Data assimilation as a key step towards the implementation of an efficient management of dissolved oxygen in land-based aquaculture

A data assimilation (DA) methodology, e.g. the continuous-discrete Kalman filter (CD-KF), was applied to the assimilation of dissolved oxygen data, in order to obtain a dynamic estimation of the oxygen demand in a land-based aquafarm. The CD-KF was implemented on a dynamic model, which included as state variables the concentration of dissolved oxygen (DO) and fish respiration rate: the latter was considered as a non-observable stochastic variable. The model was applied to a 1-month long set of observations collected at a raceway rainbow trout farm, including (1) hourly time series of water temperature and dissolved oxygen concentration in the raceway influent and effluent and (2) a daily time series of fish number and fish weight distribution. The results show that the assimilation of DO data led to a dynamic estimate of DO demand which showed changes in the daily mean and the daily pattern: these were related to changes in the feeding regime. Furthermore, the methodology provided accurate short-term predictions of the DO concentration also in the presence of short-term fluctuations, which would be very difficult to relate to external forcings in a mechanistic model. These findings indicate that DA could be effectively used to design and implement efficient and robust control systems for optimizing the oxygen supply, thus contributing to the implementation of Precision Fish Farming in land-based aquafarms

Optimization of the Spatial Distribution of Pollution Emission in Water Bodies

The environmental protection of water bodies in Europe is based on the Water Framework Directive, which combines the so called Emission Limits Value and the Water Quality Objective (QO) approaches. The first one sets limits to particular type of emissions, for example the Nitrate Directive, while the second establishes Quality Standards for Biological, Chemical and Hydromorphological Quality Elements, in order to ensure the functioning of freshwater and marine ecosystem and the sustainable use of water bodies. To this regard, mathematical models are valuable tools for reconciliating these approaches, since they allow one to establish a causal link between emission levels and the Quality Standards ("direct problem") and vice-versa ("inverse problem"). In general, Quality Elements are variables or proper combination of variables which define the "status" of a water body. For example, the "chemical status" can be defined by a set of concentrations of chemicals which are potentially harmful for the ecosystem and humans, or the biological status may be based on Quality Elements which include the density of phytoplankton, the presence/absence of Submerged Aquatic Vegetation, the presence/absence of sensitive species etc. In many instances, the Quality Standards can then be expressed as threshold values, below or above which the functioning of the ecosystem is compromised and/or the risk for human health is not acceptable. If this is the case, management policies should be aimed at improving the state of the system and meet those Standards in the near future. In order to be carried in a cost-effective manner, such interventions should be based on a quantitative understanding of the relationships between the Pressures on the system and its State. This task could be very complex in large water bodies, where transport processes play a major role in creating marked gradients and pollution sources may be spatially distributed and/or not well identified. From the scientific point of view, the problem can be stated as follows: a mathematical model should enable one to "map" the spatial distribution of inputs (emissions) into the spatial distribution of the requested output, namely the "indicator" or "metric", which is subjected to a given constraint, the Quality Standard (QS), within the computational dominion. Such analysis may reveal that the QS are not respected only in a given fraction of the water body and, in the most favorable circumstances, identify the pollution sources which cause the problem. In such a case, a selective intervention, aimed at lowering the emission levels of those sources, would probably be more cost effective than the general reduction of the emission levels in the whole area. The spatial distribution of emission sources may also affect the pollution level and, in some instances, a proper redistribution of those sources in a given area, which leaves unchanged the total load, could have positive effect on the pollution level. In this paper, we are going to investigate the above problems in the simplest possible setting, in order to provide a clear interpretation of the results in relation to the most relevant parameters. The paper is organized as follows: in the "methods" section, we present the basic equations and provide insights for solving the problem in the general case as well as in the specific one here presented. The analytical solutions are presented and discussed in the next two sessions and some concluding remarks are then summarized in the conclusive section

Estimating oxygen consumption of rainbow trout (Oncorhynchus mykiss) in a raceway: a precision fish farming approach

