Karline Soetaert

A model of early diagenetic processes from the shelf to abyssal depths

Abstract We present a numerical model of sedimentary early diagenetic processes that includes oxic and anoxic mineralization. The model belongs to the new wave of early diagenesis models that account for depth-dependent bioturbation and porosity profiles; it can be used both for calculating steady-state conditions and transient simulation. It was developed to reproduce the cycling of carbon, oxygen, and nitrogen along the ocean margin; it resolves the sediment-depth profiles of carbon, oxygen, nitrate, ammonium, and other reduced substances. Organic carbon is modeled as two degradable fractions with different first-order degradation rates and nitrogen:carbon ratios, to account for the decreasing reactivity and N/C ratio of the organic matter with depth into the sediment. The consumption of oxygen and nitrate as terminal electron acceptors is explicitly modeled, and mineralization is limited both by carbon (first order kinetics) and by oxidant availability (Michaelis-Menten type kinetics). Nitrification and oxic mineralization are decoupled, which allows the description of ammonium profiles. Mineralization processes using other oxidants (manganese oxides, iron oxides, sulphate) are lumped into one process, where degradation is only carbon limited; the terminal electron acceptors are not explicitly modeled, only the production of reduced substances is described. These substances are in part permanently removed (e.g., pyrite formation below the bioturbation zone) and partly diffuse towards the oxic layer where they react with oxygen. The values of several parameters were constrained using literature-derived relationships. The model was calibrated on a dataset obtained from the literature, which relates the magnitude of the different pathways to total organic carbon mineralization. The influence of carbon flux, bioturbation, sedimentation rate, bottomwater concentrations of oxygen, and nitrate and carbon degradability on the different mineralization pathways is examined. The relative contribution of the oxic mineralization in the model is significantly depressed under high organic flux, under low bottomwater oxygen conditions and when the bioturbation increases; higher carbon degradability has only a small positive effect, while sedimentation rate is relatively unimportant. Denitrification is mainly influenced by the nitrate concentration in the overlying bottomwater.

Denitrification in marine sediments: A model study

The rate and factors controlling denitrification in marine sediments have been investigated using a prognostic diagenetic model. The model is forced with observed carbon fluxes, bioturbation and sedimentation rates, and bottom water conditions. It can reproduce rates of aerobic mineralization, denitrification, and fluxes of oxygen, nitrate, and ammonium. The globally integrated rate of denitrification is estimated by this model to be about 230-285 Tg N yr(-1), with about 100 Tg N yr(-1) occurring in shelf sediments. This estimate is significantly higher than literature estimates (12-89 Tg N yr(- 1)), mainly because of a proposed upward revision of denitrification rates in slope and deep-sea sediments. Higher sedimentary denitrification estimates require a revision of the marine nitrogen budget and lowering of the oceanic residence time of nitrogen down to about 2 x 10(3) years and are consistent with reported low N/P remineralization ratios between 1000 and 3000 m. Rates of benthic denitrification are most sensitive to the flux of labile organic carbon arriving at the sediment-water interface and bottom water concentrations of nitrate and oxygen. Denitrification always increases when bottom water nitrate increases but may increase or decrease if oxygen in the bottom water increases. Nitrification is by far the most important source of nitrate for denitrification, except for organic-rich sediments underlying oxygen-poor and nitrate-rich water. [KEYWORDS: Organic-matter; biogeochemical cycles; early diagenesis; atmospheric co2; benthic fluxes; sea-floor; ocean; carbon;nitrogen; nutrient]

On the coupling of benthic and pelagic biogeochemical models

Abstract Mutual interaction of water column and sediment processes is either neglected or only crudely approximated in many biogeochemical models. We have reviewed the approaches to couple benthic and pelagic biogeochemical models. It is concluded that they can be classified into a hierarchical set consisting of five levels, differing in the amount of detail given to the sediment processes. The most complex approach (level 4) fully couples water column processes to a vertically resolved biogeochemical sediment model. First simplification is achieved by using a vertically integrated dynamic sediment model (level 3); next is a reflective type of boundary (level 2) where particulate material arriving at the sediment surface is instantaneously transformed into dissolved components. Then comes a set of models in which either the bottom-water concentration of dissolved substances or the sediment–water exchange is imposed (level 1). Finally, in some biogeochemical models, the bottom is plainly ignored (level 0). We have tested these various approaches in a coupled physical–pelagic–benthic biogeochemical model for oxygen, nitrogen and carbon cycling in continental shelf areas. We discuss the various model approaches with respect to their impact on the pelagic system and point out some of the inconsistencies hidden in certain formulations. We conclude that lower boundary types, in which sediment fluxes or concentrations are imposed (level 1), are especially badly designed because they fail to assure conservation of mass. Finally, we suggest as best choice a level 3 approach in which the evolution of sedimentary particulate matter is part of the solution and where the bottom fluxes of dissolved constituents are parameterised based on mass budget considerations. These simplified formulations represent the best balance between computational demand and attained accuracy.

