
}

@article{boudreau_method--lines_1996,
	title = {A method-of-lines code for carbon and nutrient diagenesis in aquatic sediments},
	volume = {22},
	issn = {00983004},
	url = {http://www.sciencedirect.com/science/article/pii/0098300495001158},
	doi = {10.1016/0098-3004(95)00115-8},
	number = {5},
	journal = {Computers \& Geosciences},
	author = {Boudreau, Bernard P.},
	month = jun,
	year = {1996},
	pages = {479--496}
}

@article{cowan_sediment-water_1996,
	title = {Sediment-{Water} {Oxygen} and {Nutrient} {Exchanges} along the {Longitudinal} {Axis} of {Chesapeake} {Bay}: {Seasonal} {Patterns}, {Controlling} {Factors} and {Ecological} {Significance}},
	volume = {19},
	issn = {01608347},
	url = {http://link.springer.com/10.2307/1352518},
	doi = {10.2307/1352518},
	number = {3},
	journal = {Estuaries},
	author = {Cowan, Jean L. W. and Boynton, Walter R.},
	month = sep,
	year = {1996},
	pages = {562}
}

@article{rao_alkalinity_2014,
	title = {Alkalinity production in intertidal sands intensified by lugworm bioirrigation},
	volume = {148},
	url = {https://www.sciencedirect.com/science/article/pii/S0272771414001711},
	doi = {10.1016/J.ECSS.2014.06.006},
	abstract = {Porewater profiles and sediment-water fluxes of oxygen, nutrients, pH, calcium, alkalinity, and sulfide were measured in intertidal sandflat sediments from the Oosterschelde mesotidal lagoon (The Netherlands). The influence of bioturbation and bioirrigation by the deep-burrowing polychaete Arenicola marina on the rates and sources of benthic alkalinity generation was examined by comparing measurements in intact and defaunated sediment cores before and after the addition of A. marina in summer and fall 2011. Higher organic matter remineralization rates, shallower O2 penetration, and greater sediment-water solute fluxes were observed in summer, consistent with higher sediment community metabolic rates at a higher temperature. Lugworm activity stimulated porewater exchange (5.1 × in summer, 1.9 × in fall), organic matter remineralization (6.2 × in summer, 1.9 × in fall), aerobic respiration (2.4 × in summer, 2.1 × in fall), alkalinity release (4.7 × in summer, 4.0 × in fall), nutrient regeneration, and iron cycling. The effects of lugworm activity on net sediment-water fluxes were similar but more pronounced in summer than in fall. Alkalinity release in fall was entirely driven by metabolic carbonate dissolution, while this process explained between 22 and 69\% of total alkalinity production in summer, indicating the importance of other processes in this season. By enhancing organic matter remineralization and the reoxidation of reduced metabolites by the sediment microbial community, lugworm activity stimulated the production of dissolved inorganic carbon and metabolic acidity, which in turn enhanced metabolic CaCO3 dissolution efficiency. In summer, evidence of microbial long distance electron transport (LDET) was observed in defaunated sediment. Thus, alkalinity production by net carbonate dissolution was likely supplemented by anaerobic respiration and LDET in summer.},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Rao, Alexandra M.F. and Malkin, Sairah Y. and Montserrat, Francesc and Meysman, Filip J.R.},
	month = jul,
	year = {2014},
	keywords = {bioirrigation, alkalinity, arenicola marina, carbonate chemistry},
	pages = {36--47}
}

@article{dalsgaard_anaerobic_2005,
	title = {Anaerobic ammonium oxidation (anammox) in the marine environment},
	volume = {156},
	issn = {09232508},
	doi = {10.1016/j.resmic.2005.01.011},
	abstract = {Anammox, anaerobic ammonium oxidation with nitrite, is now recognized as an important process in the marine nitrogen cycle. The bacteria conducting anammox are highly specialized and appear to belong to the Planctomycetales. The process has now been found in a range of environments including marine sediments, sea ice and anoxic water columns, and it may be responsible for up to 50\% of the global removal of fixed nitrogen from the oceans. ?? 2005 Elsevier SAS. All rights reserved.},
	number = {4},
	journal = {Research in Microbiology},
	author = {Dalsgaard, Tage and Thamdrup, Bo and Canfield, Donald E.},
	year = {2005},
	pmid = {15862442},
	keywords = {Anammox, Anaerobic ammonium oxidation, Review},
	pages = {457--464}
}

@article{aelion_sulfide_2010,
	title = {Sulfide {Inhibition} of {Nitrate} {Removal} in {Coastal} {Sediments}},
	volume = {33},
	issn = {1559-2723},
	url = {http://www.jstor.org/stable/40663686%0Ahttp://www.jstor.org/stable/40663686?seq=1&cid=pdf-reference#references_tab_contents%0Ahttp://about.jstor.org/terms http://link.springer.com/10.1007/s12237-010-9275-4},
	doi = {10.1007/s12237-010-9275-4},
	abstract = {Microbial nitrate (NO3∼) removal via denitrification (DNF) at high sulfide (H2S) concentrations was compared in sediment from a coastal freshwater pond in a developed area that receives salt-water influx during storm events, and a saline pond proximal to an undeveloped estuary. Sediments were incubated with added SO42∼ (1,000 μg per gram dry weight basis (gdw)) to determine whether acid volatile sulfides (AVS) were formed. DNF in the sediments was measured with NO3-N (300 μg gdw"1) alone, and with NO3-N and H2S (1,000 μg S2" gdw"1). SO42∼ addition to the freshwater sediments resulted in AVS formation (970± 307 μg S gdw"1) similar to the wetland with no added SO42∼ (986±156 μg S gdw"1). DNF rates measured with no added H2S were greater in the freshwater than the wetland site (10.6±0.6 vs. 6.4±0.1 μg N2O-N gdw"1 h"1, respectively). High H2S concentrations retained NH4-N in the undevel-oped wetland and retained NO3-N in the developed freshwater site, suggesting that potential salt-water influx Electronic supplementary material The online version of this article (doi:10.1007/sl2237-010-9275-4) contains supplementary material, which is available to authorized users.},
	number = {3},
	journal = {Estuaries and Coasts},
	author = {Aelion, C Marjorie and Warttinger, Ulrich},
	month = may,
	year = {2010},
	keywords = {Dissimilatory nitrate reduction to ammonium, Coastal sediments ·, Denitrification ·, Introduction, Nitrate removal ·, Sulfide inhibition ·},
	pages = {798--803}
}

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

@article{teal_global_2010,
	title = {Global patterns of bioturbation intensity and mixed depth of marine soft sediments},
	volume = {2},
	issn = {1864-7782},
	url = {http://www.int-res.com/abstracts/ab/v2/n3/p207-218/},
	doi = {10.3354/ab00052},
	number = {3},
	journal = {Aquatic Biology},
	author = {Teal, LR and Bulling, MT and Parker, ER and Solan, M},
	month = jun,
	year = {2010},
	keywords = {Bioturbation, Bioturbation coefficient, bioturbation rates, Global analysis, Sediment mixed depth, Sediment profile imaging, Tracer},
	pages = {207--218}
}

