Modeling eutrophication and oligotrophication of shallow-water marine systems: the importance of sediments under stratified and well-mixed conditions

A one-dimensional model that couples water-column physics with pelagic and benthic biogeochemistry in a 50-m-deep water column is used to demonstrate the importance of the sediment in the functioning of shallow systems, the eutrophication status of the system, and the system’s resilience to oligotrophication. Two physical scenarios, a well-mixed and a stratified water column, are considered and both are run along a gradient of increasing initial pelagic-dissolved inorganic nitrogen (DIN) concentration. Where the mixed layer extends to the bottom, more nutrients and less light are available for growth. Under low to moderately eutrophic conditions (pelagic DIN <30 mmol m−3), this leads to higher productivity in well-mixed waters, while the stratified system is more productive under highly eutrophic conditions. Under stratification, the build-up of nitrate and depletion of oxygen below the mixed layer does not notably change the functioning of the sediment as a sink for reactive nitrogen. In sediments underlying well-mixed waters, sedimentary denitrification, fueled mainly by in situ nitrification, is slightly more important (8–15% of total benthic mineralization) than under stratified waters (7–20%), where the influx of bottom-water nitrate is the most important nitrate source. As a consequence of this less efficient removal of reactive nitrogen, the winter DIN concentrations are higher in the stratified scenario. The model is used to estimate the long-term benefits of nutrient reduction scenarios and the timeframe under which the new steady-state condition is approached. It is shown that a 50% reduction in external nitrogen inputs ultimately results in a reduction of 60–70% of the original pelagic DIN concentration. However, as the efflux of nitrogen from the sediment compensates part of the losses in the water column, system oligotrophication is a slow process: after 20 years of reduced inputs, the pelagic DIN concentrations still remain 2.7 mmol m−3 (mixed) and 3.9 mmol m−3 (stratified) above the ultimate DIN concentrations.

Spatial and temporal patterns of the zooplankton in the Westerschelde estuary

The invertebrate zooplankton fauna of the Westerschelde (Belgium and The Netherlands) was investigated during 2 yr by means of monthly samples along a salinity gradient. Copepods were usually the most abundant holoplanktonic metazoans except in the freshwater zone where Rotifera were most numerous. The combination of a classification technique and an ordination-regression technique proved to be a valuable tool for the analysis of such an extensive data set. The presence of 4 groups was established, representing spatially distinct populations but with temporally shifting boundaries. Few zooplankton species were truly estuarine in their distribution, but many were derived from nearby coastal waters. This intrusion of marine species started in spring, reaching their most upstream distribution and highest densities in summer-early fall, then declining and retreating from the estuary, disappearing in winter. Fringing this community was a transition group with low densities, but many species. This brackish-water community consisted predominantly of the calanoid copepod Eurytemora affinis. It appeared in late fall, spread out seaward to obtain its maximum density and distribution in winter-early spring. Densities then declined and the community was absent by late summer-early fall. The freshwater zone near the port of Antwerp, Belgium, was characterized by a paucity of large zooplankters, despite the high primary production in this zone. This is probably due to the low oxygen availability in this area. A canonical correspondence analysis revealed 2 major environmental axes. The salinity gradient (mainly spatial) explained most of the variance. Strongly correlated with this factor were dissolved oxygen content and secchi disc visibility. The temperature gradient (mainly temporal) was almost perpendicular to the salinity axis, indicating little or no correlation. Of lesser importance was the load of suspended matter, which was highest in the brackish area in autumn-winter. Chlorophyll content of the water was unimportant in explaining community structure. Copepod dry weight was maximal in spring in the brackish part (500 mg m-3); a lower maximum (260 mg m-3) was observed in summer in the marine part of the estuary

Short-term fate of phytodetritus in sediments across the arabian sea oxygen minimum zone

The short-term fate of phytodetritus was investigated across the Pakistan margin of the Arabian Sea at water depths ranging from 140 to 1850 m, encompassing the oxygen minimum zone (~100–1100 m). Phytodetritus sedimentation events were simulated by adding ~44 mmol 13C-labelled algal material per m2 to surface sediments in retrieved cores. Cores were incubated in the dark, at in situ temperature and oxygen concentrations. Overlying waters were sampled periodically, and cores were recovered and sampled (for organisms and sediments) after durations of two and five days. The labelled carbon was subsequently traced into bacterial lipids, foraminiferan and macrofaunal biomass, and dissolved organic and inorganic pools. The majority of the label (20 to 100%) was in most cases left unprocessed in the sediment at the surface. The largest pool of processed carbon was found to be respiration (0 to 25% of added carbon), recovered as dissolved inorganic carbon. Both temperature and oxygen were found to influence the rate of respiration. Macrofaunal influence was most pronounced at the lower part of the oxygen minimum zone where it contributed 11% to the processing of phytodetritus

