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The Baltic Sea is a severely disturbed marine ecosystem previously used as a dumping ground for chemical warfare agents (CWA), which are now known to enter its food web. We have performed a modelling exercise using a calibrated and validated Central Baltic Ecopath with Ecosim (EwE) model to recreate the potential environmental pathways of the infamous Clark I (diphenylchlorarsine). Observations from modelling timestamps covering recent times correspond with in situ detections in sediments and Atlantic cod (Gadus morhua). Under applied modelling conditions and scenarios, there is an active transfer of Clark I from sediments through the Baltic Sea food-web. According to our results, Clark I bioaccumulates within the Baltic Sea food web exclusively throughout the detritus-based food chain. The EwE model for the Central Baltic Sea also allows the simulation of changes in the food web under multiple anthropogenic stressors and management efforts, including recommendations from the Helsinki Commission Baltic Sea Action Plan (HELCOM BSAP). Among all investigated scentarios and factors, the commercial fishing is the most impactful on Clark I accumulation rate and contamination transfer within the Baltic Sea food web. The study indicates the need to extend the existing monitoring approach by adding additional species representing a broader range of ecological niches and tiers within the food chains. From the environmental perspective, the remediation of Chemical Weapons by removal should be considered as part of the integrated management of the Baltic Sea.

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This study aims to comprehensively understand the Gosikhurd Dam ecosystem (GDE) ecosystem by employing the Ecopath with Ecosim software (version 6.6.5) to construct a trophic mass balancing model. This model consisted of 16 functional groups of organisms, and their interactions and trophic levels were explored. The study focuses on various performance indicators to assess the ecosystem's maturity and complexity. To achieve these objectives, monthly fish samples were collected from June 2022 to May 2023. Performance indicators such as the connectance index (CI), system omnivory index (SOI), Finn's cycling index (FCI), mean path length (FML), ascendency, overhead, and Shannon diversity index were calculated to assess ecosystem maturity and complexity. The Finn's cycling index (FCI) and the mean path length (FML) were calculated as 1.81 and 2.20, respectively, indicating the ecosystem's responsiveness to environmental changes and overall system health and stability. Ascendency and overhead values were also analysed, with ascendency being relatively higher (41.58%), reflecting a system that utilises less than half of its total capacity. The overhead value (58.42%) indicated that the ecosystem is relatively stable and capable of adapting to external perturbations. Furthermore, the Shannon diversity index was 1.67, illustrating less diversity and validating the ecosystem's immaturity. The study identifies critical species and their roles in shaping the ecosystem dynamics, highlighting the importance of zooplankton, zoobenthos, and tilapia as keystone species. These indices propound that GDE is in its developmental stage and lacks complexity compared to mature ecosystems. The findings provide valuable insights into the current state of the ecosystem and can guide future management and conservation efforts.

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Ecosystem services link the status of biodiversity and its functioning to societal goods and benefits contributing to human wellbeing. As such, they can play a key role in preserving the environment and managing natural resources and ecosystems to conserve nature's contributions to people. Identification of the main threats acting on the natural environment, and how these may impact its capacity to supply ecosystem services, is fundamental to the maintenance of these services. To that end, we present a novel approach based on a cumulative impacts assessment that 1) covers all relevant human activities and their pressures, 2) links impacts to the biotic groups that make up biodiversity and 3) provides an estimation of the Service Supply Potential based on the functioning of these biotic groups. Key proxy metrics to estimate this Service Supply Potential were identified from a literature review and quantified using a food web model (Ecopath with Ecosim). In addition to this quantitative information, the assessment of the capacity to supply ecosystem services was supplemented with expert judgement-based information to reflect the societal preferences that drive the allocation of human capital and turn these services into societal goods and benefits. As a proof of concept, the method was applied to the North Sea ecosystem. Results showed that, overall, the capacity of the North Sea to supply Cultural ecosystem services was most threatened, with an average potential decline of 50 % compared to an undisturbed situation. This was followed by the Provisioning ecosystem services with 46 % and the Regulation & Maintenance with 38 %. The main anthropogenic threats (excluding climate change) to the North Sea capacity to supply ecosystem services come primarily from fishing contributing to 51 % of the overall threat. Of the remaining 18 sectoral activities another 23 % was contributed by mining, non-renewable energy, tourism, and agriculture.