@article{turnewitsch_bioturbation_2000,
	title = {Bioturbation in the abyssal {Arabian} {Sea}: influence of fauna and food supply},
	volume = {47},
	issn = {09670645},
	url = {http://www.sciencedirect.com/science/article/pii/S0967064500000527},
	doi = {10.1016/S0967-0645(00)00052-7},
	abstract = {In order to evaluate bioturbation in abyssal Arabian-Sea sediments of the Indus fan profiles of 210Pb (half-life: 22.3yr) and 234Th (half-life: 24.1d) were measured in cores collected during September and October 1995 and April 1997, respectively. The density and composition of epibenthic megafauna and lebensspuren were determined in vertical seafloor photographs during April 1997. Mean eddy-diffusive mixing coefficients according to the distribution of excess 210Pb ( 210Pb-DB) were 0.072±0.028, 0.068±0.055, 0.373±0.119, 0.037±0.009 and 0.079±0.119cm2yr−1 in the northern, western, central, eastern and southern abyssal Arabian sea, respectively. Mean eddy-diffusive mixing coefficients according to the distribution of excess 234Th (234Th-DB) were 0.53, 1.64 and 0.47cm2yr−1 in the northern, western and central abyssal Arabian Sea, respectively. Mobile epibenthic megafauna at the western, northern, central and southern study sites were dominated by ophiuroids, holothurians, ophiuroids and natant decapods (the respective densities were 100, 82, 29 and 6 individuals 1000m−2). The northern study site was characterized by a high abundance of spoke traces and fecal casts. The central site showed spoke traces and many tracks. The southern site displayed the highest abundance of spoke traces, whereas at the western site hardly any lebensspuren were observed. There is evidence for at least two functional endmember communities in the Arabian Sea. In the northwestern Arabian Sea (WAST) vertical particle displacement seems to be dominated by macrofauna and primarily eddy-diffusive. In the southern Arabian Sea (SAST) non-local and `incidental' mixing due to spoke-trace producers might become more important and superimpose reduced eddy-diffusive mixing. With respect to biological data CAST is an intermediate location. Given the biological data, average 210Pb-DB is higher and decimeter-scale variability of 210Pb-DB smaller at CAST than expected. These findings indicate that in a mixture of both endmember communities the organisms may interact in way that increases values of biodiffusivity, as reflected by 210Pb-DB, and reduces decimeter-scale 210Pb-DB heterogeneity in comparison to the simple sum of the isolated effects of the endmembers. For time scales {\textbackslash}textless100years there was no evidence for a relationship between food supply (POC flux) and bioturbation intensity, as reflected by 210Pb-DB and 234Th-DB. Bioturbation intensity should be controlled primarily by the composition of the benthic fauna, its specific adaptation to the environmental setting, and the abundance of each species of the benthic community. Food supply can have only an indirect influence on bioturbation intensity. In certain parts of the ocean the a priori overall positive relationship between POC flux and biodiffusivity might include restricted intervals displaying no or even negative relations.},
	number = {14},
	journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
	author = {Turnewitsch, Robert and Witte, Ursula and Graf, Gerhard},
	month = jan,
	year = {2000},
	pages = {2877--2911}
}

@article{volkenborn_effects_2007,
	title = {Effects of bioturbation and bioirrigation by lugworms ({Arenicola} marina) on physical and chemical sediment properties and implications for intertidal habitat succession},
	volume = {74},
	url = {https://www.sciencedirect.com/science/article/pii/S0272771407001394},
	doi = {10.1016/J.ECSS.2007.05.001},
	abstract = {Sediment destabilization by sediment-reworking organisms is common in coastal aquatic environments, but the potential of bioturbation to inhibit shoreline succession has not been suggested previously. The lugworm Arenicola marina is a widespread and dominant large burrower at European Atlantic shores, and a major source of bioturbation and bioirrigation on the extensive intertidal flats in the Wadden Sea (eastern North Sea). The hypothesis that lugworm activities inhibit the successive development from sandy to muddy sediments in depositional embayments has been tested by a large-scale exclusion field experiment. Changes in sediment properties indicate a progressive clogging of interstices with fine particles and organic matter, resulting in lower sediment permeability in exclusion areas compared to lugworm inhabited control areas. Chlorophyll content in the surface layer was consistently higher in the absence of lugworms. Lack of sub-surface irrigation in the absence of lugworms combined with reduced sediment permeability resulted in increased concentrations of ammonium, phosphate, silicate, and sulphide in the pore-water. Concentrations {\textbackslash}textgreater100μM of sulphide gave rise to toxic conditions for macrofauna. The effects of lugworms on sediment characteristics were more conspicuous in fine than in medium sand. It is concluded that A. marina contributes to the maintenance of permeable sand and thereby sustaining suitable conditions for the lugworm population itself. Without this “ecosystem engineer” mud flats would greatly expand at the expense of sand flats in the Wadden Sea.},
	number = {1-2},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Volkenborn, N. and Hedtkamp, S.I.C. and van Beusekom, J.E.E. and Reise, K.},
	month = aug,
	year = {2007},
	pages = {331--343}
}

@article{diaz_marine_1995,
	title = {Marine benthic hypoxia: {A} review of its ecological effects and the behavioural responses of benthic macrofauna},
	volume = {33},
	issn = {0078-3218},
	abstract = {In this review the effects of hypoxia on benthic fauna are summarized and detailed information is given on (1) the impact on community structure and function in fjords, estuaries, coastal and offshore areas (2) behavioural changes (3) recovery processes (4) ecosystem energy flow implications, and (5) tolerance in experimental studies. There is no other environmental variable of such ecological importance to coastal marine ecosystems that has changed so drastically in such a short period as dissolved oxygen. While hypoxic and anoxic environments have existed through geological time, their occurrence in shallow coastal and estuarine areas appears to be increasing, most likely accelerated by human activities. Ecological problems associated with the occurrence of low oxygen are increasing on a global scale. The oxygen budgets of most major estuarine and coastal ecosystems have been adversely affected mainly through the process of eutrophication, which acts as an accelerant or enhancing factor to hypoxia and anoxia, and when coupled with adverse meteorological and hydrodynamic events, hypoxia increases in frequency and severity. The area of hypoxic and anoxic bottom water is even increasing within systems that historically are considered oxygen stressed. Many ecosystems that are now severely stressed by hypoxia appear to be near or at a threshold. Should oxygen concentrations become slightly lower, catastrophic events may overcome the systems and alter the productivity base that leads to fisheries species. Examples of such events are becoming increasingly common. At what point permanent damage will result is difficult to say. To dare there is no large system that has recovered after development of persistent hypoxia or anoxia. The only exception may be small systems where pollution inputs have ceased and recovery initiated from surrounding non-affected areas. The expanding occurrence of hypoxia and anoxia continues to bring about significant structural changes in benthic communities and to affect benthic-pelagic coupling. Restoring ecosystem balance and reversing the trend of increasing hypoxia and anoxia will require dealing with the global problem of coastal eutrophication and determining how to reduce the production of organic matter in sensitive estuarine and coastal areas.},
	journal = {Oceanography and Marine Biology - an Annual Review},
	author = {Diaz, Rj J and Rosenberg, Rutger},
	year = {1995},
	pages = {245--303}
}

