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6 november 2020, Contains fulltext : 226343.pdf (publisher's version ) (Open Access)

Despite the scientific consensus on the extinction crisis and its anthropogenic origin, the quantification of historical trends and of future scenarios of biodiversity and ecosystem services has been limited, due to the lack of inter-model comparisons and harmonized scenarios. Here, we present a multi-model analysis to assess the impacts of land-use and climate change from 1900 to 2050. During the 20th century provisioning services increased, but biodiversity and regulating services decreased. Similar trade-offs are projected for the coming decades, but they may be attenuated in a sustainability scenario. Future biodiversity loss from land-use change is projected to keep up with historical rates or reduce slightly, whereas losses due to climate change are projected to increase greatly. Renewed efforts are needed by governments to meet the 2050 vision of the Convention on Biological Diversity.

“Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.

The lake ecosystem model PCLake is a process-based model that was developed to simulate water quality based on ecological interactions in shallow, non-stratifying lakes in the temperate climate zone. Here we present PCLake+, which extends the PCLake model to cover a wide range of freshwater lakes that differ in stratification regime and climate-related processes. To this end, the model was extended with a hypolimnion layer that can be invoked and configured by forcing functions or by simple built-in empirical relationships that impose stratification. Further adjustments to the original PCLake model have been made with respect to the calculation of 1) light irradiation in the water column, 2) evaporation processes and 3) phenology of macrophytes. The simulation output of PCLake+ for different types of lakes complies well with generally accepted limnological knowledge, thus holding promise for future contributions to ecological theory and application to lakes around the globe.

Food production for a growing world population relies on application of fertilisers and pesticides on agricultural lands. However, these substances threaten surface water quality and thereby endanger valued ecosystem services such as drinking water supply, food production and recreational water use. Such deleterious effects do not merely arise on the local scale, but also on the regional scale through transport of substances as well as energy and biota across the catchment. Here we argue that aquatic ecosystem models can provide a process-based understanding of how these transports by water and organisms as vectors affect – and are affected by – ecosystem state and functioning in networks of connected lakes. Such a catchment scale approach is key to setting critical limits for the release of substances by agricultural practices and other human pressures on aquatic ecosystems. Thereby, water and food production and the trade-offs between them may be managed more sustainably.

To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land use and climate change on biodiversity and ecosystem services (i.e. nature's contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs) to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenarios selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem service models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modelling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modelling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

“Everything changes and nothing stands still” (Heraclitus). Here we review three major improvements to freshwater aquatic ecosystem models — and ecological models in general — as water quality scenario analysis tools towards a sustainable future. To tackle the rapid and deeply connected dynamics characteristic of the Anthropocene, we argue for the inclusion of eco-evolutionary, novel ecosystem and social-ecological dynamics. These dynamics arise from adaptive responses in organisms and ecosystems to global environmental change and act at different integration levels and different time scales. We provide reasons and means to incorporate each improvement into aquatic ecosystem models. Throughout this study we refer to Lake Victoria as a microcosm of the evolving novel social-ecological systems of the Anthropocene. The Lake Victoria case clearly shows how interlinked eco-evolutionary, novel ecosystem and social-ecological dynamics are, and demonstrates the need for transdisciplinary research approaches towards global sustainability.

To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land-use and climate change on biodiversity and ecosystem services (i.e., nature's contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs) – SSP1xRCP2.6, SSP3xRCP6.0, SSP5xRCP8.6 – to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenario selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem services models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modeling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modeling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

Algal blooms increasingly threaten lake and reservoir water quality at the global scale, caused by ongoing climate change and nutrient loading. To anticipate these algal blooms, models to project future algal blooms worldwide are required. Here we present the state-of-the-art in algal projection modelling and explore the requirements of an ideal algal projection model. Based on this, we identify current challenges and opportunities for such model development. Since most building blocks are present, we foresee that algal projection models for any lake on earth can be developed in the near future. Finally, we think that algal bloom projection models at a global scale will provide a valuable contribution to global policymaking, in particular with respect to SDG 6 (clean water and sanitation).

Quantitative evidence of sudden shifts in ecological structure and function in large shallow lakes is rare, even though they provide essential benefits to society. Such ‘regime shifts’ can be driven by human activities which degrade ecological stability including water level control (WLC) and nutrient loading. Interactions between WLC and nutrient loading on the long-term dynamics of shallow lake ecosystems are, however, often overlooked and largely underestimated, which has hampered the effectiveness of lake management. Here, we focus on a large shallow lake (Lake Chaohu) located in one of the most densely populated areas in China, the lower Yangtze River floodplain, which has undergone both WLC and increasing nutrient loading over the last several decades. We applied a novel methodology that combines consistent evidence from both paleolimnological records and ecosystem modeling to overcome the hurdle of data insufficiency and to unravel the drivers and underlying mechanisms in ecosystem dynamics. We identified the occurrence of two regime shifts: one in 1963, characterized by the abrupt disappearance of submerged vegetation, and another around 1980, with strong algal blooms being observed thereafter. Using model scenarios, we further disentangled the roles of WLC and nutrient loading, showing that the 1963 shift was predominantly triggered by WLC, whereas the shift ca. 1980 was attributed to aggravated nutrient loading. Our analysis also shows interactions between these two stressors. Compared to the dynamics driven by nutrient loading alone, WLC reduced the critical P loading and resulted in earlier disappearance of submerged vegetation and emergence of algal blooms by approximately 26 years and 10 years, respectively. Overall, our study reveals the significant role of hydrological regulation in driving shallow lake ecosystem dynamics, and it highlights the urgency of using multi-objective management criteria that includes ecological sustainability perspectives w