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Mercury is a naturally occurring heavy metal that has also been associated with anthropogenic sources such as cement production or hydrocarbon extraction. Mercury is a contaminant of concern as it can have a significant negative impact on organismal health when ingested. In aquatic environments, it bioaccumulates up the foodweb, where it then has the potential to impact human health. With the offshore hydrocarbon platforms in the North Sea nearing decommissioning, they must be assessed as a potential source for the environmental release of mercury. International treaties govern the handling of materials placed in the ocean. Studies have assessed the ecologic and economic benefits of (partial) in situ abandonment of the infrastructure as artificial reefs. This can be applied to pipelines after substantial cleaning to remove mercury accumulation from the inner surface. This work outlines the application of an approach to modelling marine mercury bioaccumulation for decommissioning scenarios in the North Sea. Here, in situ decommissioning of cleaned pipelines was unlikely to have a negative impact on the North Sea food web or human health. However, significant knowledge gaps have been determined, which must be addressed before all negative impacts on ecosystems and organismal health can be excluded.

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Many oceanic areas are still in need of baseline information on their structure and functioning. This is particularly important due to the ever-increasing impacts of global changes, which have led to the decline of marine life, and top predators in particular. The study of the structure and functioning of food webs can help understand the consequences of the disappearance of this group in marine ecosystems. Here, we develop a mass-balanced model for the marine Exclusive Economic Zone of the archipelago of Madeira, with emphasis on the role of marine megafauna in this ecosystem. A total of 50 functional groups were defined, representing coastal and open ocean areas, and epipelagic and deep-sea levels. The total biomass of the Madeira system was calculated at 52.68 t km-2, with lower trophic level organisms comprising 89.9 % of its biomass. Marine megafauna, namely pelagic sharks and coastal birds had the highest impacts across other trophic levels and were classified as keystone species, together with monk seals. The food web was characterized by a linear-like food chain, with a large proportion of specialized organisms, including dolphins, shearwaters, and large pelagic fish. The low mean trophic level of the system was 2.03, much lower than that of fisheries (4.3) targeting mainly tunas and Black scabbardfish. Considering the importance of marine megafauna in this food web and the threats they are facing; monitoring studies of key species in the region should be a priority. This study can now be used to build a needed ecosystem-based fisheries management and integrate conservation measures to declining species.

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Background: The Black Sea is one of the most anthropogenically disturbed marine ecosystems in the world because of introduced species, fisheries overexploitation, nutrient enrichment via pollution through river discharge, and the impacts of climate change. It has undergone significant ecosystem transformations since the 1960s. The infamous anchovy and alien warty comb jelly Mnemiopsis leidyi shift that occurred in 1989 is the most well-known example of the drastic extent of anthropogenic disturbance in the Black Sea. Although a vast body of literature exists on the Black Sea ecosystem, a holistic look at the multidecadal changes in the Black Sea ecosystem using an ecosystem- and ecology-based approach is still lacking. Hence, this work is dedicated to filling this gap. Methods: First, a dynamic food web model of the Black Sea extending from 1960 to 1999 was established and validated against time-series data. Next, an ecological network analysis was performed to calculate the time series of synthetic ecological indicators, and a regime shift analysis was performed on the time series of indicators. Results: The model successfully replicated the regime shifts observed in the Black Sea. The results showed that the Black Sea ecosystem experienced four regime shifts and was reorganized due to effects instigated by overfishing in the 1960s, eutrophication and establishment of trophic dead-end organisms in the 1970s, and overfishing and intensifying interspecies trophic competition by the overpopulation of some r-selected organisms (i.e., jellyfish species) in the 1980s. Overall, these changes acted concomitantly to erode the structure and function of the ecosystem by manipulating the food web to reorganize itself through the introduction and selective removal of organisms and eutrophication. Basin-wide, cross-national management efforts, especially with regard to pollution and fisheries, could have prevented the undesirable changes observed in the Black Sea ecosystem and should be immediately employed for management practices in the basin to prevent such drastic ecosystem fluctuations in the future.