Meiobenthic distribution and nematode community structure in five European estuaries

Meiofauna from the intertidal zone of five European estuaries (Ems, Westerschelde, Somme, Gironde, Tagus) was investigated. Samples represented a cross section of various benthic habitats from near-freshwater to marine, from pure silts to fine-sandy bottoms. The meiobenthic community comprised everywhere a fauna strongly dominated by nematodes, with meiobenthic density increasing with increasing salinity. The Ems differed from the other estuaries due to the presence of a well developed community of Copepods, Gastrotrichs, large Ciliates and/or soft-shelled Foraminiferans in some sites. The Westerschelde stood out due to the near-absence of harpacticoid copepods and, as in the Tagus, the lower meiobenthic densities in the marine part of the estuary. For nematode community analysis, we also included data from the Tamar which were obtained from the literature (Warwick & Gee, 1984). This resulted in the enumeration of 220 species, belonging to 102 genera, each with a characteristic distribution along the salinity, sedimentary and latitudinal gradients. Using the multivariate technique CANOCO, a zonation along these different physicochemical determinants was observed as well although salinity and sediment characteristic (scale of hundreds of meters to kilometers) proved to be more important in explaining community structure than latitudinal differences (scale of hundreds of kilometers). Nematode diversity was nearly entirely determined on the genus level and was positively related to salinity. Deviations from this general trend in the Gironde and the Tamar were attributed to sedimentary characteristics or to low macrobenthic predation. The presence of a typical opportunistic colonizing nematode species Pareurodiplogaster pararmatus in the low-salinity region of the Gironde could indicate (organic?) pollution or disturbance of the intertidal mud-flats.

Carbon flows through a benthic food web: Integrating biomass, isotope and tracer data.

The herbivorous, detrital and microbial pathways are major components of marine food webs. Although it is commonly recognized that these pathways can be linked in several ways, elucidating carbon transfers between or within these pathways remains a challenge. Intertidal flat communities are driven by a wide spectrum of organic matter sources that support these different pathways within the food web. Here we reconstruct carbon pathways using inverse analysis based on mass balancing, stable isotope signatures and tracer data. Data were available on biomass, total carbon production and processing, integrated diet information from stable isotope signatures and the transfer of recently produced carbon through the food web from an isotope tracer study. The integration of these data improved the quality of the inverse food web reconstruction considerably, as demonstrated explicitly by an uncertainty analysis. Deposition of detritus (detrital pathway) from the water column and subsequent assimilation and respiration by bacteria and to a lesser extent by microbenthos (microbial pathway) dominated the food web. Secondary production was dominated by bacteria (600 mg C m −2 d −1 ), but transfer to higher trophic levels was limited to 9% and most bacterial carbon was recycled back to dissolved organic carbon (DOC) and detritus. Microbenthos secondary production (77 mg C m −2 d −1 ) was supported by DOC (73%) and detritus (26%) and was entirely transferred up the food web. The higher trophic levels consisting of nematodes, meiobenthos (copepods, ostracods and foraminifera) and macrobenthos fed highly selectively and relied primarily on microphytobenthos and pelagic primary production (herbivorous pathway). Deposit feeding is a common feeding mode among these sediment dwelling fauna, but detritivory was negligible due to this selective feeding. This strong resource selectivity implies that the herbivorous and detrital-microbial pathways function more or less autonomously, with limited interaction.

On the oxidation and burial of organic carbon in sediments of the Iberian margin and Nazaré Canyon (NE Atlantic)