All over the world freshwater ecosystems like ponds, ditches and lakes suffer from nutrient-driven regime shifts from submerged plants to dominance by algae or free-floating plants. Although freshwaters are often connected and part of a network, most of our current knowledge on regime shifts comes from studies of isolated ecosystems. The few studies that have assessed the spatial manifestation of regime shifts overlooked the hydrological fact that the water flow through connected waters typically increases in the downstream direction. Here, we use a complex ecosystem model to show that this increase in flow does not lead to spatial differences in ecosystem state. We support these findings with a simple, analytically tractable, nutrient retention model on connected waterbodies. The model shows that all bodies have the same nutrient concentration despite spatial gradients in the flow of water as well as nutrients carried by the water. As a consequence, each connected waterbody is equally vulnerable to a regime shift, implying a regime shift to be system-wide. Furthermore, it appeared that each connected waterbody behaves the same as an isolated waterbody, implying that the vast body of theory on isolated systems, like alternative stable states theory, can still be useful for connected systems. Although these findings are violated when there is heterogeneity in lateral runoff or waterbody characteristics—leading to spatial differences in ecosystem state and therefore to differences in the vulnerability to a regime shift—they show that the typical downstream build-up of water flow does not necessarily lead to differences in ecological state, and thereby provide a basic concept to better understand the ecology of connected freshwaters.

The Netherlands is well-known for its extended networks of drainage ditches, with a total ditch length of about 300.000 km. Their main function is to enable agriculture by draining water. Nonetheless, ditches also have important ecological functions. They serve as ecological corridors and harbor a high biodiversity in which water plants play a crucial role. The last decades, the ecological quality of ditches is at stake. Enhanced nutrient inputs promoted the invasion by dense mats of free-floating plants like duckweed. Underneath these mats the water becomes dark and anoxic, which severely constrains aquatic life. In this thesis I developed new concepts to better understand, predict and combat the dominance by free-floating plants in ditches. The following questions are addressed. Are floating plants a self-stabilizing state - an alternative stable state - which would make it more difficult to combat floating-plant dominance (chapter 2)? Does it make sense to fight floating-plant dominance by reducing nitrogen (N) inputs to the ditches or will it lead to an invasion of floating plants that can fix N2 from the atmosphere (chapter 3)? What about spatial aspects, does the vulnerability of a ditch to floating plants depend on the position of a ditch in a polder, like its distance to the polder outlet (chapter 4)? To answer these questions, I used ecological models that predict the abundance of free-floating plants based on the competition for nutrients and light with other plants such as submerged plants, and where possible validated these models with field data. Starting from the ecosystem model PCDitch, I developed and combined models with different complexity to see how theoretical concepts, developed in minimal models, translate to the ecosystem level. Chapter 5 deals with a method that facilitates this up- and downscaling in model complexity. Are floating plants an alternative stable state? To answer this question I extended mechanistic resource competition theory

Dynamical ecosystem models are important tools that can help ecologists understand complex systems, and turn understanding into predictions of how these systems respond to external changes. This thesis revolves around PCLake, an integrated ecosystem model of shallow lakes that is used by both scientists and water quality managers to understand and predict eutrophication effects in shallow lake ecosystems. Shallow lakes provide some of the clearest examples of alternative stable states in natural systems. PCLake can be used to calculate the critical nutrient loading, that is, the nutrient loading where an abrupt regime shift occurs from a clear aquatic plant dominated state to a turbid phytoplankton dominated state, or vice versa. Four different aspects of modelling with PCLake are addressed in this thesis: (1) making the model better accessible for the modelling community, (2) improving the model, (3) developing scientific theory, and (4) exploring new applications for water quality management. Following a general introduction to the thesis in chapter 1, the Database Approach To Modelling (DATM) is introduced in chapter 2. DATM is invented to make dynamic models more accessible. The idea of DATM is that the mathematical equations of a model are stored in a database independently of program language and software specific information. From the database, the information can be automatically translated, augmented and compiled into working model code of various different modelling frameworks (software programs). In chapter 3 the weak link between ecosystem models and real ecosystems is discussed in relation to model calibration and improvement. In a previous stage PCLake has been calibrated using data of more than 40 lakes to obtain a best overall fit, which has greatly increased the scope of the model by making it suitable for more generalized studies on temperate shallow lakes. However, because of this calibration, adding missing functional components to the model at a, Vier verschillende aspecten van het modelleren met PCLake staan centraal in dit onderzoek: het ontsluiten van het model, het verbeteren van het model, het uitbouwen van ecologische theorie, en het uitwerken van een nieuwe toepassing in het waterkwaliteitsbeheer.