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We used the Ecopath with Ecosim ecosystem model to assess the future effects of multiple stressors on sardine and the Portuguese continental shelf ecosystem. We assessed individual and combined impacts of changes in sardine fishing pressure, biomass of sardine competitors and predators and sea surface temperature (SST). This study demonstrated that the greatest impact on sardine stock is caused by projected SST rise whose effect is dominant and detrimental to sardine stock regardless of other conditions, including sardine fishing at maximum sustainable yield (FMSY). The largest impact on ecosystem stability, maturity and diversity of flows was observed under the forced-biomass scenarios that simulate changes in biomass of sardine predators and competitors. Moreover, these stressors alongside FMSY are projected to play an important role in the future evolution of the sardine stock. Results presented in this study can assist long-term and strategic management of the Iberian sardine stock.

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The ecological roles of the species in the food web are studied through the Ecopath with Ecosim modelling approach. In this modelling approach, the food web is described by means of functional groups, each representing a species, a life stage of a species, or a group of species with similar trophic, ecological and physiological features. Links between the groups are formally described by a set of linear equations, informed with ecological and fishing data. Here, the data input collected to implement 3 Ecopath models in the Northern Ionian Sea (Central Mediterranean Sea) from 1995 to 2015 are reported. This dataset applied to study the ecological roles of the demersal Chondrichthyes in the study area could be useful to explore different fishing management scenarios. A large dataset of over 300 taxa is shown detailing the ecological inputs, such as Biomass (kg km-2), Production and Consumption rates (y-1), Diet information (weight in %), and fishing data represented by Landings and Discards (t km-2 y-1). In particular, the fishery data described the catches of trawls, longlines, passive nets, other gears and purse seine. In addition, a description of the aggregation method of the species is shown.

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To explore the historical evolution and current status of the EwE (Ecopath with Ecosim) modelling research, the core dataset and extended dataset were collected by topic retrieval and citation indexing methods from the "Web of Science" from 1984 to 2020. The bibliometric analysis and mapping knowledge were performed by CiteSpace software, focusing on literature distribution, research forces, research theme, and hotspot evolution. The results showed that the annual publications in the EwE model researches were increasing, covering multi-disciplinary fields. Christensen, Walters, and Pauly were representative scholars with an important role in model development and relevant international cooperation. In the early stage, EwE model was usually applied to solve ecosystem problems, including spatial-temporal dynamic of structure and function, and the ecosystem effects of fisheries. Currently, marine resource management, ecosystem modelling, marine protected areas and ecosystem indicators had become the key themes. The research hotspots shifted from model development and food web structure to ecosystem forecasting and resource management, which would provide scientific evidence for ecosystem-based aquatic resource management and the construction of protected area in marine.

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The expansion of fisheries and its increased efficiency are causing severe detrimental impacts on marine species and ecosystems, that can be categorised into operational and ecological effects. While impacts directly caused by fishing activities have been extensively documented, it is difficult to set an empirical link between fisheries and changes in predator biomass and abundance. Therefore, exploring the functioning of ecosystems as a whole, the interactions between the different species within them and the impact of human activities, is key to understanding the ecological effects of fisheries on top predators and ecosystems, and to develop effective conservation measures, while ensuring a more sustainable exploitation of fishing resources. For instance, mass balance models, such as Ecopath with Ecosim, have proven to be a useful tool to develop more holistic fisheries management and conservation strategies. In this study, Ecopath with Ecosim was used to investigate the temporal dynamics of the Rías Baixas shelf ecosystem (North-West Spain) between 2005 and 2017. Additionally, nine 30-year forward projecting simulations covering the period 2018-2047 were developed to examine the effects of differing fisheries management strategies on common dolphins (Delphinus delphis), bottlenose dolphins (Tursiops truncatus) and harbour porpoises (Phocoena phocoena). Results from these models suggest that when intense fishing increases it poses a major threat to the conservation of these top predators in the area, by reducing the variety of their available prey and potentially enhancing competition amongst them. The study highlights the applicability of Ecopath with Ecosim to develop cetacean conservation measures and despite its small spatial scale, it provides a general framework that can be used to assess cetacean conservation in larger and impacted areas.

