A system identification view on two aquatic topics: phytoplankton dynamics and water mass mixing

The general aim of this study is to modify or improve existing modelling procedures in order to extract more or more reliable information from observations at hand. In practice, this means that much attention is directed to quantifying uncertainties, since these enable to draw a line between what is significant and what should not be interpreted. Two applications were considered: tracer experiments modelled by compartmental models (Part A) and a multivariate water mass mixing model (Part B). However, the focus lies on the methods used and developed to improve the models and their inferences. Indeed, the merit of this work is not to have enabled the estimation of flux rates and mixing fractions, but to have enabled their accurate estimation, together with an estimate of the associated uncertainty. Very briefly, these are the main achievements: (i) Inclusion of the input uncertainties in the estimation of model parameters and their uncertainties.(ii) Model selection method based on the statistical interpretation of the residual Weighted Least Squares cost function.(iii) Improvement of Optimum Multiparameter analysis for large-scale reconstruction of mixing water mass distributions.(iv) Construction of an algorithm to estimate heteroscedastic noise variances, from residuals but corrected for model errors.(v) Verification of identifiability of given experiment-model combinations

Identification of the accretion rate for annually resolved archives

International audienceThe past environment is often reconstructed by measuring a given proxy (e.g. ?18O) in an environmental archive, i.e. a species which gradually accumulates mass and records the current environment during this mass formation (e.g. corals, shells, trees, etc...). When such an environmental proxy is measured, its values are known as a function of distance. However, to relate the data to environmental variations, the date associated with each measurement, i.e. the time base, should be known. This is not straightforward solved, since species usually do not grow at constant rates. In this paper, we investigate this problem for annually resolved archives, which exhibit a certain periodicity. Such signals are often found in clams or corals. Due to variations in accretion rate the data along the distance axis have a disturbed periodic profile. A method is developed to extract information about the accretion rate, such that the original (periodic) signal as function of time can be recovered. Simultaneously the exact shape of the periodic signal is estimated. The final methodology is quasi-independent of choices made by the investigator. Every step in the procedure is described in detail and finally, the method is exemplified on a real world example

Finite element modelling of the Scheldt estuary and the adjacent Belgian/Dutch coastal zone with application to the transport of fecal bacteria

A fundamental problem in coastal modelling is the need to simultaneously consider large- and small-scale processes, especially when local dynamics or local environmental issues are of interest. The approach widely resorted to is based on a nesting strategy by which coarse grid large scale model provide boundary conditions to force fine resolution local models. This is probably the best solution for finite difference methods, needing structured grids. However, the use of structured grids leads to a marked lack of flexibility in the spatial resolution. Another solution is to take advantage of the potential of the more modern finite element methods, which allow the use of unstructured grids in which the mesh size may vary over a wide spectrum. With these methods only one model is required to describe both the larger and the smaller scales.Such a model is use herein, namely the Second-generation Louvain-la-Neuve Ice-ocean Model (SLIM, http://www.climate.be/SLIM). For one of its first realistic applications, the Scheldt Estuary area is studied. The hydrodynamics is primarily forced by the tide and the neatest way to take it into account is to fix it at the shelf break. This results in a multi-scale problem since the domain boundary lies at the shelf break, and covers about 1000km of the North Sea and 60km of the actual estuary, and ends with a 100km long section of the Scheldt River until Ghent where the river is not more than 50 m wide.Two-dimensional elements are used to simulate the hydrodynamics from the shelf break to Antwerp (80km upstream of the mouth) and one-dimensional elements for the riverine part between Antwerp and Ghent.For first application we consider the transport of faecal bacteria (Escherichia coli) which is an important water quality indicator.The model will be described in detail and the simulation results will be discussed. This modelling exercise actually falls within the framework of the interdisciplinary project TIMOTHY (http://www.climate.be/TIMOTHY) dedicated to the modelling of ecological indicators in the Scheldt area

Timing and placing samplings to optimally calibrate a reactive transport model: exploring the potential for <i>Escherichia coli</i> in the Scheldt estuary

For the calibration of any model, measurements are necessary. As measurements are expensive, it is of interest to determine beforehand which kind of samples will provide the maximum of information. Using a criterion related to the Fisher information matrix, it is possible to design a sampling scheme that will enable the most precise model parameter estimates. This approach was applied to a reactive transport model (based on SLIM) of Escherichia coli in the Scheldt Estuary. As this estuary is highly influenced by the tide, it is expected that careful timing of the samples with respect to the tidal cycle will have an effect on the quality of the data. The timing and also the positioning of samples were optimised according to the proposed criterion. In the investigated case studies the precision of the estimated parameters could be improved by up to a factor of ten, confirming the usefulness of this approach to maximize the amount of information that can be retrieved from a fixed number of samples

Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses.