Complex lake ecosystem models can assist lake managers in developing management plans counteracting the eutrophication symptoms that are expected to be a result of climate change. We applied the ecological model PCLake based on 22 years of data from shallow, eutrophic Lake Søbygaard, Denmark and simulated multiple combinations of increasing temperatures (0-6 °C), reduced external nutrient loads (0%-98%) with and without internal phosphorus loading. Simulations suggest nitrogen to be the main limiting nutrient for primary production, reflecting ample phosphorus release from the sediment. The nutrient loading reduction scenarios predicted increased diatom dominance, accompanied by an increase in the zooplankton:phytoplankton biomass ratio. Simulations generally showed phytoplankton to benefit from a warmer climate and the fraction of cyanobacteria to increase. In the 6 °C warming scenario, a nutrient load reduction of as much as 60% would be required to achieve summer chlorophyll-a levels similar to those of the baseline scenario with present-day temperatures.

Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5–10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.

A principal aim of ecologists is to identify critical levels of environmental change beyond which ecosystems undergo radical shifts in their functioning. Both food-web theory and alternative stable states theory provide fundamental clues to mechanisms conferring stability to natural systems. Yet, it is unclear how the concept of food-web stability is associated with the resilience of ecosystems susceptible to regime change. Here, we use a combination of food web and ecosystem modelling to show that impending catastrophic shifts in shallow lakes are preceded by a destabilizing reorganization of interaction strengths in the aquatic food web. Analysis of the intricate web of trophic interactions reveals that only few key interactions, involving zooplankton, diatoms and detritus, dictate the deterioration of food-web stability. Our study exposes a tight link between food-web dynamics and the dynamics of the whole ecosystem, implying that trophic organization may serve as an empirical indicator of ecosystem resilience.

Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka–Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance

Alteration of natural flow regime is considered a major threat to biodiversity in river floodplain ecosystems. Measurements of quantitative relationships between flow regime change and biodiversity are, however, incomplete and inconclusive. This hampers the assessment of human impact on riverine floodplain wetlands in global biodiversity evaluations. We systematically reviewed the scientific literature and extracted information from existing data sets for a meta-analysis to unravel a general quantitative understanding of the ecological consequences of altered flow regimes. From 28 studies we retrieved both ecological and hydrological data. Relative mean abundance of original species (mean species abundance, MSA) and relative species richness were used as effect size measures of biodiversity intactness. The meta-analysis showed that alteration of a natural flow regime reduces the MSA by more than 50 % on average, and species richness by more than 25 %. Impact on species richness and abundance tends to be related to the degree of hydrological alteration. These results can be used in strategic quantitative assessments by incorporating the relationships into global models on environmental change and biodiversity such as GLOBIO-aquatic.

The amount of terrestrial particulate organic matter (t-POM) entering lakes is predicted to increase as a result of climate change. This may especially alter the structure and functioning of ecosystems in small, shallow lakes which can rapidly shift from a clear-water, macrophyte-dominated into a turbid, phytoplankton-dominated state. We used the integrative ecosystem model PCLake to predict how rising t-POM inputs affect the resilience of the clear-water state. PCLake links a pelagic and benthic food chain with abiotic components by a number of direct and indirect effects. We focused on three pathways (zoobenthos, zooplankton, light availability) by which elevated t-POM inputs (with and without additional nutrients) may modify the critical nutrient loading thresholds at which a clear-water lake becomes turbid and vice versa. Our model results show that (1) increased zoobenthos biomass due to the enhanced food availability results in more benthivorous fish which reduce light availability due to bioturbation, (2) zooplankton biomass does not change, but suspended t-POM reduces the consumption of autochthonous particulate organic matter which increases the turbidity, and (3) the suspended t-POM reduces the light availability for submerged macrophytes. Therefore, light availability is the key process that is indirectly or directly changed by t-POM input. This strikingly resembles the deteriorating effect of terrestrial dissolved organic matter on the light climate of lakes. In all scenarios, the resilience of the clear-water state is reduced thus making the turbid state more likely at a given nutrient loading. Therefore, our study suggests that rising t-POM input can add to the effects of climate warming making reductions in nutrient loadings even more urgent., The amount of terrestrial particulate organic matter (t-POM) entering lakes is predicted to increase as a result of climate change. This may especially alter the structure and functioning of ecosystems in small, shallow lakes which can rapidly shift from a clear-water, macrophyte-dominated into a turbid, phytoplankton-dominated state. We used the integrative ecosystem model PCLake to predict how rising t-POM inputs affect the resilience of the clear-water state. PCLake links a pelagic and benthic food chain with abiotic components by a number of direct and indirect effects. We focused on three pathways (zoobenthos, zooplankton, light availability) by which elevated t-POM inputs (with and without additional nutrients) may modify the critical nutrient loading thresholds at which a clear-water lake becomes turbid and vice versa. Our model results show that (1) increased zoobenthos biomass due to the enhanced food availability results in more benthivorous fish which reduce light availability due to bioturbation, (2) zooplankton biomass does not change, but suspended t-POM reduces the consumption of autochthonous particulate organic matter which increases the turbidity, and (3) the suspended t-POM reduces the light availability for submerged macrophytes. Therefore, light availability is the key process that is indirectly or directly changed by t-POM input. This strikingly resembles the deteriorating effect of terrestrial dissolved organic matter on the light climate of lakes. In all scenarios, the resilience of the clear-water state is reduced thus making the turbid state more likely at a given nutrient loading. Therefore, our study suggests that rising t-POM input can add to the effects of climate warming making reductions in nutrient loadings even more urgent.