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Increasing human population size and mobility have accelerated the translocation of nonnative species globally, which has become a major threat to conservation of biodiversity and ecosystem services. Introduced species can disrupt species interactions of the recipient ecosystem, triggering system-wide events, and amplify or dampen effects of existing pressures. We show how two pervasive intercontinental invasive consumers in North American lakes, dreissenids (filter-feeding mussels) and Bythotrephes (carnivorous zooplankton), nonlinearly modify consumer-resource dynamics and undermine management interventions to rebuild cold-water predatory fish biomass. Synthesizing 30 yr (1986-2015) of lake-wide monitoring data with a dynamic mass-balance food-web model (consisting of 61 species and trophic groups), we reconstructed historical food-web dynamics of Lake Simcoe, a large, temperate lake in Ontario, Canada that has shifted from a turbid to clear-water state. We then analyzed patterns of biomass fluctuations of three recreationally harvested, ecologically connected populations; lake trout (Salvelinus namaycush, a piscivore), lake whitefish (Coregonus clupeaformis, a benthivore), and cisco (C. artedi, a planktivore) before and after the invasions by testing hypotheses on their delayed recoveries under management interventions-predator manipulations (fishery removal and stocking) and nutrient (phosphorus) load reduction. Analyses suggest that fishery harvest primarily regulated early recovery trajectories of the piscivore and planktivore, weakening top-down control prior to the establishment of the invasive consumers. By contrast, the benthivore biomass patterns were shaped, in part, by the invasive mussels (via diet shift), independently of management actions. Although improved water quality (with reduced hypoxia in deeper water) and, in turn, higher macrophyte production are projected to expand the predation refuge for young fish, intensified planktivory (by Bythotrephes) and herbivory (by dreissenids) have triggered shifts in community composition (from pelagic to demersal dominance). These system-wide shifts, in turn, have substantially diminished ecosystem productivity, thereby shrinking fishery yields. Novel consumers can rewire food webs, disrupt energy flows, and suppress predator recoveries, underscoring the need to account for altered ecological reality when sustainably managing fishery resources in invaded ecosystems.

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Modeling is a useful approach to learn about the capacity of the systems to recover after disturbances. In October 2011, a submarine volcanic eruption in The Punta Restinga-Mar de Las Calmas Marine Protected Area (RMC-MPA) caused catastrophic mass mortality. We modeled the recovery dynamics of the fully protected (no-take zone), partially protected (buffer zone), and unprotected (fished zone) areas to evaluate their resilience and their potential to restore fishing resources. Recovery varied with species and levels of protection. Benthic macroalgae and parrotfish populations recovered the fastest. Piscivore fishes, macroinvertebrate feeders, and macroinvertebrate detritivores required more extended recovery periods. The levels of protection played a significant role in recovery, with the no-take zone showing more resilience than the buffer and fished zones. Our results suggest that no-take zones are crucial in the recovery process after catastrophic events. Regular monitoring of benthic communities provided the necessary data to model these communities and to point to the regulation of the artisanal fleet activity in restricted fishing areas as a mechanism to further enhance the recovery of fishing stocks.

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We developed numerical simulations of potential future ecological states of the Baltic Sea ecosystem at the end of century under five scenarios. We used a spatial food web (Ecospace) model, forced by a physical-biogeochemical model. The scenarios are built on consistent storylines that describe plausible developments of climatic and socioeconomic factors in the Baltic Sea region. Modelled species diversity and fish catches are driven by climate- and nutrient load-related changes in habitat quality and by fisheries management strategies. Our results suggest that a scenario including low greenhouse gas concentrations and nutrient pollution and ecologically focused fisheries management results in high biodiversity and catch value. On the other hand, scenarios envisioning increasing societal inequality or economic growth based on fossil fuels, high greenhouse gas emissions and high nutrient loads result in decreased habitat quality and diminished biodiversity. Under the latter scenarios catches are high but they predominantly consist of lower-valued fish.