@article{zehr_nitrogen_2011,
	title = {Nitrogen fixation by marine cyanobacteria},
	volume = {19},
	issn = {0966842X},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0966842X10002155},
	doi = {10.1016/j.tim.2010.12.004},
	number = {4},
	journal = {Trends in Microbiology},
	author = {Zehr, Jonathan P.},
	month = apr,
	year = {2011},
	pages = {162--173}
}

@article{dalsgaard_anaerobic_2005-1,
	title = {Anaerobic ammonium oxidation (anammox) in the marine environment},
	volume = {156},
	issn = {09232508},
	doi = {10.1016/j.resmic.2005.01.011},
	abstract = {Anammox, anaerobic ammonium oxidation with nitrite, is now recognized as an important process in the marine nitrogen cycle. The bacteria conducting anammox are highly specialized and appear to belong to the Planctomycetales. The process has now been found in a range of environments including marine sediments, sea ice and anoxic water columns, and it may be responsible for up to 50\% of the global removal of fixed nitrogen from the oceans. ?? 2005 Elsevier SAS. All rights reserved.},
	number = {4},
	journal = {Research in Microbiology},
	author = {Dalsgaard, Tage and Thamdrup, Bo and Canfield, Donald E.},
	year = {2005},
	pmid = {15862442},
	keywords = {Anammox, Anaerobic ammonium oxidation, Review},
	pages = {457--464}
}

@article{hargrave_assessing_nodate,
	title = {Assessing {Benthic} {Impacts} of {Organic} {Enrichment} from {Marine} {Aquaculture}},
	volume = {99},
	issn = {1573-2932},
	url = {http://link.springer.com/article/10.1023/A:1018332632372},
	doi = {10.1023/A:1018332632372},
	language = {en},
	number = {1-4},
	journal = {Water, Air, and Soil Pollution},
	author = {Hargrave, B.T. and Phillips, G.A. and Doucette, L.I. and White, M.J. and Milligan, T.G. and Wildish, D.J. and Cranston, R.E.},
	pages = {641--650}
}

@article{duplisea_modelling_2001,
	title = {Modelling potential impacts of bottom trawl fisheries on soft sediment biogeochemistry in the {North} {Sea}},
	volume = {2},
	url = {http://pubs.rsc.org/en/content/articlehtml/2001/gt/b108342b},
	abstract = {Bottom trawling causes physical disturbance to sediments particularly in shelf areas. The disturbance due to trawling is most significant in deeper areas with softer sediments where levels of natural disturbance due to wave and tidal action are low. In heavily fished areas, trawls may impact the same area of seabed more than four times per year. A single pass of a beam trawl, the heaviest gear routinely used in shelf sea fisheries, can kill 5–65\% of the resident fauna and mix the top few cm of sediment. We expect that sediment community function, carbon mineralisation and biogeochemical fluxes will be strongly affected by trawling activity because the physical effects of trawling are equivalent to those of an extreme bioturbator, and yet, unlike bioturbating macrofauna, trawling does not directly contribute to community metabolism. We used an existing box-model of a generalised soft sediment system to examine the effects of trawling disturbance on carbon mineralisation and chemical concentrations. We contrasted the effects of a natural scenario, where bioturbation is a function of macrobenthos biomass, with an anthropogenic impact scenario where physical disturbance results from trawling rather than the action of bioturbating macrofauna. Simulation results suggest that the effects of low levels of trawling disturbance will be similar to those of natural bioturbators but that high levels of trawling disturbance prevent the modelled system from reaching equilibrium due to large carbon fluxes between oxic and anoxic carbon compartments. The presence of macrobenthos in the natural disturbance scenario allowed sediment chemical storage and fluxes to reach equilibrium. This is because the macrobenthos are important carbon consumers in the system whose presence reduces the magnitude of available carbon fluxes. In soft sediment systems, where the level physical disturbance due to waves and tides is low, model results suggest that intensive trawling disturbance could cause large fluctuations in benthic chemical fluxes and storage.},
	journal = {Geochem. Trans.},
	author = {Duplisea, Daniel E. and Jennings, Simon and Malcolm, Stephen J and Parker, Right and Sivyer, David B.},
	month = dec,
	year = {2001},
	keywords = {bioturbation, trawling, modelling, fishing},
	pages = {112--117}
}

@article{canfield_review_2010,
	title = {{REVIEW} {The} {Evolution} and {Future} of {Earth} ' s {Nitrogen} {Cycle}},
	volume = {330},
	issn = {0036-8075},
	doi = {10.1126/science.1186120},
	abstract = {Atmospheric reactions and slow geological processes controlled Earth's earliest nitrogen cycle, and by ∼2.7 billion years ago, a linked suite of microbial processes evolved to form the modern nitrogen cycle with robust natural feedbacks and controls. Over the past century, however, the development of new agricultural practices to satisfy a growing global demand for food has drastically disrupted the nitrogen cycle. This has led to extensive eutrophication of fresh waters and coastal zones as well as increased inventories of the potent greenhouse gas nitrous oxide (N2O). Microbial processes will ultimately restore balance to the nitrogen cycle, but the damage done by humans to the nitrogen economy of the planet will persist for decades, possibly centuries, if active intervention and careful management strategies are not initiated.},
	journal = {Science},
	author = {Canfield, Donald E and Glazer, Alexander N and Falkowski, Paul G},
	year = {2010},
	pmid = {20929768},
	pages = {192--196}
}

@article{sanz-lazaro_diversity_2011,
	title = {Diversity {Patterns} of {Benthic} {Macrofauna} {Caused} by {Marine} {Fish} {Farming}},
	volume = {3},
	issn = {1424-2818},
	url = {http://www.mdpi.com/1424-2818/3/2/176},
	doi = {10.3390/d3020176},
	abstract = {This paper reviews the patterns observed in the diversity and structure of the macrofauna benthic community under the influence of fish farming. First, we explain the effects of organic enrichment on the sediment and the consequences for the inhabiting communities. We describe the diversity trends in spatial and temporal gradients affected by fish farming and compare them with those described by the Pearson and Rosenberg model. We found that in general terms, the trends of diversity and other community parameters followed the Pearson and Rosenberg model but they can vary to some extent due to sediment local characteristics or to secondary disturbances. We also show the different mechanisms by which wild fish can affect macrofauna diversity patterns under fish farming influence. In addition, we comment the importance of the macrofauna diversity in the ecosystem functions and propose some guidelines to measure functional diversity related to relevant processes at ecosystem level. We propose more research efforts in the main topics commented in this review to improve management strategies to guarantee a good status of the diversity and ecosystem functioning of sediments influenced by fish farming.},
	number = {2},
	journal = {Diversity},
	author = {Sanz-Lázaro, Carlos and Marín, Arnaldo and Sanz-Lázaro, Carlos and Marín, Arnaldo},
	month = apr,
	year = {2011},
	keywords = {aquaculture, abundance, benthic diversity, biomass, community structure, ecosystem functioning, functional diversity, macrofauna, organic enrichment, Pearson, Rosenberg model, sediment metabolic capacity, Shannon, spatial and temporal patterns, species richness, Wienner},
	pages = {176--199}
}