Many lakes worldwide are experiencing great change due to eutrophication. Consequently, species composition changes, toxic algal blooms proliferate, and drinking water supplies dwindle. The transition to the deteriorated state can be catastrophic with an abrupt change from macrophyte to phytoplankton domination. This has been shown repeatedly in small lakes. Whether such alternative stable states also exist in large shallow lakes is less clear, however. Here we discuss the characteristics that give rise to alternative stable states in large shallow lakes either in the lake as whole or restricted to specific regions of the lake. We include the effect of lake size, spatial heterogeneity and internal connectivity on a lake's response along the eutrophication axis. As a case study, we outline the eutrophication history of Lake Taihu (China) and illustrate how lake size, spatial heterogeneity and internal connectivity can explain the observed spatial presence of different states. We discuss whether these states can be alternatively stable by comparing the data with model output (PCLake). These findings are generalised for other large, shallow lakes. We conclude that locations with prevailing size effects generally lack macrophytes; and, therefore, alternative stable states are unlikely to occur there. However, most large shallow lakes have macrophytes whose presence remains unexplained when only size effect is taken into account. By including spatial heterogeneity in the analysis, the presence of macrophytes and alternative stable states in large shallow lakes is better understood. Finally, internal connectivity is important because a high internal connectivity reduces the stability of alternative states.

Many lakes worldwide are experiencing great change due to eutrophication. Consequently, species composition changes, toxic algal blooms proliferate, and drinking water supplies dwindle. The transition to the deteriorated state can be catastrophic with an abrupt change from macrophyte to phytoplankton domination. This has been shown repeatedly in small lakes. Whether such alternative stable states also exist in large shallow lakes is less clear, however. Here we discuss the characteristics that give rise to alternative stable states in large shallow lakes either in the lake as whole or restricted to specific regions of the lake. We include the effect of lake size, spatial heterogeneity and internal connectivity on a lake's response along the eutrophication axis. As a case study, we outline the eutrophication history of Lake Taihu (China) and illustrate how lake size, spatial heterogeneity and internal connectivity can explain the observed spatial presence of different states. We discuss whether these states can be alternatively stable by comparing the data with model output (PCLake). These findings are generalised for other large, shallow lakes. We conclude that locations with prevailing size effects generally lack macrophytes; and, therefore, alternative stable states are unlikely to occur there. However, most large shallow lakes have macrophytes whose presence remains unexplained when only size effect is taken into account. By including spatial heterogeneity in the analysis, the presence of macrophytes and alternative stable states in large shallow lakes is better understood. Finally, internal connectivity is important because a high internal connectivity reduces the stability of alternative states.

Lake Victoria (in East Africa) is the world's second largest fresh-water system. Over the past century the ecosystem has undergone drastic changes. Some 30 years after the introduction of Nile perch and tilapia in the 1950s, the highly diverse community of native haplochromines collapsed, leaving a system dominated by only four species: the native cyprinid dagaa and shrimp Caridina nilotica, as well as the introduced Nile perch and Nile tilapia. More recently, an unexpected resurgence of haplochromines has been reported. To better grasp these changes in terms of ecosystem functioning and of changes in growth of trophic groups, we created mass-balances of the food web near Mwanza (Tanzania) before, during and after the Nile perch boom (1977, 1987 and 2005), using the application ECOPATH. We connected these mass-balances with a dynamic model assuming linear trends in net growth rates of the trophic groups. Our analysis suggests that the Nile perch boom initially altered the biomass distribution over trophic levels. Also, results indicate that not only fishing but also changes at the detritivores' trophic level might have played an important role in driving changes in the system. Both the mass-balances and the dynamic model connecting them reveal that after a major distortion during the Nile perch boom, the biomass distribution over the main trophic levels had largely recovered to its original state by 2005. However, no such return appeared in terms of community structure. Biodiversity in the new state is dramatically lower, consisting of introduced species and a few native surviving species. We conclude that at an aggregate level Lake Victoria's ecosystem has proved to be resilient in the sense that its overall trophic structure has apparently recovered after a major perturbation. By contrast, its intricate functional structure and associated biodiversity have proven to be fragile and seem unlikely to recover., Lake Victoria (in East Africa) is the world's second largest fresh-water system. Over the past century the ecosystem has undergone drastic changes. Some 30 years after the introduction of Nile perch and tilapia in the 1950s, the highly diverse community of native haplochromines collapsed, leaving a system dominated by only four species: the native cyprinid dagaa and shrimp Caridina nilotica, as well as the introduced Nile perch and Nile tilapia. More recently, an unexpected resurgence of haplochromines has been reported. To better grasp these changes in terms of ecosystem functioning and of changes in growth of trophic groups, we created mass-balances of the food web near Mwanza (Tanzania) before, during and after the Nile perch boom (1977, 1987 and 2005), using the application ECOPATH. We connected these mass-balances with a dynamic model assuming linear trends in net growth rates of the trophic groups. Our analysis suggests that the Nile perch boom initially altered the biomass distribution over trophic levels. Also, results indicate that not only fishing but also changes at the detritivores' trophic level might have played an important role in driving changes in the system. Both the mass-balances and the dynamic model connecting them reveal that after a major distortion during the Nile perch boom, the biomass distribution over the main trophic levels had largely recovered to its original state by 2005. However, no such return appeared in terms of community structure. Biodiversity in the new state is dramatically lower, consisting of introduced species and a few native surviving species. We conclude that at an aggregate level Lake Victoria's ecosystem has proved to be resilient in the sense that its overall trophic structure has apparently recovered after a major perturbation. By contrast, its intricate functional structure and associated biodiversity have proven to be fragile and seem unlikely to recover.

Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing importance of numerical aquatic ecosystem models while also noting the difficulties, up until now, of the aquatic scientific community to make significant advances in these models during the past two decades. Through a common forum for aquatic ecosystem modellers we aim to (i) advance collaboration within the aquatic ecosystem modelling community, (ii) enable increased use of models for research, policy and ecosystem-based management, (iii) facilitate a collective framework using common (standardised) code to ensure that model development is incremental, (iv) increase the transparency of model structure, assumptions and techniques, (v) achieve a greater understanding of aquatic ecosystem functioning, (vi) increase the reliability of predictions by aquatic ecosystem models, (vii) stimulate model inter-comparisons including differing model approaches, and (viii) avoid ‘re-inventing the wheel’, thus accelerating improvements to aquatic ecosystem models. We intend to achieve this as a community that fosters interactions amongst ecologists and model developers. Further, we outline scientific topics recently articulated by the scientific community, which lend themselves well to being addressed by integrative modelling approaches and serve to motivate the progress and implementation of an open source model framework., Here, we communicate a point of departure in the development of aquatic ecosystem models, namely a new community-based framework, which supports an enhanced and transparent union between the collective expertise that exists in the communities of traditional ecologists and model developers. Through a literature survey, we document the growing importance of numerical aquatic ecosystem models while also noting the difficulties, up until now, of the aquatic scientific community to make significant advances in these models during the past two decades. Through a common forum for aquatic ecosystem modellers we aim to (i) advance collaboration within the aquatic ecosystem modelling community, (ii) enable increased use of models for research, policy and ecosystem-based management, (iii) facilitate a collective framework using common (standardised) code to ensure that model development is incremental, (iv) increase the transparency of model structure, assumptions and techniques, (v) achieve a greater understanding of aquatic ecosystem functioning, (vi) increase the reliability of predictions by aquatic ecosystem models, (vii) stimulate model inter-comparisons including differing model approaches, and (viii) avoid ‘re-inventing the wheel’, thus accelerating improvements to aquatic ecosystem models. We intend to achieve this as a community that fosters interactions amongst ecologists and model developers. Further, we outline scientific topics recently articulated by the scientific community, which lend themselves well to being addressed by integrative modelling approaches and serve to motivate the progress and implementation of an open source model framework.

A feature of meromictic lakes is that several physicochemical and biological gradients affect the vertical distribution of different organisms. The vertical stratification of physical, chemical and biological components in saline, fishless meromictic lakes Shira and Shunet (Siberia, Russia) is quite different mainly because both mean depth and maximum depth of lakes differ as well as their salinity levels differ. The chemocline of the Lake Shira, as in many meromictic lakes, is inhabited by bacterial community consisting of purple sulphur and heterotrophic bacteria. As the depth of the chemocline is variable, the bacterial community does not attain high densities. The mixolimnion in Lake Shira, which is thermally stratified in summer, also creates different habitat for various species. The distribution of phytoplankton is non-uniform with its biomass peak in the metalimnion. The distribution of zooplankton is also heterogeneous with rotifers and juvenile copepods inhabiting the warmer epilimnion and older copepods found in the cold but oxic hypolimnion. The amphipod Gammarus lacustris which can be assigned to the higher trophic link in the fishless lake’s ecosystem, such as Lake Shira, is also distributed non-uniformly, with its peak density generally observed in the thermocline region. The chemocline in Lake Shunet is located at the depth of 5 m, and unlike in Lake Shira, due to a sharp salinity gradient between the mixolimnion and monimolimnion, this depth is very stable. The mixolimnion in Lake Shunet is relatively shallow and the chemocline is inhabited by (1) an extremely dense bacterial community; (2) a population of Cryptomonas sp.; and (3) ciliate community comprising several species. As the mixolimnion of Lake Shunet is not thermally stratified for long period, the phytoplankton and zooplankton populations are not vertically stratified. The gammarids, however, tend to concentrate in a narrow layer located 1–2 m above the chemocline. We believe that in addit, A feature of meromictic lakes is that several physicochemical and biological gradients affect the vertical distribution of different organisms. The vertical stratification of physical, chemical and biological components in saline, fishless meromictic lakes Shira and Shunet (Siberia, Russia) is quite different mainly because both mean depth and maximum depth of lakes differ as well as their salinity levels differ. The chemocline of the Lake Shira, as in many meromictic lakes, is inhabited by bacterial community consisting of purple sulphur and heterotrophic bacteria. As the depth of the chemocline is variable, the bacterial community does not attain high densities. The mixolimnion in Lake Shira, which is thermally stratified in summer, also creates different habitat for various species. The distribution of phytoplankton is non-uniform with its biomass peak in the metalimnion. The distribution of zooplankton is also heterogeneous with rotifers and juvenile copepods inhabiting the warmer epilimnion and older copepods found in the cold but oxic hypolimnion. The amphipod Gammarus lacustris which can be assigned to the higher trophic link in the fishless lake’s ecosystem, such as Lake Shira, is also distributed non-uniformly, with its peak density generally observed in the thermocline region. The chemocline in Lake Shunet is located at the depth of 5 m, and unlike in Lake Shira, due to a sharp salinity gradient between the mixolimnion and monimolimnion, this depth is very stable. The mixolimnion in Lake Shunet is relatively shallow and the chemocline is inhabited by (1) an extremely dense bacterial community; (2) a population of Cryptomonas sp.; and (3) ciliate community comprising several species. As the mixolimnion of Lake Shunet is not thermally stratified for long period, the phytoplankton and zooplankton populations are not vertically stratified. The gammarids, however, tend to concentrate in a narrow layer located 1–2 m above the chemocline. We believe that in addit

