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

Primary, new and export production in the NW Pacific subarctic gyre during the vertigo K2 experiments

Author Posting. © Elsevier B.V., 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 55 (2008): 1594-1604, doi:10.1016/j.dsr2.2008.04.013.This paper presents results on tracer experiments using 13C and 15N to estimate uptake rates of dissolved inorganic carbon (DIC) and nitrogen (DIN). Experiments were carried out at station K2 (47°N, 161°E) in the NW Pacific subarctic gyre during July-August 2005. Our goal was to investigate relationships between new and export production. New production was inferred from the tracer experiments using the f ratio concept (0-50m); while export production was assessed with neutrally buoyant sediment traps (NBSTs) and the e ratio concept (at 150m). During trap deployments, K2 was characterized both by changes in primary production (523 to 404 mg C m-2 d-1), new production (119 to 67 mg C m-2 d-1), export production (68 to 24 mg C m-2 d-1) and phytoplankton composition (high to low proportion of diatoms). The data indicate that 17 to 23% of primary production is exportable to deeper layers (f ratio) but only 6 to 13% collected as a sinking particle flux at 150m (e ratio). Accordingly, > 80% of the carbon fixed by phytoplankton would be mineralized in the upper 50m (1 – f), while < 11% would be within 50-150m (f – e). DIN uptake flux amounted to 0.5 mM m-2 h-1, which was equivalent to about 95% particulate nitrogen (PN) remineralized and/or grazed within the upper 150 m. Most of the shallow PN remineralization occurred just above the depth of the deep chlorophyll maximum (DCM), where a net ammonium production was measured. Below the DCM, while nitrate uptake rates became negligible because of light limitation, ammonium uptake did continue to be significant. The uptake of ammonium by heterotrophic bacteria was estimated to be 14-17% of the DIN assimilation. Less clear are the consequences of this uptake on the phytoplankton community and biogeochemical processes, e.g. new production. It was suggested that competition for ammonium could select for small cells and may force large diatoms to use nitrate. This implies that under Fe stress as observed here, ammonium uptake is preferred and new production progressively suppressed despite the surplus of nitrate.This research was supported by the Research Foundation Flanders through grant G.0021.04 and Vrije Universiteit Brussel via grant GOA 22, as well as the US National Science Foundation programs in Chemical and Biological Oceanography

Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments

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

Tephrochronology and its application: A review

Tephrochronology (from tephra, Gk ‘ashes’) is a unique stratigraphic method for linking, dating, and synchronizing geological, palaeoenvironmental, or archaeological sequences or events. As well as utilising the Law of Superposition, tephrochronology in practise requires tephra deposits to be characterized (or ‘fingerprinted’) using physical properties evident in the field together with those obtained from laboratory analyses. Such analyses include mineralogical examination (petrography) or geochemical analysis of glass shards or crystals using an electron microprobe or other analytical tools including laser-ablation-based mass spectrometry or the ion microprobe. The palaeoenvironmental or archaeological context in which a tephra occurs may also be useful for correlational purposes. Tephrochronology provides greatest utility when a numerical age obtained for a tephra or cryptotephra is transferrable from one site to another using stratigraphy and by comparing and matching inherent compositional features of the deposits with a high degree of likelihood. Used this way, tephrochronology is an age-equivalent dating method that provides an exceptionally precise volcanic-event stratigraphy. Such age transfers are valid because the primary tephra deposits from an eruption essentially have the same short-lived age everywhere they occur, forming isochrons very soon after the eruption (normally within a year). As well as providing isochrons for palaeoenvironmental and archaeological reconstructions, tephras through their geochemical analysis allow insight into volcanic and magmatic processes, and provide a comprehensive record of explosive volcanism and recurrence rates in the Quaternary (or earlier) that can be used to establish time-space relationships of relevance to volcanic hazard analysis. The basis and application of tephrochronology as a central stratigraphic and geochronological tool for Quaternary studies are presented and discussed in this review. Topics covered include principles of tephrochronology, defining isochrons, tephra nomenclature, mapping and correlating tephras from proximal to distal locations at metre- through to sub-millimetre-scale, cryptotephras, mineralogical and geochemical fingerprinting methods, numerical and statistical correlation techniques, and developments and applications in dating including the use of flexible depositional age-modelling techniques based on Bayesian statistics. Along with reference to wide-ranging examples and the identification of important recent advances in tephrochronology, such as the development of new geoanalytical approaches that enable individual small glass shards to be analysed near-routinely for major, trace, and rare-earth elements, potential problems such as miscorrelation, erroneous-age transfer, and tephra reworking and taphonomy (especially relating to cryptotephras) are also examined. Some of the challenges for future tephrochronological studies include refining geochemical analytical methods further, improving understanding of cryptotephra distribution and preservation patterns, improving age modelling including via new or enhanced radiometric or incremental techniques and Bayesian-derived models, evaluating and quantifying uncertainty in tephrochronology to a greater degree than at present, constructing comprehensive regional databases, and integrating tephrochronology with spatially referenced environmental and archaeometric data into 3-D reconstructions using GIS and geostatistics