@article{pohle_assessment_2001,
	title = {Assessment of regional benthic impact of salmon mariculture within the {Letang} {Inlet}, {Bay} of {Fundy}},
	volume = {58},
	issn = {10543139},
	url = {http://icesjms.oxfordjournals.org/content/58/2/417.abstract},
	doi = {10.1006/jmsc.2000.1039},
	abstract = {Between 1994 and 1999, impact on the benthic fauna has been evaluated in two areas with intensive salmon net-pen aquaculture (Lime Kiln Bay, Bliss Harbour). A third embayment (Deadmans Harbour), which lacked significant aquaculture activity, served as a reference site. Changes in benthic community structure were investigated using multivariate, distributional, and univariate analyses. Such changes reflect cumulative stress from various sources, including organic enrichment and chemical therapeutants. Changes at the Deadmans Harbour reference site indicated a general improvement in ecosystem quality during the study period. Lime Kiln Bay experienced an increase in aquaculture activity during the first few years, followed by a complete cessation in 1998. Analyses indicated increased biological stress on the benthic community, suggesting major environmental alterations did take place in that bay. Diversity declined significantly between 1994 and 1995, with a corresponding significant increase in sediment organic content. Analysis of indicator species corroborated the enrichment trend. Sedimentary microbial biomass and organic matter concentrations decreased from 1997 to 1999, reflecting the cessation of fish farming, but the benthos did not recover during this period. It is concluded that benthic impact in Lime Kiln Bay persisted until 1999 even though organic loading decreased. Enrichment levels in Bliss Harbour were elevated from the beginning of the study onwards and the impact persisted throughout the study. The observed differences in community structure within the three embayments were not attributable to differences in sediment types, temperature, salinity, or water depth.},
	number = {2},
	journal = {ICES Journal of Marine Science},
	author = {Pohle, G},
	month = apr,
	year = {2001},
	pages = {417--426}
}

@article{king_incorporating_2008,
	title = {Incorporating cumulative effects into environmental assessments of mariculture: {Limitations} and failures of current siting methods},
	volume = {28},
	issn = {01959255},
	doi = {10.1016/j.eiar.2007.12.002},
	abstract = {Assessing and evaluating the cumulative impacts of multiple marine aquaculture facilities has proved difficult in environmental assessment. A retrospective review of 23 existing mariculture farms in southwestern New Brunswick was conducted to determine whether cumulative interactions would have justified site approvals. Based on current scientific evidence of cumulative effects, six new criteria were added to a set of far-field impacts and other existing criteria were expanded to include regional and cumulative environmental impacts in Hargrave's [Hargrave BT. A traffic light decision system for marine finfish aquaculture siting. Ocean Coast Manag 2002; 45:215–35.] Traffic Light Decision Support System (DSS) presently used in Canadian aquaculture environmental assessments. Before mitigation, 19 of the 23 sites failed the amended set of criteria and after considering mitigation, 8 sites failed. Site and ecosystem indices yielded varying site acceptability scores; however, many sites would not have been approved if siting decisions had been made within a regional management framework and cumulative impact criteria were considered in the site evaluation process.},
	number = {8},
	journal = {Environmental Impact Assessment Review},
	author = {King, Sarah C. and Pushchak, Ronald},
	year = {2008},
	pages = {572--586}
}

@article{gilbert_influence_2003,
	title = {The influence of macrofaunal burrow spacing and diffusive scaling on sedimentary nitrification and denitrification: {An} experimental simulation and model approach},
	volume = {61},
	url = {http://www.ingentaselect.com/rpsv/cgi-bin/cgi?ini=xref&body=linker&reqdoi=10.1357/002224003321586426},
	doi = {10.1357/002224003321586426},
	number = {1},
	journal = {Journal of Marine Research},
	author = {Gilbert, Franck and Aller, Robert C. and Hulth, Stefan},
	month = jan,
	year = {2003},
	keywords = {ecology, modelling, N-cycling},
	pages = {101--125}
}

@article{magalhaes_impact_2007,
	title = {Impact of trace metals on denitrification in estuarine sediments of the {Douro} {River} estuary, {Portugal}},
	volume = {107},
	issn = {03044203},
	doi = {10.1016/j.marchem.2007.02.005},
	abstract = {Denitrification influences the nitrogen budget in estuaries by removing fixed nitrogen from the inorganic pool; rates are dependent on both geological and geographic conditions as well as increasing anthropogenic impacts. In this study the effects of copper (Cu), chromium (Cr), zinc (Zn), cadmium (Cd) and lead (Pb), on the denitrification pathway were evaluated in subtidal and intertidal sediments of the Douro River estuary. Dinitrogen, N2O and NO2- production rates were measured in triplicate slurries of field samples under different treatments of metal concentrations. Results demonstrated that similar metal amendments led to different site responses for denitrification, suggesting that variations in sediment properties (metal concentrations, grain size, organic matter content, etc.) and/or differences in denitrifying community tolerance modulate the level of metal toxicity. Denitrifying communities in subtidal muddy sediments were not affected by increasing concentrations of metals. In contrast, intertidal sandy sites revealed high sensitivity to almost all trace metals tested; almost complete inhibition by Cr (95\%) and Cu (85\%) was observed for 98 and 79????g per gram of wet sediment respectively, and by Zn (92\%) at the highest concentration added (490????g per gram of wet sediment). Moreover, the addition of trace metals stimulated N2O and NO2- accumulation in intertidal sandy (Zn, Cu, Cr and Cd) and muddy sediments (Cu and Zn), demonstrating a pronounced inhibitory effect on specific steps within the denitrification enzymatic system. In summary, the results obtained suggest that, according to the type of estuarine sediment, trace metals cannot only reduce total N removal from an estuary via denitrification but also can enhance the release of N2O, a powerful greenhouse gas. ?? 2007 Elsevier B.V. All rights reserved.},
	number = {3},
	journal = {Marine Chemistry},
	author = {Magalhães, Catarina and Costa, Joana and Teixeira, Catarina and Bordalo, Adriano A.},
	year = {2007},
	pmid = {3917912},
	keywords = {Denitrification, Estuarine sediments, Nitrous oxide, Trace metals},
	pages = {332--341}
}

@article{rutting_functional_2008,
	title = {Functional role of {DNRA} and nitrite reduction in a pristine south {Chilean} {Nothofagus} forest},
	volume = {90},
	issn = {0168-2563},
	url = {http://link.springer.com/10.1007/s10533-008-9250-3},
	doi = {10.1007/s10533-008-9250-3},
	number = {3},
	journal = {Biogeochemistry},
	author = {Rütting, T. and Huygens, D. and Müller, C. and Van Cleemput, O. and Godoy, R. and Boeckx, P.},
	month = sep,
	year = {2008},
	keywords = {15N tracing model, dissimilatory nitrate reduction ammonium (DNRA), Markov chain Monte Carlo sampling, N retention, nitrite (NO2-), Nothofagus betuloides},
	pages = {243--258}
}