The equine disease strangles, which is characterized by the formation of abscesses in the lymph nodes of the head and neck, is one of the most frequently diagnosed infectious diseases of horses around the world. The causal agent, Streptococcus equi subspecies equi, establishes a persistent infection in approximately 10 % of animals that recover from the acute disease. Such 'carrier' animals appear healthy and are rarely identified during routine veterinary examinations pre-purchase or transit, but can transmit S. equi to naïve animals initiating new episodes of disease. Here, we report the analysis and visualization of phylogenomic and epidemiological data for 670 isolates of S. equi recovered from 19 different countries using a new core-genome multilocus sequence typing (cgMLST) web bioresource. Genetic relationships among all 670 S. equi isolates were determined at high resolution, revealing national and international transmission events that drive this endemic disease in horse populations throughout the world. Our data argue for the recognition of the international importance of strangles by the Office International des Épizooties to highlight the health, welfare and economic cost of this disease. The Pathogenwatch cgMLST web bioresource described herein is available for tailored genomic analysis of populations of S. equi and its close relative S. equi subspecies zooepidemicus that are recovered from horses and other animals, including humans, throughout the world. This article contains data hosted by Microreact

Residence time, exposure time and connectivity in the Scheldt Estuary

Residence times and exposure times are computed for 13 boxes in the Scheldt Estuary, using the high-resolution tracer-transport model SLIM. The concepts are clearly defined and related to how they should be computed. First, the timescale values are compared with results published previously that were obtained with a simple box model, and an unexpected difference is revealed. This may suggest that a high-resolution model is necessary, even for the computation of such integrated quantities as residence or exposure times. Secondly, the newly computed residence times are compared to the exposures times to illustrate their intrinsic differences. From this difference, it is possible to propose a return coefficient, expressing the fraction of the exposure time that is due to “returning water”, i.e. water which has already left the estuary at least once. Finally, the estuarine exposure times are decomposed into the different box exposure times, resulting in a connectivity matrix. This matrix expresses how much time is spent in each of the estuarine subdomains during the water parcels' journey through the estuary

A comparative study of methods to reconstruct a periodic time series from an environmental proxy record

The past environment is often reconstructed by measuring a certain proxy (e.g. delta O-18) in an environmental archive, i.e. a biogenic or abiogenic accreting structure which gradually accumulates mass and records the current environment during this mass formation (e.g. corals, shells, trees, ice cores, speleothems, etc.). Proxy analysis usually yields a record along a distance axis. However, to relate the data to environmental variations, the date associated with each data point has to be known too. This transformation from distance to time is not straightforward to solve, since accretion mostly proceeds at a varying and unknown rate. To solve this problem some hypotheses about the growth rate or the time series must be made. Depending on the application, different assumptions may be appropriate, resulting in or requiring a particular method to perform this transformation. The actual method used can hugely influence the final result and hence the interpretation of the data in terms of frequency and timing of events. However, no comparative study has been made so far, and most of the existing methods haven't been thoroughly assessed. Therefore, this paper aims to evaluate and compare the most popular methods. To keep the review manageable the scope was limited to those records where it can be assumed that the time series is periodic. Examples of periods include tidal, seasonal and ENSO (El Nino Southern Oscillation) cycles, and even cycles of thousands of years could be considered, as long as they are resolved in the measured record. Six methods to reconstruct the time base for periodic proxy records are compared in this review. Their performance in the presence of stochastic and systematic errors is tested on simulations and linked to the methods' underlying assumptions. As a final comparison, all methods are applied to a real world example. The goal of this overview is to provide an objective structure and comparison of the methods mostly used, so that the users are aware of the underlying assumptions and their consequences

Arsenic speciation in the River Zenne, Belgium

Arsenic species have been assessed in the Zenne River, a sewage contaminated tributary of the Scheldt estuary, in winter 2003. The highest total dissolved As concentrations were found in the middle part of the river with values up to 3.6 mu g L(-1). Particulate As concentrations increase towards the mouth of the River with highest levels of 2 mu g L(-1). A very good correlation between the % of dissolved As and % of dissolved Fe was observed. They both linearly decrease with the amount of dissolved oxygen.In the middle part of the Zenne River where the oxygen levels were lowest, even below 1 mg L(-1), As(III) was the dominant species. In the other parts (upstream and downstream) of the river, As(V) was dominant. A linear relation between the measured redox values and those calculated via the As(III)/As(V) couple exists, but the range of measured Eh values is much larger than the calculated ones. No methylated dissolved As species were found during our survey

Modelling <i>Escherichia coli</i> concentrations in the tidal Scheldt river and estuary

Recent observations in the tidal Scheldt River and Estuary revealed a poor microbiological water quality and substantial variability of this quality which can hardly be assigned to a single factor. To assess the importance of tides, river discharge, point sources, upstream concentrations, mortality and settling a new model (SLIM-EC) was built. This model was first validated by comparison with the available field measurements of Escherichia coli (E. coli, a common fecal bacterial indicator) concentrations. The model simulations agreed well with the observations, and in particular were able to reproduce the observed long-term median concentrations and variability. Next, the model was used to perform sensitivity runs in which one process/forcing was removed at a time. These simulations revealed that the tide, upstream concentrations and the mortality process are the primary factors controlling the long-term median E. coli concentrations and the observed variability. The tide is crucial to explain the increased concentrations upstream of important inputs, as well as a generally increased variability. Remarkably, the wastewater treatment plants discharging in the study domain do not seem to have a significant impact. This is due to a dilution effect, and to the fact that the concentrations coming from upstream (where large cities are located) are high. Overall, the settling process as it is presently described in the model does not significantly affect the simulated E. coli concentrations