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The Galápagos Archipelago is home to a diverse range of marine bioregions due to the confluence of several cold and warm water currents, resulting in some of the most productive tropical marine ecosystems in the world. These ecosystems are strongly influenced by El Niño events which can reduce primary production by an order of magnitude, dramatically reducing energy available throughout the food web. Fisheries are an important component of the local economy, although artisanal and illegal overfishing have dramatically reduced the productivity of invertebrate and finfish resources in recent decades, resulting in reductions in catches for local fishers. The regionally-endemic sailfin grouper (Myctereoperca olfax), locally known as bacalao, was once the most important fished species in the Galápagos, but is now listed as vulnerable by the IUCN due to its limited range and dramatic declines in catch over time. It is unknown how reduction of this predatory species has affected ecosystem structure and function. In the absence of stock assessments, we used an estimate of unfished bacalao biomass from fishers' ecological knowledge along with unfished biomass estimates of other heavily exploited stocks-lobster (Panulirus penicillatus and P. gracilis) and sea cucumber (Isostichopus fuscus)-to create historical, unfished versions of existing modern day ecosystem models. We used the unfished and modern versions of the ecosystem models to test the ecosystem effects of bacalao exploitation at the Bolivar Channel, located in the cold, west upwelling bioregion of the archipelago during both El Niño and non El Niño years, and at Floreana Island, in the warmer, central bioregion. Fishers' ecological knowledge indicates that at present, the biomass of bacalao is at least seven times lower than when unfished. This reduced bacalao biomass is linked with a greatly reduced ecosystem role compared to when unfished, and ecosystem role is further reduced in El Niño years. Allowing bacalao populations to rebuild to at least half of unfished biomass would partially restore their role within these ecosystems, while also resulting in greater fisheries catches. Comparing ecosystem impacts caused by fishing and El Niño, fishing has had a greater negative impact on bacalao ecosystem role than regular El Niño events.

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Eutrophication is a leading cause of impairment of lentic water bodies throughout the world. To inhibit algal blooms and remove excess nutrients, a 10,000 m2 restoration project consisting of vegetation establishment and fish manipulation was conducted in the eutrophic bay of the Yantian Reservoir, southern China. Three Ecopath models were constructed to assess the recovery effects at an ecosystem level, and time series data were simulated to propose a fishery policy. During the restoration, 1) the redundant primary production flowing back to detritus decreased due to the increased predation of four stocked fish with different feeding habits; 2) the transfer efficiencies (TEs) through trophic levels increased due to the reinforced energy flows along the planktivorous, herbivorous, and molluscivorous food chains; 3) the groups that had the highest keystoneness shifted from carnivorous fish to invertivorous fish and omnivorous shrimp, indicating the shift of mixed trophic impacts from top-down to wasp-waist control; and 4) the changing indices of path length, flow fluxes, matter cycling, and network information showed that the restored system was more mature, developed, and organized than before. To sustain the long-term energy balance and functioning of the ecosystem, the maximum fishing yields (0.37-8.53 g/m2/year) were determined to maintain the relative biomass (close to 1) of stocked fish and wild tilapia by harvesting their annual production.

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Ecotracer is a tool in the Ecopath with Ecosim (EwE) software package used to simulate and analyze the transport of contaminants such as methylmercury or radiocesium through aquatic food webs. Ecotracer solves the contaminant dynamic equations simultaneously with the biomass dynamic equations in Ecosim/Ecospace. In this paper, we give a detailed description of the Ecotracer module and analyze the performance on two problems of differing complexity. Ecotracer was modified from previous versions to more accurately model contaminant excretion, and new numerical integration algorithms were implemented to increase accuracy and robustness. To test the mathematical robustness of the computational algorithm, Ecotracer was tested on a simple problem for which we know an analytical solution. These results demonstrated the effectiveness of the program numerics. A much more complex model, the release of the cesium radionuclide 137Cs from the Fukushima Dai-ichi nuclear accident, was also modeled and analyzed. A comparison of the Ecotracer results to sampled 137Cs measurements in the coastal ocean area around Fukushima show the promise of the tool but also highlight some important limitations.