3openInternationalItalian coauthor/editorThe Precision Fish Farming (PFF) approach was applied to the estimation of fish oxygen consumption of rainbow trout in a raceway farm. A dynamic model, simulating the evolution of Dissolved Oxygen concentration, was identified: the daily oscillation of fish oxygen consumption rate was simulated by means of a sinusoidal function. The model was applied to the data set collected during a four-week field study, which was carried out in July 2019. Water temperature and Dissolved Oxygen concentration were measured with an hourly frequency in farm influent and effluent. Fish biomass was monitored on a daily basis by combining the data provided by a state-of-the art system for non-invasive estimation of fish weight distribution with mortality counting. The monitoring period was partitioned into two time-windows, as fish was not fed during the first two weeks. These windows were further partitioned into a calibration and validation set. Three model parameters, i.e. the average daily respiration rate, the amplitude of its daily oscillation, and its phase were estimated by fitting the model output to the time series of DO concentration in the effluent. The results of the calibration show that: 1) the daily average oxygen consumption rate is consistent with the literature; 2) the amplitude of the daily oscillation when fish is regularly fed is more than twice that estimated for fasting fish. The results of the validation suggest that the model could be used to implement a cost-effective automatic control of oxygen supply, based on the short-term prediction of oxygen demandopenRoyer, E.; Faccenda, F.; Pastres, R.Royer, E.; Faccenda, F.; Pastres, R

Linking food web functioning and habitat diversity for an ecosystem based management: A Mediterranean lagoon case-study

We propose a modelling approach relating the functioning of a transitional ecosystem with the spatial extension of its habitats. A test case is presented for the lagoon of Venice, discussing the results in the context of the application of current EU directives. The effects on food web functioning due to changes related to manageable and unmanageable drivers were investigated. The modelling procedure involved the use of steady-state food web models and network analysis, respectively applied to estimate the fluxes of energy associated with trophic interactions, and to compute indices of food web functioning. On the long term (hundred years) temporal scale, the model indicated that the expected loss of salt marshes will produce further changes at the system level, with a lagoon showing a decrease in the energy processing efficiency. On the short term scale, simulation results indicated that fishery management accompanied by seagrass restoration measures would produce a slight transition towards a more healthy system, with higher energy cycling, and maintaining a good balance between processing efficiency and resilience. Scenarios presented suggest that the effectiveness of short term management strategies can be better evaluated when contextualized in the long term trends of evolution of a system. We also remark the need for further studying the relationship between habitat diversity and indicators of food web functioning

Testing the robustness of primary production models in shallow coastal areas: a case study

In this paper we investigate the robustness of a dynamic model, which describes the dynamic of the seagrass Zostera marina, with respect to the inter-annual variability of the two main forcing functions of primary production models in eutrophicated environments. The model was previously applied to simulate the seasonal evolution of this species in the Lagoon of Venice during a specific year and calibrated against time series of field data. In the this paper, we present and discuss the results which were obtained by forcing the model using time series of site-specific daily values concerning the solar radiation intensity and water temperature. The latter was estimated by means of a regression model, whose input variable was a site-specific time series of the air temperature. The regression model was calibrated using a year-long time series of hourly observations. The Z marina model was first partially recalibrated against the same data set that was used in the original paper. Subsequently, the model was forced using a 7-year-long time series of the driving functions, in order to check the reliability of its long-term predictions. Even though the calibration gave satisfactory results, the multi-annual trends of the output variables were found to be in contrast with the observed evolution of the seagrass biomasses. Since detailed information about the air temperature and solar radiation are often available, these findings suggest that the testing of the ecological consistency of the evolution of primary production models in the long term would provide additional confidence in their results, particularly in those cases in which the scarcity of field data does not allow one to perform a formal corroboration/validation of these models

Testing a model of pacific oysters’ (Crassostrea gigas) growth in the adriatic sea: Implications for aquaculture spatial planning

Assessing the potential biomass yield is a key step in aquaculture site selection. This is challenging, especially for shellfish, as the growth rate depends on both trophic status and water temperature. Individual ecophysiological models can be used for mapping potential shellfish growth in coastal areas, using as input spatial time series of remotely sensed SST and chlorophyll-a. This approach was taken here to estimate the potential for developing oyster (Crassostrea gigas) farming in the western Adriatic Sea. Industry relevant indicators (i.e., shell length, total individual weight) and days required to reach marketable size were mapped using a dynamic energy budget model, finetuned on the basis of site-specific morphometric data collected monthly for a year. Spatially scaled-up results showed that the faster and more uniform growth in the northern Adriatic coastal area, compared with the southern one, where chlorophyll-a levels are lower and summer temperatures exceed the critical temperature limit for longer periods. These results could be used in planning the identification of allocated zones for aquaculture, (AZA), taking into account also the potential for farming or co-farming C. gigas. In perspective, the methodology could be used for getting insights on changes to the potential productivity indicators due to climatic changes

Ecosystem functioning and ecological status in the Venice lagoon, which relationships?