Abstract As a contribution to the EC-OMEX-II program, sediment carbon and nitrogen budgets are presented for the Iberian Margin (northeastern Atlantic). The budgets for degradable organic carbon and associated nitrogen were calculated from sediment and pore water properties, using a steady-state version of a numerical coupled diagenetic model, OMEXDIA. Data were collected throughout the major upwelling period along five transects, four of which were located on the open margin and one positioned in a major submarine canyon, the Nazare Canyon. A comparison of in situ oxygen profiles measured with monocathodic microelectrodes and with Clark type microelectrodes showed that monocathodic electrodes overestimate the oxygen concentration gradient near the sediment–water interface. This artifact probably results from the loss in sensitivity of the monocathodic microelectrode during profiling. Shipboard time course measurements with Clark type electrodes demonstrated transient conditions upon sediment retrieval on deck and indicated enhanced rates of oxygen consumption in the surface sediment, presumably as a result of lysis or exudation of oxidisable substrates by infauna. As a result, oxygen fluxes calculated from shipboard oxygen profiles overestimated in situ fluxes by up to a factor of 5 for water depths >1000 m. The sediments from the canyon and from a depositional area on the shelf were enriched in organic carbon (3–4.5 wt%) relative to the open margin stations (0.5–2 wt%) and showed C/N ratios exceeding Redfield stoichiometry for marine organic matter, indicating there was deposition of organic carbon of terrestrial origin in these areas. The oxidation of organic carbon on the open margin declined from ~11 gCm −2 y −1 on the shelf to 2 gCm −2 y −1 at 5000 m water depth, and was dominated by aerobic oxidation. The reactivity of the degradable organic carbon at the time of deposition was −1 on the shelf, and declined to −1 offshore. The burial of refractory organic carbon at the stations along the open margin transects also declined with increasing water depth from ~5 gCm −2 y −1 on the shelf to −2 y −1 at 2000 m depth, whereas the burial of particulate inorganic carbon declined from ~20 gCm −2 y −1 to −2 y −1 . A comparison of the estimated total organic carbon deposition and predicted delivery for the shelf suggest that 58 to 165 gCm −2 y −1 is oxidized in the water column, laterally advected, or focused into one of the canyons. Anaerobic oxidation, denitrification and, therefore, total oxidation of organic carbon was enhanced within the canyon relative to the open margin. Total organic carbon oxidation decreased with water depth from 22 gCm −2 y −1 at the head of the canyon to 3 gCm −2 y −1 over its fan. The reactivity of the organic carbon deposited in the canyon was lower than those of the shelf stations, suggesting that the canyon is being enriched in older, laterally advected organic matter. The burial of refractory organic carbon in sediments from the Nazare Canyon was considerably higher than in the sediments from the open margin; it also decreased with depth from 20 gCm −2 y −1 at 343 m to ~2.5 gCm −2 y −1 at 4298 m water depth. The burial of particulate inorganic carbon was slightly lower than that of refractory organic carbon. The burial of refractory organic carbon and the deposition of degradable organic carbon were both positively correlated with the sedimentation rates for the Iberian Margin, and indicated burial efficiencies were 0.6 to 48%. A single trend for burial efficiency versus sedimentation rate for both the canyon and the open margin indicates that the sedimentation rate was the master variable for the geographical distribution of organic carbon oxidation and carbon preservation on the NW Iberian Margin.

Nitrogen dynamics in the Westerschelde estuary (SW Netherlands) estimated by means of the ecosystem model MOSES

A tentative nitrogen budget for the Westerschelde (SW Netherlands) is constructed by means of a simulation model with thirteen spatial compartments. Biochemical and chemical processes in the water column are dynamically modeled; fluxes of dissolved constituents across the water-bottom interface are expressed by means of diagenetic equations.The model is calibrated on a large amount of observed variables in the estuary (1980–1986) with relatively fine temporal and spatial detail. Additional constraints are imposed by the stoichiometric coupling of carbon, nitrogen and oxygen flows and the required conservation of mass. The model is able to reproduce rather well the observed distributions of nitrate, ammonium, oxygen and Kjeldahl nitrogen both in time and space. Also, model output of biochemical oxygen demand and total organic carbon falls within observed ranges.By far the most pervasive process in the nitrogen cycle of the estuary is nitrification which mainly takes place in the water column of the upper estuarine part. On average about three times as much nitrate is leaving the estuary at the sea side compared to what enters from the river and from waste discharges. Ammonium on the other hand is consumed much faster (nitrification) than it is regenerated and only about one third of the total import leaves the estuary at the sea side. The budget for detrital nitrogen reveals import from the river, from wastes and from the sea. Phytoplankton uptake of inorganic nitrogen is negligible in the model.About 21% of total nitrogen, 33% of inorganic nitrogen, is removed from the estuary (mainly to the atmosphere through denitrification) and the load of nitrogen net exported to the sea amounts to about 51 000 tonnes per year. Total denitrification in our model is lower than what was estimated in the literature from the late seventies, where a nitrogen removal up to 40–50% of the total inorganic load was reported. Part of the differences could be methodological, but inspection of the nutrient profiles that led to these conclusions show them to be different to the ones used in our study. The oxygen deficient zone has moved upstream since the late seventies, entrailing the zone of denitrification into the riverine part of the Schelde. The nitrification process now starts immediately upon entering the estuary.