@article{lubos_polerecky_*_high_2006,
	title = {High {Temporal} {Resolution} {Oxygen} {Imaging} in {Bioirrigated} {Sediments}},
	url = {https://pubs.acs.org/doi/abs/10.1021/es060494l},
	doi = {10.1021/ES060494L},
	abstract = {A technique is presented for temporal characterization of the bioirrigation activity of benthic macrofauna and for quantitative estimation of its effects on the oxygen exchange between the sediment and the overlying water. The technique is based on high temporal resolution (15−30 s) oxygen imaging aided by a planar oxygen optode and can be applied under laboratory and field conditions, both freshwater and marine. It allows direct observation of the complex 2D oxygen dynamics in the sediment around the burrow while the animal dwells undisturbed in its natural environment. The conditions to which the animal is exposed can easily be controlled or manipulated. Chironomus plumosus, widely distributed freshwater insect larvae, were used in a case study. Their bioirrigation activity was divided into a random succession of pumping intervals (duration 5.4 ± 1.7 min) and rest periods (duration 9.2 ± 5.8 min). The burrow ventilation resulted in a highly variable volume of the oxygenated sediment surrounding the burr...},
	author = {Lubos Polerecky, *, † and and Nils Volkenborn, ‡ and Peter Stief†, {\textbackslash}S},
	year = {2006},
	keywords = {oxygen, bioirrigation, chironomid, fresh water, imaging, methods}
}

@article{paerl_atmospheric_2002,
	title = {Atmospheric deposition of nitrogen: {Implications} for nutrient over-enrichment of coastal waters},
	volume = {25},
	issn = {0160-8347},
	doi = {10.1007/BF02804899},
	abstract = {Atmospheric deposition of nitrogen (AD-N) is a significant source of nitrogen enrichment to nitrogen (N)-limited estuarine and coastal waters downwind of anthropogenic emissions. Along the eastern U.S. coast and eastern Gulf of Mexico, AD-N currently accounts for 10\% to over 40\% of new N loading to estuaries. Extension of the regional acid deposition model (RADM) to coastal shelf waters indicates that 11, 5.6, and 5.6 kg N ha-1 may be deposited on the continental shelf areas of the northeastern U.S. coast, southeast U.S. coast, and eastern Gulf of Mexico, respectively. AD-N approximates or exceeds riverine N inputs in many coastal regions. From a spatial perspective, AD-N is a unique source of N enrichment to estuarine and coastal waters because, for a receiving water body, the airshed may exceed the watershed by 10-20 fold. AD-N may originate far outside of the currently managed watersheds. AD-N may increase in importance as a new N source by affecting waters downstream of the oligohaline and mesohaline estuarine nutrient filters where large amounts of terrestrially-supplied N are assimilated and denitrified. Regionally and globally, N deposition associated with urbanization (NOx, peroxyacetyl nitrate, or PAN) and agricultural expansion (NH4 + and possibly organic N) has increased in coastal airsheds. Recent growth and intensification of animal (poultry, swine, cattle) operations in the midwest and mid-Atlantic regions have led to increasing amounts of NH4 + emission and deposition, according to a three decadal analysis of the National Acid Deposition Program network. In western Europe, where livestock operations have dominated agricultural production for the better part of this century, NH4 + is the most abundant form of AD-N. AD-N deposition in the U.S. is still dominated by oxides of N (NOx) emitted from fossil fuel combustion; annual NH4 + deposition is increasing, and in some regions is approaching total NO3 - deposition. In receiving estuarine and coastal waters, phytoplankton community structural and functional changes, associated water quality, and trophic and biogeochemical alterations (i.e., algal blooms, hypoxia, food web, and fisheries habitat disruption) are frequent consequences of N-driven eutrophication. Increases in and changing proportions of various new N sources regulate phytoplankton competitive interactions, dominance, and successional patterns. These quantitative and qualitative aspects of AD-N and other atmospheric nutrient sources (e.g., iron) may promote biotic changes now apparent in estuarine and coastal waters, including the proliferation of harmful algal blooms, with cascading impacts on water quality and fisheries.},
	number = {4},
	journal = {Estuaries},
	author = {Paerl, Hans W. and Dennis, Robin L. and Whitall, David R.},
	year = {2002},
	pages = {677--693}
}

@article{meysman_bio-irrigation_2006,
	title = {Bio-irrigation in permeable sediments: {An} assessment of model complexity},
	volume = {64},
	url = {http://openurl.ingenta.com/content/xref?genre=article&issn=0022-2402&volume=64&issue=4&spage=589},
	doi = {10.1357/002224006778715757},
	number = {4},
	journal = {Journal of Marine Research},
	author = {Meysman, Filip J. R. and Galaktionov, Oleksiy S. and Gribsholt, Britta and Middelburg, Jack J.},
	month = jul,
	year = {2006},
	keywords = {bioirrigation, mechanistic, modelling, improved models},
	pages = {589--627}
}

@article{brin_effects_2015,
	title = {Effects of experimental warming and carbon addition on nitrate reduction and respiration in coastal sediments},
	volume = {125},
	issn = {1573515X},
	doi = {10.1007/s10533-015-0113-4},
	abstract = {Climate change may have differing effects on microbial processes that control coastal N availability. We conducted a microcosm experiment to explore effects of warming and carbon availability on nitrate reduction pathways in marine sediments. Sieved continental shelf sediments were incubated for 12 weeks under aerated seawater amended with nitrate (∼50 μM), at winter (4 °C) or summer (17 °C) temperatures, with or without biweekly particulate organic C additions. Treatments increased diffusive oxygen consumption as expected, with somewhat higher effects of C addition compared to warming. Combined warming and C addition had the strongest effect on nitrate flux across the sediment water interface, with a complete switch early in the experiment from influx to sustained efflux. Supporting this result, vial incubations with added 15N-nitrate indicated that C addition stimulated potential rates of dissimilatory nitrate reduction to ammonium (DNRA), but not denitrification. Overall capacity for both denitrification and DNRA was reduced in warmed treatments, possibly reflecting C losses due to increased respiration with warming. Anammox potential rates were much lower than DNRA or denitrification, and were slightly negatively affected by warming or C addition. Overall, results indicate that warming and C addition increased ammonium production through remineralization and possibly DNRA. This stimulated nitrate production through nitrification, but without a comparable increase in nitrate consumption through denitrification. The response to C of potential DNRA rates over denitrification, along with a switch to nitrate efflux, raises the possibility that DNRA is an important and previously overlooked source of internal N cycling in shelf sediments.},
	number = {1},
	journal = {Biogeochemistry},
	author = {Brin, Lindsay D. and Giblin, Anne E. and Rich, Jeremy J.},
	year = {2015},
	keywords = {Denitrification, Anammox, Dissimilatory nitrate reduction to ammonium, Climate change, Continental shelf, Warming},
	pages = {81--95}
}