The BenBioDen database, a global database for meio-, macro- and megabenthic biomass and densities

Benthic fauna refers to all fauna that live in or on the seafloor, which researchers typically divide into size classes meiobenthos (32/64 µm–0.5/1 mm), macrobenthos (250 µm–1 cm), and megabenthos (>1 cm). Benthic fauna play important roles in bioturbation activity, mineralization of organic matter, and in marine food webs. Evaluating their role in these ecosystem functions requires knowledge of their global distribution and biomass. We therefore established the BenBioDen database, the largest open-access database for marine benthic biomass and density data compiled so far. In total, it includes 11,792 georeferenced benthic biomass and 51,559 benthic density records from 384 and 600 studies, respectively. We selected all references following the procedure for systematic reviews and meta-analyses, and report biomass records as grams of wet mass, dry mass, or ash-free dry mass, or carbon per m2 and as abundance records as individuals per m2. This database provides a point of reference for future studies on the distribution and biomass of benthic fauna

Book Review : M. Henry. H. Stevens: A Primer of Ecology with R. Springer-Verlag, New York, 2009.

no abstract

Reactive transport in aquatic ecosystems: rapid model prototyping in the open source software R

The concentrations of many natural compounds are altered by chemical and biological transformations, and physical processes such as adsorption and transport. Their fate can be predicted using reactive transport models that describe reaction and advective and dispersive movement of these components in their natural environment. Recently a number of software packages have been implemented in the open source software R that allow one to implement reactive transport models. Central to this is the ReacTran R-package, a comprehensive collection of functions for modeling reactive components that may be distributed over multiple phases, whose dynamics are coupled through biological and geochemical reactions, and that are transported in one-, two- or three-dimensional domains with simple geometries. Dedicated solution methods are in R-packages deSolve and rootSolve. The modeling packages facilitate the simulation of reaction and transport of components for spatial scales ranging from micrometers to kilometers and spanning multiple time-scales. As they are influenced in similar ways, the same functions can solve biogeochemical models of the sediment, groundwater, rivers, estuaries, lakes or water columns, experimental setups, or even describe reaction and transport within flat, cylindrical or spherical bodies, such as organisms, aggregates, or the dispersion of individuals on flat surfaces and so on. We illustrate the use of R for reactive transport modeling by three applications spanning several orders of magnitude with respect to spatial and temporal scales. They comprise (1) a model of an experimental flow-through sediment reactor, where fitting so-called breakthrough curves are used to derive sulfate reduction rates in an estuarine sediment, (2) a conservative and reactive tracer addition experiment in a small stream, which implements the concept of river spiraling, and (3) a 2-D and 3-D model that describes oxygen dynamics in the upper layers of the sediment, interspersed with several hotspots of increased reaction intensities. The packages ReacTran, deSolve and rootSolve are implemented in the software R and thus available for all popular platforms (Linux, Windows, Mac). Models implemented using this software are short and easily readable, yet they are efficiently solved. This makes R extremely well suited for rapid model prototyping.

Estimating Estuarine Residence Times in the Westerschelde (the Netherlands) Using a Box Model with Fixed Dispersion Coefficients

The residence time of the water masses in the Westerschelde estuary was determined using a simple compartment-model that simulates the advective-diffusive transport of a conservative dissolved substance (chlorinity). The residence time of a water parcel in the upstream part of the estuary (i.e, the time needed for this water parcel to leave the estuary) varied from about 50 days in winter to about 70 days in summer. The most seaward compartment had residence times of about 10-15 days. Dispersive coefficients that are fixed in time were able to reproduce the observed salinity distributions very well in the Westerschelde. They were obtained by calibration on observed chlorinities. It is argued that the apparent relationship of dispersive coefficients with freshwater flow, which is observed in certain studies, could (partly) reflect the deviation from steady state conditions which are required assumptions to calculate these dispersive coefficients directly from salinity profiles. [KEYWORDS: Residence times; westerschelde; estuary Scales

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 51000 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. [KEYWORDS: Nitrogen; budget; nitrification; denitrification; westerschelde; estuary Organic-carbon; north-sea; nitrifying bacteria; southern bight; st-lawrence; denitrification; sediments; budget]