The implementation of management measures for improving the ecological status within an Ecosystem Based Management approach represents one the of the main challenges in coastal and transitional water environments. In general terms, ecological status and ecosystem functioning are expected to be positively associated, being good ecological processes a sort of prerequisite for the ecosystem health, but often relationships between ecosystem functioning indicators and the metrics used to define ecological status resulted to be rather puzzling. Moreover, the Biological Quality Elements (BQEs) do not show a consistent response to the changes in the ecosystem. This situation does not allow to recognize where interventions are really needed, hindering the definition of effective management strategies. In the present paper, a spatially explicit food web model of the Venice lagoon (with the resolution of 300 m) is used to simulate changes in the ecological status and related them to different management scenarios. Functional changes in the food web were investigated by comparing values of a set of 12 indicators derived by the ecological network analysis. In general, results highlighted on one hand the need for more discussion about the implementation of the WFD, at least in complex and spatially heterogeneous transitional waters environments, as the Venice lagoon; on the other, results remark the opportunity to support the BQEs monitoring with an ecological modelling approach. These models are certainly not the panacea for addressing questions about the environmental management, as they have inherent uncertainties (on parameters, structure, processes etc.); however, they can prove useful for selecting among different policy choices, since they offer the opportunity to simulate the mean effects, preliminarily verifying the efficacy of the proposed interventions

A stratified compartmental model for the transmission of Sparicotyle chrysophrii (Platyhelminthes: Monogenea) in gilthead seabream (Sparus aurata) fish farms †

The rapid development of intensive fish farming has been associated with the spreading of infectious diseases, pathogens and parasites. One such parasite is Sparicotyle chrysophrii (Platyhelminthes: Monogenea), which commonly infects cultured gilthead seabream (Sparus aurata)-a vital species in Mediterranean aquaculture. The parasite attaches to fish gills and can cause epizootics in sea cages with relevant consequences for fish health and associated economic losses for fish farmers. In this study, a novel stratified compartmental epidemiological model of S. chrysophrii transmission was developed and analysed. The model accounts for the temporal progression of the number of juvenile and adult parasites attached to each fish, as well as the abundance of eggs and oncomiracidia. We applied the model to data collected in a seabream farm, where the fish population and the number of adult parasites attached to fish gills were closely monitored in six different cages for 10 months. The model successfully replicated the temporal dynamics of the distribution of the parasite abundance within fish hosts and simulated the effects of environmental factors, such as water temperature, on the transmission dynamics. The findings highlight the potential of modelling tools for farming management, aiding in the prevention and control of S. chrysophrii infections in Mediterranean aquaculture

Mechanical clam dredging in Venice lagoon: ecosystem effects evaluated with a trophic mass-balance model

Harvesting of the invasive Manila clam, Tapes philippinarum, is the main exploitative activity in the Venice lagoon, but the mechanical dredges used in this free-access regime produce a considerable disturbance of the lagoon ecosystem. An ecosystem approach to study the complex effects of clam harvesting was implemented using a trophic mass-balance model. The trophic relations in the ecosystem were quantified with a mixed trophic impact analysis and further evaluated by considering different explanations for the ‘‘Tapes paradox’’, which consists of the apparent population enhancement of Manila clams by dredging and the apparent nutritional advantages that this species receives from re-suspended organic matter. The key-role played by this introduced species is highlighted by a network analysis that indicates a ‘‘wasp-waist control’’ of the system by Manila clams. The model constructed to characterise the present state of the Venice lagoon ecosystem is compared with models produced for a reconstructed past lagoon and a projected future lagoon. The future model was obtained by simulating the elimination of clam dredging in 10 years. The three different models were compared using thermodynamic and informational indices. Simulating the elimination of clam dredging produced a 33% increase in artisanal fishery catches, carried out by means of static gears, even with no change in fishing effort. These simulations also forecast an increase in the mean trophic level of the artisanal fishery catches as a positive effect of eliminating mechanical clam harvesting