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Network analysis is used to address diverse ecological, social, economic, and epidemiological questions, but few efforts have been made to combine these field-specific analyses into interdisciplinary approaches that effectively address how complex systems are interdependent and connected to one another. Identifying and understanding these cross-boundary connections improves natural resource management and promotes proactive, rather than reactive, decisions. This research had two main objectives; first, adapt the framework and approach of infectious disease network modeling so that it may be applied to the socio-ecological problem of spreading aquatic invasive species, and second, use this new coupled model to simulate the spread of the invasive Chinese mystery snail (Bellamya chinensis) in a reservoir network in Southeastern Nebraska, USA. The coupled model integrates an existing social network model of how anglers move on the landscape with new reservoir-specific ecological network models. This approach allowed us to identify 1) how angler movement among reservoirs aids in the spread of B. chinensis, 2) how B. chinensis alters energy flows within individual-reservoir food webs, and 3) a new method for assessing the spread of any number of non-native or invasive species within complex, social-ecological systems.

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Lake buffering zones play a special role in spatial arrangement of the lake watershed, and the wetland in buffering zones also is of great significance in basin ecological health and lake water environmental quality. Taking Zhushanhu wetland ecosystem in the area of lake buffering zone of Zhushan Bay, Lake Taihu as the research object, the biotic components were divided into 16 functional groups to construct the Ecopath with Ecosim (EWE) model, and the characteristics and state of the ecosystem and the interrelation between the functional groups were analyzed. The results showed that the range of effective trophic level in Zhushanhu wetland ecosystem was 1-3.72, tro-phic flows were mainly concentrated in the first 4 trophic levels, and most of the food chains started from submerged plants and detritus. The total energy conversion efficiency of the wetland ecosystem was 5.1%, being lower than the "1/10 law", indicating that the current energy conversion efficiency was low. The average transmission efficiency of material throughput in the ecosystem was 4.3%. The sum of all production in the ecosystem was 2496.66 t·km-2·a-1, and the total system throughput was 10145.2 t·km-2·a-1. The characteristic parameters of ecosystem showed that the current ecosystem was at the immature stage.

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Understanding ecosystem responses to global and local anthropogenic impacts is paramount to predicting future ecosystem states. We used an ecosystem modeling approach to investigate the independent and cumulative effects of fishing, marine protection, and ocean acidification on a coastal ecosystem. To quantify the effects of ocean acidification at the ecosystem level, we used information from the peer-reviewed literature on the effects of ocean acidification. Using an Ecopath with Ecosim ecosystem model for the Wellington south coast, including the Taputeranga Marine Reserve (MR), New Zealand, we predicted ecosystem responses under 4 scenarios: ocean acidification + fishing; ocean acidification + MR (no fishing); no ocean acidification + fishing; no ocean acidification + MR for the year 2050. Fishing had a larger effect on trophic group biomasses and trophic structure than ocean acidification, whereas the effects of ocean acidification were only large in the absence of fishing. Mortality by fishing had large, negative effects on trophic group biomasses. These effects were similar regardless of the presence of ocean acidification. Ocean acidification was predicted to indirectly benefit certain species in the MR scenario. This was because lobster (Jasus edwardsii) only recovered to 58% of the MR biomass in the ocean acidification + MR scenario, a situation that benefited the trophic groups lobsters prey on. Most trophic groups responded antagonistically to the interactive effects of ocean acidification and marine protection (46%; reduced response); however, many groups responded synergistically (33%; amplified response). Conservation and fisheries management strategies need to account for the reduced recovery potential of some exploited species under ocean acidification, nonadditive interactions of multiple factors, and indirect responses of species to ocean acidification caused by declines in calcareous predators.

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Anthropogenic stress has been shown to reduce coral coverage in ecosystems all over the world. A phase shift towards an algae-dominated system may accompany coral loss. In this case, the composition of the reef-associated fish assemblage will change and human communities relying on reef fisheries for income and food security may be negatively impacted. We present a case study based on the Raja Ampat Archipelago in Eastern Indonesia. Using a dynamic food web model, we simulate the loss of coral reefs with accompanied transition towards an algae-dominated state and quantify the likely change in fish populations and fisheries productivity. One set of simulations represents extreme scenarios, including 100% loss of coral. In this experiment, ecosystem changes are driven by coral loss itself and a degree of habitat dependency by reef fish is assumed. An alternative simulation is presented without assumed habitat dependency, where changes to the ecosystem are driven by historical observations of reef fish communities when coral is lost. The coral-algal phase shift results in reduced biodiversity and ecosystem maturity. Relative increases in the biomass of small-bodied fish species mean higher productivity on reefs overall, but much reduced landings of traditionally targeted species.

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