A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others (‘reinventing the wheel’). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available (‘having tunnel vision’). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and trait-based models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its ‘leading principle’, there are many opportunities for combining approaches. We take the point of view that a single ‘right’ approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view, A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others (‘reinventing the wheel’). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available (‘having tunnel vision’). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and trait-based models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its ‘leading principle’, there are many opportunities for combining approaches. We take the point of view that a single ‘right’ approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view

A one-dimensional ecological model of the meromictic brackish Lake Shira (Russia, Khakasia) was developed. The model incorporates state-of-the-art knowledge about the functioning of the lake ecosystem using the most recent field observations and ideas from PCLake, a general ecosystem model of shallow freshwater lakes. The model of Lake Shira presented here takes into account the vertical dynamics of biomasses of the main species of algae, zooplankton and microbial community, as well as the dynamics of oxygen, detritus, nutrients and hydrogen sulphide from spring to autumn. Solar radiation, temperature and diffusion are modelled using real meteorological data. The parameters of the model were calibrated to the field data, after applying different methods of sensitivity analysis to the model. The resulting patterns of phytoplankton and nutrients dynamics show a good qualitative and quantitative agreement with the field observations during the whole summer season. Results are less satisfactory with respect to the vertical distribution of zooplankton biomass. We hypothesize that this is due to the fact that the current model does not take the sex and age structure of zooplankton into account. The dynamics of oxygen, hydrogen sulphide and the modelled positions of the chemocline and thermocline are again in good agreement with field data. This resemblance confirms the validity of the approach we took in the model regarding the main physical, chemical and ecological processes. This general model opens the way for checking various hypotheses on the functioning of the Lake Shira ecosystem in future investigations and for analysing options for management of this economically important lake., A one-dimensional ecological model of the meromictic brackish Lake Shira (Russia, Khakasia) was developed. The model incorporates state-of-the-art knowledge about the functioning of the lake ecosystem using the most recent field observations and ideas from PCLake, a general ecosystem model of shallow freshwater lakes. The model of Lake Shira presented here takes into account the vertical dynamics of biomasses of the main species of algae, zooplankton and microbial community, as well as the dynamics of oxygen, detritus, nutrients and hydrogen sulphide from spring to autumn. Solar radiation, temperature and diffusion are modelled using real meteorological data. The parameters of the model were calibrated to the field data, after applying different methods of sensitivity analysis to the model. The resulting patterns of phytoplankton and nutrients dynamics show a good qualitative and quantitative agreement with the field observations during the whole summer season. Results are less satisfactory with respect to the vertical distribution of zooplankton biomass. We hypothesize that this is due to the fact that the current model does not take the sex and age structure of zooplankton into account. The dynamics of oxygen, hydrogen sulphide and the modelled positions of the chemocline and thermocline are again in good agreement with field data. This resemblance confirms the validity of the approach we took in the model regarding the main physical, chemical and ecological processes. This general model opens the way for checking various hypotheses on the functioning of the Lake Shira ecosystem in future investigations and for analysing options for management of this economically important lake.