@article{sweetman_benthic_2014,
	title = {Benthic ecosystem functioning beneath fish farms in different hydrodynamic environments},
	volume = {59},
	issn = {00243590},
	url = {http://doi.wiley.com/10.4319/lo.2014.59.4.1139},
	doi = {10.4319/lo.2014.59.4.1139},
	abstract = {To quantify how fish farming modifies short-term benthic carbon cycling in fjord environments and the role of hydrodynamics in modifying effects on the benthos, we assessed benthic ecosystem structure and respiration and used isotope labeled algae as a tracer to quantify C flow over 48 h through macrofauna and bacteria in sediments collected from beneath fish farm sites in (1) high water-flow areas, (2) low water-flow areas, and (3) two appropriate control sites situated downstream from the farms. Bacterial biomass was significantly greater in sediments collected from the fish farm sites relative to the controls. This was also true for sediment oxygen consumption (SOC) rates averaged over each 48 h investigation, which were significantly correlated with total benthic (macrofauna and bacteria) biomass. Short-term C-uptake rates by macrofauna were elevated in both fish farm treatments compared with bacterial C uptake and were significantly higher in sediments from the low flow fish farm site relative to both controls. While SOC rates were significantly higher in experiments using sediments from the low flow fish farm site; faunal abundance, biomass uptake, C uptake, bacterial biomass, and metabolism in sediments from both fish farm treatments were not significantly different from one another. Fish farming can dramatically alter benthic ecosystem functioning, and significant effects can occur around fish farms irrespective of the water-flow regime the farms are moored in. © 2014, by the Association for the Sciences of Limnology and Oceanography, Inc.},
	number = {4},
	journal = {Limnology and Oceanography},
	author = {Sweetman, Andrew K. and Norling, Karl and Gunderstad, Carina and Haugland, Barbro T. and Dale, Trine},
	year = {2014},
	pages = {1139--1151}
}

@article{callier_sedimentation_2006,
	title = {Sedimentation rates in a suspended mussel farm ({Great}-{Entry} {Lagoon}, {Canada}): {Biodeposit} production and dispersion},
	volume = {322},
	issn = {01718630},
	doi = {10.3354/meps322129},
	abstract = {Experimental and field studies were carried out to characterise biodeposit dynamics in a suspended mussel Mytilus edulis L. farm in Great-Entry Lagoon, eastern Canada. We assessed: (1) the quantity and quality of biodeposits produced by different age classes of mussels, (2) the size-dependent sinking velocity of faeces and (3) the variation in sedimentation rates at different spatial and temporal scales. Individual 0+ mussels produced on average only 63\% of the mass of biodeposits (32.4 mg dry wt d(-1) ind.(-1)) that 1+ mussels did (51.5 mg dry wt d(-1) ind.(-1)). In contrast, the amount of biodeposits produced per unit body weight (dry weight of soft tissue) was greater for 0+ than for 1+ mussels. Faecal pellet sinking velocity ranged from 0.27 to 1.81 cm s(-1) for mussels ranging in size from 3 to 7 cm, and was best correlated with faecal pellet width. Sedimentation rates were greater within the farm than at reference sites, supporting the hypothesis that mussel farming increases sedimentation rates. Variations in sedimentation were also observed at small spatial scales and through time. Prior to the harvesting of 1+ mussels, sedimentation rates directly under the 1+ mussel lines were about twice those 10 m distant, between the lines, and in other zones (reference sites and sites in the lease with 0+ mussels). These observations and sedimentation patterns along transects leading away from the mussel farm suggest that biodeposits from the farm are not dispersed broadly. The estimated initial dispersal of faecal pellets ranges from 0-7.4 m (1+ mussels) to 7-24.4 m (0+ mussels).},
	number = {Hargrave 2005},
	journal = {Marine Ecology Progress Series},
	author = {Callier, Myriam D. and Weise, Andr??a M. and McKindsey, Christopher W. and Desrosiers, Gaston},
	year = {2006},
	pmid = {15},
	keywords = {Aquaculture, Faeces, Biodeposit production, Dispersion, Mytilus edulis, Sedimentation rates, Sinking velocity, Spatial scale},
	pages = {129--141}
}

@article{middelburg_empirical_1997,
	title = {Empirical relationships for use in global diagenetic models},
	volume = {44},
	issn = {09670637},
	url = {http://80-www.aslo.org/lo/toc/vol_52/issue_6/2496.pdf http://journal.frontiersin.org/article/10.3389/fmicb.2014.00460/abstract http://www.sciencedirect.com/science/article/pii/S0022098102005294 http://doi.wiley.com/10.1111/jwas.12128 http://www.sciencedir},
	doi = {10.1016/S0967-0637(96)00101-X},
	abstract = {Most of the organic matter found in the sea is degraded in the seabed. A number of different bacteria are responsible for organic matter degradation. Through their metabolic processes bacteria form inorganic nitrogen and phosphorus compounds that are thus made available for new production. They also produce a number of waste products, such as hydrogen sulphide, that have a great impact on the marine environment. After many years of research, our knowledge of the processes going on in the seabed is substantial. This knowledge forms the basis of a new mathematical model linking the complex material cycles taking place in the seabed and describing the exchange of oxygen and nutrients between seabed and seawater. The construc- tion of the model is described in this report. This report was prepared as a contribu- tion towards developing NERI's expertise within the field of mathematical model- ling.},
	number = {2},
	journal = {Deep Sea Research Part I: Oceanographic Research Papers},
	author = {Middelburg, Jack J. and Soetaert, Karline and Herman, Peter M.J.},
	month = feb,
	year = {1997},
	pmid = {3917912},
	keywords = {Ammonium, Nitrate, Nitrogen, Denitrification, Aquaculture, Water quality, Anammox, DNRA, Gulf of Mexico, Hypoxia, Benthic enrichment, Biogeochemistry, Cage aquaculture, Mariculture, Meta-analysis, Sediment types, Benthic-pelagic coupling, Atlantic salmon, Bacteria, Nutrients, Modelling, bioturbation, Benthos, denitrification, benthic fluxes, Bacteria: metabolism, Cyanobacteria, Cyanobacteria: metabolism, Nitrogen Fixation, Nitrogen Fixation: physiology, Seawater, Soil Microbiology, Salmo salar, Environment, Sediment, Benthic fluxes, Dissimilatory nitrate reduction to ammonium, nitrogen cycle, Sediment oxygen demand, Review, Sulfide, Isotope pairing technique, Benthic mineralization, Organic carbon, Oxygen, Benthic microalgae, Flux rates, Bioturbation, Estuarine sediments, Nitrous oxide, Trace metals, Climate change, Continental shelf, Warming, Albemarle, amazon, Ammonium uptake, Animals, anoxic sediment, Aquaculture impact, atlantic forest, background info, Bioassay, Biogeochemical cycling, Bioturbation with Aquaculture, Bivalve, Bottom anoxia, British Columbia, Carbon isotopes, Carbon mineralization, Denitriﬁcation, DEPOMOD, Diagenetic model, Diatom, Dissolved inorganic carbon, diversity, Ecosystem, ecosystem services, Emersion period, Environmental Monitoring, Environmental Restoration and Remediation, Estuarine, Fallow, Fallowing, farmers, Fatty acids, Feeding, Feeds, Fish cages, fish ecology, Fish meal, fishermen, floodplain forests, Geologic Sediments, Geologic Sediments: chemistry, Greenhouse effect, Greenshell™ mussel, Husbandry, hypoxia, Infaunal Trophic Index, Invertebrates, Invertebrates: classification, Invertebrates: growth \& development, local ecological knowledge, Loch Creran, Louisiana shelf, Macrofauna, Macroinvertebrates, Marine, Marine ecosystems, Methane, microcosm, Microphytobenthic production, Microphytobenthos, Netpen, nit, Nitric oxide, nitrification, nitrogen budget, Nitrogen cycling, nitrogen isotope, Nitrogen isotopes, nrfA, Nutrient, Nutrient cycling, Nutrient exchange, Nutrient fluxes and denitrification, organic loading, oxygen concentration, Particle tracking, Phosphorus, Population Dynamics, Precipitation, pyrosequencing, qPCR, Recovery, Remediation, Removal, Resuspension, RTM, S, Salmon, Salt marsh creek, Sediment oxygen consumption, Spatio-Temporal Analysis, Stable isotopes, Sterols, Transient simulation, Turnover rates, Water, Water Pollutants, Water Pollutants: analysis, Water Pollution, Water Pollution: statistics \& numerical data, Zinc},
	pages = {327--344}
}