The role of the benthic biota in sedimentary metabolism and sediment-water exchange processes in the Goban Spur area (NE Atlantic)

We provide an overview of the role of biological processes in the Benthic boundary layer (BBL) and in sediments on the cycling of particulate organic material in the Goban Spur area (Northeast Atlantic). The benthic fauna, sediment and BBL characteristics were studied along a transect ranging from 208 to 4460 m water depth in different seasons over 3 years. Near-bottom flow velocities are high at the upper part of the slope (1000–1500 m), and high numbers of filter-feeding taxa are found there such that organic carbon normally passing this area during high flow conditions is probably trapped, accumulated, and/or remineralised by the fauna. Overall metabolism in shelf and upper slope sediments is dominated by the macrofauna. More than half of the organic matter flux is respired by macrofauna, with a lower contribution of metazoan meiofauna (4%) and anoxic and suboxic bacterial mineralisation (21%); the remainder (23%) being channelled through nanobiota and oxic bacteria. By its feeding activity and movement, the macrofauna intensely reworks the sediments on the shelf and upper slope. Mixing intensity of bulk sediment and of organic matter are of comparable magnitude. The benthos of the lower slope and abyssal depth is dominated by the microbiota, both in terms of total biomass (>90%) and carbon respiration (about 80%). The macrofauna (16%), meiofauna (4%) and megafauna (0.5%) only marginally contribute to total carbon respiration at depths below 1400 m. Because large animals have a lower share in total metabolism, mixing of organic matter within the sediments is reduced by a factor of 5, whereas mixing of bulk sediment is one to two orders of magnitude lower than on the shelf. The food quality of organic matter in the sediments in the shallowest part of the Goban Spur transect is significantly higher than in sediments in the deeper parts. The residence time of mineralisable carbon is about 120 d on the shelf and compares well with the residence time of the biota. In the deepest station, the mean residence time of mineralisable carbon is more than 3000 d, an order of magnitude higher than that of biotic biomass.

Similar rapid response to phytodetritus deposition in shallow and deep-sea sediments

The short-term benthic response to an input of fresh organic matter was examined in vastly contrasting benthic environments (estuarine intertidal to deep-sea) using 13C-labeled diatoms as a tracer of labile carbon. Benthic processing was assessed in major compartments through 13C-enrichment in CO2, in bacteria-specific phospholipids and in fauna tissue. A rapid response was evident in all environments. Under warm bottom water (14–18°C), similar quantities of the added carbon were respired within 24 hours in shallow and deep-sea sediments. However, the speed and magnitude of respiration were strongly reduced under low bottom water temperature (4–6°C), both in a shallow and a deep-sea site. Rapid carbon respiration even in deep-sea sediments almost devoid of fauna highlights the key role of bacteria, the most ubiquitous benthic component, in this short-term respiration of fresh organic matter. However, when present, fauna rapidly ingest algal material, thereby increasing the amount of carbon processed and directly extending carbon flow pathways.

Modeling 210Pb-derived mixing activity in ocean margin sediments : Diffusive versus nonlocal mixing

The influence of sediment mixing on activity versus depth profiles of the radionuclide *iOPb in the upper 20 cm of the sediments has been investigated along a depth transect (208 m4500 m, 17 stations) in the OMEX study area (Goban Spur, NE Atlantic Ocean). A hierarchical family of bioturbation!nonlocal exchange models was derived. Each member of the hierarchy includes all processes of the previous model, and adds a one- or two-parameter process. The significance of the additional parameters is tested using a one-tailed F-test. It was found that (1) in five cases there is a significant improvement when direct injection of part of the flux into deeper sediment layers (nonlocal exchange) is added to the diffusive mixing model. (2) In these five cases, the best model required only two additional parameters, compared to the diffusive mixing model. More elaborate models, including additional parameters did not result in a significantly better fit. (3) In four cases, the inclusion of diffusive mixing (bioturbation) to an advection/decay model does not result in a significant better fit of modeled versus measured *l”Pb activity-depth profiles. Using the simplest nonlocal exchange model, the amount of particulates that are directly injected at depth into the sediment was estimated and compared with the amount incorporated at the sediment surface. Along the OMEX transect, between 8-86% of the total flux enters the sediment by nonlocal exchange rather than by mere bioturbation/advection at the sediment surface. The importance of nonlocal exchange decreases with increasing water depth. To allow comparison with other measurements, we have also calculated the diffusive mixing coefficient using the classical bioturbation model. The sediments in the OMEX area have low bioturbation coefficients, especially at the deeper sites. Finally our models have also been used to reproduce and to explore some aberrant *‘OPb profiles reported in the literature.