There is a vast body of knowledge that eutrophication of lakes may cause algal blooms. Among lakes, shallow lakes are peculiar systems in that they typically can be in one of two contrasting (equilibrium) states that are self-stabilizing: a ‘clear’ state with submerged macrophytes or a ‘turbid’ state dominated by phytoplankton. Eutrophication may cause a switch from the clear to the turbid state, if the P loading exceeds a critical value. The ecological processes governing this switch are covered by the ecosystem model PCLake, a dynamic model of nutrient cycling and the biota in shallow lakes. Here we present an extensive analysis of the model, using a three-step procedure. (1) A sensitivity analysis revealed the key parameters for the model output. (2) These parameters were calibrated on the combined data on total phosphorus, chlorophyll-a, macrophytes cover and Secchi depth in over 40 lakes. This was done by a Bayesian procedure, giving a weight to each parameter setting based on its likelihood. (3) These weights were used for an uncertainty analysis, applied to the switchpoints (critical phosphorus loading levels) calculated by the model. The model was most sensitive to changes in water depth, P and N loading, retention time and lake size as external input factors, and to zooplankton growth rate, settling rates and maximum growth rates of phytoplankton and macrophytes as process parameters. The results for the ‘best run’ showed an acceptable agreement between model and data and classified nearly all lakes to which the model was applied correctly as either ‘clear’ (macrophyte-dominated) or ‘turbid’ (phytoplankton-dominated). The critical loading levels for a standard lake showed about a factor two uncertainty due to the variation in the posterior parameter distribution. This study calculates in one coherent analysis uncertainties in critical phosphorus loading, a parameter that is of great importance to water quality managers., There is a vast body of knowledge that eutrophication of lakes may cause algal blooms. Among lakes, shallow lakes are peculiar systems in that they typically can be in one of two contrasting (equilibrium) states that are self-stabilizing: a ‘clear’ state with submerged macrophytes or a ‘turbid’ state dominated by phytoplankton. Eutrophication may cause a switch from the clear to the turbid state, if the P loading exceeds a critical value. The ecological processes governing this switch are covered by the ecosystem model PCLake, a dynamic model of nutrient cycling and the biota in shallow lakes. Here we present an extensive analysis of the model, using a three-step procedure. (1) A sensitivity analysis revealed the key parameters for the model output. (2) These parameters were calibrated on the combined data on total phosphorus, chlorophyll-a, macrophytes cover and Secchi depth in over 40 lakes. This was done by a Bayesian procedure, giving a weight to each parameter setting based on its likelihood. (3) These weights were used for an uncertainty analysis, applied to the switchpoints (critical phosphorus loading levels) calculated by the model. The model was most sensitive to changes in water depth, P and N loading, retention time and lake size as external input factors, and to zooplankton growth rate, settling rates and maximum growth rates of phytoplankton and macrophytes as process parameters. The results for the ‘best run’ showed an acceptable agreement between model and data and classified nearly all lakes to which the model was applied correctly as either ‘clear’ (macrophyte-dominated) or ‘turbid’ (phytoplankton-dominated). The critical loading levels for a standard lake showed about a factor two uncertainty due to the variation in the posterior parameter distribution. This study calculates in one coherent analysis uncertainties in critical phosphorus loading, a parameter that is of great importance to water quality managers.

To study the interaction between species- and ecosystem-level impacts of climate change, we focus on the question of how climate-induced shifts in key species affect the positive feedback loops that lock shallow lakes either in a transparent, macrophyte-dominated state or, alternatively, in a turbid, phytoplankton-dominated state. We hypothesize that climate warming will weaken the resilience of the macrophyte-dominated clear state. For the turbid state, we hypothesize that climate warming and climate-induced eutrophication will increase the dominance of cyanobacteria. Climate change will also affect shallow lakes through a changing hydrology and through climate change-induced eutrophication. We study these phenomena using two models, the full ecosystem model PCLake and a minimal dynamic model of lake phosphorus dynamics. Quantitative predictions with the complex model show that changes in nutrient loading, hydraulic loading and climate warming can all lead to shifts in ecosystem state. The minimal model helped in interpreting the non-linear behaviour of the complex model. The main output parameters of interest for water quality managers are the critical nutrient loading at which the system will switch from clear to turbid and the much lower critical nutrient loading – due to hysteresis – at which the system switches back. Another important output parameter is the chlorophyll-a level in the turbid state. For each of these three output parameters we performed a sensitivity analysis to further understand the dynamics of the complex model PCLake. This analysis showed that our model results are most sensitive to changes in temperature-dependence of cyanobacteria, planktivorous fish and zooplankton. We argue that by combining models at various levels of complexity and looking at multiple aspects of climate changes simultaneously we can develop an integrated view of the potential impact of climate change on freshwater ecosystems., To study the interaction between species- and ecosystem-level impacts of climate change, we focus on the question of how climate-induced shifts in key species affect the positive feedback loops that lock shallow lakes either in a transparent, macrophyte-dominated state or, alternatively, in a turbid, phytoplankton-dominated state. We hypothesize that climate warming will weaken the resilience of the macrophyte-dominated clear state. For the turbid state, we hypothesize that climate warming and climate-induced eutrophication will increase the dominance of cyanobacteria. Climate change will also affect shallow lakes through a changing hydrology and through climate change-induced eutrophication. We study these phenomena using two models, the full ecosystem model PCLake and a minimal dynamic model of lake phosphorus dynamics. Quantitative predictions with the complex model show that changes in nutrient loading, hydraulic loading and climate warming can all lead to shifts in ecosystem state. The minimal model helped in interpreting the non-linear behaviour of the complex model. The main output parameters of interest for water quality managers are the critical nutrient loading at which the system will switch from clear to turbid and the much lower critical nutrient loading – due to hysteresis – at which the system switches back. Another important output parameter is the chlorophyll-a level in the turbid state. For each of these three output parameters we performed a sensitivity analysis to further understand the dynamics of the complex model PCLake. This analysis showed that our model results are most sensitive to changes in temperature-dependence of cyanobacteria, planktivorous fish and zooplankton. We argue that by combining models at various levels of complexity and looking at multiple aspects of climate changes simultaneously we can develop an integrated view of the potential impact of climate change on freshwater ecosystems.