@article{katsev_effects_2007,
	title = {Effects of progressive oxygen depletion on sediment diagenesis and fluxes: {A} model for the lower {St}. {Lawrence} {River} {Estuary}},
	volume = {52},
	issn = {00243590},
	url = {http://doi.wiley.com/10.4319/lo.2007.52.6.2555},
	doi = {10.4319/lo.2007.52.6.2555},
	number = {6},
	journal = {Limnology and Oceanography},
	author = {Katsev, Sergei and Chaillou, Gwénaëlle and Sundby, Bjørn and Mucci, Alfonso},
	year = {2007},
	keywords = {Bioturbation},
	pages = {2555--2568}
}

@article{kalantzi_benthic_2006-1,
	title = {Benthic impacts of fish farming: {Meta}-analysis of community and geochemical data},
	volume = {52},
	issn = {0025326X},
	doi = {10.1016/j.marpolbul.2005.09.034},
	abstract = {A number of 41 papers dealing with the benthic effects of fish farming were reviewed and the values of the variables studied were extracted to be used in a meta-analysis of effects. The papers used covered a wide range of farmed species, geographic regions, management practices and specific site characteristics (e.g., depth, exposure, and sediment type). Therefore, the total data-set may not be considered as biased towards a particular set of conditions as is often the case with data collected in a single study. More than 120 biological and geochemical variables were monitored, occasionally using different sampling and analytical protocols for the same variables. The rank correlation analysis between all possible pairs of variables in the data set showed a large number of significant positive or negative correlations, reflecting the response of these variables to benthic organic enrichment. The use of stepwise regression showed that most biological and geochemical variables are determined by a combination of distance from the farm with bottom depth and/or latitude. Results of stepwise regression, repeated separately for each type of sediment, showed that although the general pattern was similar among different types of sediments, the coefficients varied considerably indicating changes of the distance affected by settling particulate organic material for different sediment types. The overall conclusion is that the complicated interactions between variables and the lack of data, such as current speed, induce difficulties in setting common or uniform environmental quality standards for benthic effects of fish farming and these should take into account the existing considerable differences between geographic regions, depth zones and sediment types. ?? 2005 Elsevier Ltd. All rights reserved.},
	number = {5},
	journal = {Marine Pollution Bulletin},
	author = {Kalantzi, Ioanna and Karakassis, Ioannis},
	year = {2006},
	pmid = {16257014},
	keywords = {Benthic enrichment, Biogeochemistry, Cage aquaculture, Mariculture, Meta-analysis, Sediment types},
	pages = {484--493}
}

@article{gardner_nitrogen_2009,
	title = {Nitrogen dynamics at the sediment-water interface in shallow, sub-tropical {Florida} {Bay}: {Why} denitrification efficiency may decrease with increased eutrophication},
	volume = {95},
	issn = {01682563},
	doi = {10.1007/s10533-009-9329-5},
	abstract = {Nitrogen (N) dynamics at the sediment�water interface were examined in four regions of Florida Bay to provide mechanistic information on the fate and effects of increased N inputs to shallow, subtropical, coastal environments. Dissimilatory nitrate (NO3 -) reduction to ammonium (DNRA) was hypothesized to be a significant mechanism retaining bioreactive N in this warm, saline coastal ecosystem. Nitrogen dynamics, phosphorus (P) fluxes, and sediment oxygen demand (SOD) were measured in northcentral (Rankin Key; eutrophic), north-eastern (Duck Key; high N to P seston ratios), north-western (Murray Key; low N to P ratios), and central (Rabbit Key; typical central site) Florida Bay in August 2004, January 2005, and November 2006. Site water was passed over intact sediment cores, and changes in oxygen (O2), phosphate (o-PO4 3-), ammonium (NH4), NO3, nitrite (NO2), and N2 concentrations were measured, without and with addition of excess NO3 - or NH4 ? to inflow water. These incubations provided estimates of SOD, nutrient fluxes, N2 production, and potential DNRA rates. Denitrification rates were lowest in summer, when SOD was highest. DNRA rates and NH4 fluxes were high in summer at the eutrophic Rankin site, when denitrification rates were low and almost no N2 came from added 15NO3 -. Highest NH4 accumulation, resulting from DNRA, occurred at Rabbit Key during a picocyanobacteria bloom in November. NH4 accumulation rates among the stations correlated with SOD in August and January, but not in November during the algal bloom. These mechanistic results help explain why bioreactive N supply rates are sometimes high in Florida Bay and why denitrification efficiency may decrease with increased NO3 - inputs in sub-tropical coastal environments.},
	number = {2},
	journal = {Biogeochemistry},
	author = {Gardner, Wayne S. and McCarthy, Mark J.},
	year = {2009},
	pmid = {12658535},
	keywords = {Denitrification, DNRA, Florida Bay, Nitrogen transformations, Subtropical/tropical ecosystems},
	pages = {185--198}
}

@article{bernard_dissimilatory_2015,
	title = {Dissimilatory nitrate reduction to ammonium ({DNRA}) seasonally dominates {NO}3 − reduction pathways in an anthropogenically impacted sub-tropical coastal lagoon},
	volume = {125},
	issn = {0168-2563},
	url = {http://link.springer.com/10.1007/s10533-015-0111-6},
	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.},
	month = aug,
	year = {2015},
	keywords = {Denitrification, Anammox, DNRA, Sediment oxygen demand, Nitrogen cycling},
	pages = {47--64}
}