Shallow lakes typically can be in one of two contrasting states: a clear state with submerged macrophytes or a turbid state dominated by phytoplankton. Eutrophication may cause a switch from the clear to the turbid state, if the phosphorus loading exceeds a critical value. Recovery of the clear state is difficult as the critical loading for the switch back during oligotrophication is often lower. A system of interacting ecological processes makes both states stabilize themselves causing the observed hysteresis. The ecosystem of shallow lakes is analysed with PCLake, a dynamic model of nutrient cycling and biota – including phytoplankton, macrophytes and a simplified food web. The model was used to calculate the switchpoints in terms of critical phosphorus loading levels for a number of lake types. It turned out that the predicted critical phosphorus loadings differ per lake type, e.g. they decrease with lake area, mean depth and retention time, increase with relative marsh area and fishing intensity, and differ per sediment type. The findings were grossly comparable with empirical evidence. These outcomes were also used to build a metamodel. The results may be useful for lake management, by comparing the critical loadings for a given lake with the actual loading. If the actual loading clearly exceeds the upper switchpoint, nutrient reduction measures are recommended. If the loading approaches the upper switchpoint, or is in the intermediate range, a manager could try to increase the critical loading values of the lake, e.g. by hydromorphological measures. If the loading is well between the two switchpoints, an alternative is to force a switch by direct food web management., Shallow lakes typically can be in one of two contrasting states: a clear state with submerged macrophytes or a turbid state dominated by phytoplankton. Eutrophication may cause a switch from the clear to the turbid state, if the phosphorus loading exceeds a critical value. Recovery of the clear state is difficult as the critical loading for the switch back during oligotrophication is often lower. A system of interacting ecological processes makes both states stabilize themselves causing the observed hysteresis. The ecosystem of shallow lakes is analysed with PCLake, a dynamic model of nutrient cycling and biota – including phytoplankton, macrophytes and a simplified food web. The model was used to calculate the switchpoints in terms of critical phosphorus loading levels for a number of lake types. It turned out that the predicted critical phosphorus loadings differ per lake type, e.g. they decrease with lake area, mean depth and retention time, increase with relative marsh area and fishing intensity, and differ per sediment type. The findings were grossly comparable with empirical evidence. These outcomes were also used to build a metamodel. The results may be useful for lake management, by comparing the critical loadings for a given lake with the actual loading. If the actual loading clearly exceeds the upper switchpoint, nutrient reduction measures are recommended. If the loading approaches the upper switchpoint, or is in the intermediate range, a manager could try to increase the critical loading values of the lake, e.g. by hydromorphological measures. If the loading is well between the two switchpoints, an alternative is to force a switch by direct food web management.

Many lakes have experienced a transition from a clear into a turbid state without macrophyte growth due to eutrophication. There are several measures by which nitrogen (N) and phosphorus (P) concentrations in the surface water can be reduced. We used the shallow lake model PCLake to evaluate the effects of three measures (reducing external nutrient loading, increasing relative marsh area, and increasing exchange rate between open water and marsh) on water quality improvement. Furthermore, the contribution of different retention processes was calculated. Settling and burial contributed more to nutrient retention than denitrification. The model runs for a typical shallow lake in The Netherlands showed that after increasing relative marsh area to 50%, total phosphorous (TP) concentration in the surface water was lower than the Maximum Admissible Risk (MAR, a Dutch government water quality standard) level, in contrast to total nitrogen (TN) concentration. The MAR levels could also be achieved by reducing N and P load. However, reduction of nutrient concentrations to MAR levels did not result in a clear lake state with submerged vegetation. Only a combination of a more drastic reduction of the present nutrient loading, in combination with a relatively large marsh cover (approximately 50%) would lead to such a clear state. We therefore concluded that littoral marsh areas can make a small but significant contribution to lake recovery., Many lakes have experienced a transition from a clear into a turbid state without macrophyte growth due to eutrophication. There are several measures by which nitrogen (N) and phosphorus (P) concentrations in the surface water can be reduced. We used the shallow lake model PCLake to evaluate the effects of three measures (reducing external nutrient loading, increasing relative marsh area, and increasing exchange rate between open water and marsh) on water quality improvement. Furthermore, the contribution of different retention processes was calculated. Settling and burial contributed more to nutrient retention than denitrification. The model runs for a typical shallow lake in The Netherlands showed that after increasing relative marsh area to 50%, total phosphorous (TP) concentration in the surface water was lower than the Maximum Admissible Risk (MAR, a Dutch government water quality standard) level, in contrast to total nitrogen (TN) concentration. The MAR levels could also be achieved by reducing N and P load. However, reduction of nutrient concentrations to MAR levels did not result in a clear lake state with submerged vegetation. Only a combination of a more drastic reduction of the present nutrient loading, in combination with a relatively large marsh cover (approximately 50%) would lead to such a clear state. We therefore concluded that littoral marsh areas can make a small but significant contribution to lake recovery.