@article{jennings_effects_2002,
	title = {Effects of chronic trawling disturbance on the production of infaunal communities},
	volume = {243},
	url = {http://www.int-res.com/abstracts/meps/v243/p251-260/},
	doi = {10.3354/meps243251},
	abstract = {Trawling causes widespread physical disturbance in shallow shelf seas. While the impacts of trawling on the biomass and community structure of benthic fauna are well known, no existing studies have quantified the effects of trawling disturbance on the absolute production of small benthic infauna. We investigated the effects of beam trawling disturbance on the production of small benthic infauna (AFDM {\textbackslash}textgreater 0.78 to 62.5 mg) at 9 sites that were subject to a 17.5-fold range in annual trawling disturbance, using a size-based approach that could be applied to other soft-bottom systems. We developed a generalised additive model to test for relationships between trawling disturbance and infaunal production and size structure, after accounting for differences in sediment characteristics and depth. The statistical power of our analyses to detect linear and non-linear relationships between production and disturbance, including increased production at intermediate levels of disturbance, was high ({\textbackslash}textgreater90\% probability of detecting a 50\% change in production across the range of disturbance). The analyses showed that trawling frequencies of 0.35 to 6.14 times yr-1 did not have a significant effect on the production of small infauna or polychaetes. This result contrasts with order of magnitude decreases in the production of large infauna, and shows that small polychaetes with fast life histories are less vulnerable to trawling disturbance. Since small infaunal polychaetes are a key source of food for flatfishes, we conclude that beam trawling disturbance does not have a positive or negative effect on their food supply.},
	journal = {Marine Ecology Progress Series},
	author = {Jennings, S and Nicholson, MD and Dinmore, TA and Lancaster, JE},
	month = nov,
	year = {2002},
	keywords = {ecology, community ecology, trawling},
	pages = {251--260}
}

@article{kobayashi_fish_2015,
	title = {Fish to 2030: {The} {Role} and {Opportunity} for {Aquaculture}},
	volume = {19},
	issn = {1365-7305},
	url = {http://www.tandfonline.com/doi/abs/10.1080/13657305.2015.994240},
	doi = {10.1080/13657305.2015.994240},
	abstract = {Seafood sector can contribute to the global food supply in an important way, and provide an important source of animal protein. Based on observed regional trends in seafood production and consumption and using a global, partial-equilibrium, multi-market model, this study investigates what the global seafood market may look like in 2030. The model projects that the total fish supply will increase from 154 million tons in 2011 to 186 million tons in 2030, with aquaculture entirely responsible for the increase. The fastest aquaculture growth is expected for tilapia and shrimp, while the largest expansion is expected in India, Latin America and Caribbean and Southeast Asia. Fast-growing seafood demand in China and elsewhere represents a critical opportunity for global fisheries and aquaculture to improve their management and achieve sustainable seafood economy.},
	number = {3},
	journal = {Aquaculture Economics \& Management},
	author = {Kobayashi, Mimako and Msangi, Siwa and Batka, Miroslav and Vannuccini, Stefania and Dey, Madan M and Anderson, James L},
	year = {2015},
	keywords = {feed management, market outlook, multi-market modeling, seafood trade},
	pages = {282--300}
}

@article{porubsky_benthic_2009-2,
	title = {Benthic metabolism and the fate of dissolved inorganic nitrogen in intertidal sediments},
	volume = {83},
	issn = {02727714},
	doi = {10.1016/j.ecss.2009.04.012},
	abstract = {We determined patterns of benthic metabolism and examined the relative importance of denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) as sinks for nitrate (NO3-) in intertidal sediments in the presence and absence of benthic microalgal (BMA) activity. By influencing the activity of BMA, light regulated the metabolic status of the sediments, and, in turn, exerted strong control on sediment nitrogen dynamics and the fate of inorganic nitrogen. A pulsed addition of 15N-labeled NO3- tracked the effect and fate of dissolved inorganic nitrogen (DIN) in the system. Under illuminated conditions, BMA communities influenced benthic fluxes directly, via DIN uptake, and indirectly, by altering the oxygen penetration depth. Under dark hypoxic and anoxic conditions, the fate of water column NO3- was determined largely by three competing dissimilatory reductive processes; DNF, DNRA, and, on one occasion, anaerobic ammonium oxidation (anammox). Mass balance of the added 15N tracer illustrated that DNF accounted for a maximum of 48.2\% of the 15NO3- reduced while DNRA (a minimum of 11.4\%) and anammox (a minimum of 2.2\%) accounted for much less. A slurry experiment was employed to further examine the partitioning between DNF and DNRA. High sulfide concentrations negatively impacted rates of both processes, while high DOC:NO3- ratios favored DNRA over DNF. ?? 2009 Elsevier Ltd. All rights reserved.},
	number = {4},
	journal = {Estuarine, Coastal and Shelf Science},
	author = {Porubsky, W.P. P. and Weston, N.B. B. and Joye, S.B. B.},
	year = {2009},
	keywords = {anammox, denitrification, benthic microalgae, dissimilatory nitrate reduction to ammonium, intertidal sediments},
	pages = {392--402}
}

@article{bernard_dissimilatory_2015-1,
	title = {Dissimilatory nitrate reduction to ammonium ({DNRA}) seasonally dominates {NO}3- reduction pathways in an anthropogenically impacted sub-tropical coastal lagoon},
	volume = {125},
	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 (Nﬁxation, denitriﬁcation, anammox, and DNRA) and benthic ﬂuxes were measured at three sites over a year toinvestigatethehypothesisthatDNRA,byproducing 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 lmol N m-2 h-1) compared to denitriﬁcation (study average 7.7 lmol 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.},
	journal = {Biogeochemistry},
	author = {Bernard, Rebecca J. and Mortazavi, Behzad and Kleinhuizen, Alice A.},
	year = {2015},
	keywords = {Anammox, DNRA, Denitriﬁcation, Nitrogen cycling, S},
	pages = {47--64}
}

@book{v._a._hartmann_oceans_2009,
	title = {{OCEANS} 2009},
	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. We expect areas of rapid deposition (organics and inorganic sediment) and low bottom water oxygen to be colonized by- a few organisms that are concentrated near the sediment-water interface, remaining above the depth of the redox potential discontinuity (RPD). In contrast, well oxygenated areas are expected to have developed diverse benthic communities that have attained the equilibrium stage of succession, which includes larger, deeper burrowing fauna. The diverse, deeper-burrowing benthos helps to create and maintain a deeper RPD. As a consequence of the vertical zonation and faunal diversity differences between stressed and recovered areas, several sediment properties may be affected. SPI photographs show that RPD depths in the four provinces vary from 2 to 6 cm below the sediment surface in the spring, before hypoxia has developed. The x-radiographs depict the extent of recent sedimentation and bioturbation at each province. Featured in the x-radiographs are: event layers, shell fragments, voids above and below event layers, vertical, horizontal, and complex burrows. Preliminary radiochemistry results for the April 2009 cruise indicate shallow depths of sediment mixing at all sites on a temporal scale of ∼1 year (Be-7), though provinces HO and FH show a deeper mixing depth (2.25 cm) over this period than provinces BH or NO (1.25 and 1.75 cm, respectively). This may reflect a competitive advantage of discrete macrobenthic organisms who are better able to tolerate hypoxic conditions, a rapid re-colonization of previously hypoxic bottom sediments, or both. Results from the April 2009 cruise are presented as baseline data to establish benthic macrofauna densities and sediment properties before development of hypoxia. A second cruise was conducted in September to assess the effects of seasonal hypoxia at these same four provinces