Wolf M. Mooij

Worldwide, anthropogenic activities threaten surface water quality by aggravating eutrophication and increasing total nitrogen to total phosphorus (TN:TP) ratios. In hydrologically connected systems, water quality management may benefit from in-ecosystem nutrient retention by preventing nutrient transport to downstream systems. However, nutrient retention may also alter TN:TP ratios with unforeseen consequences for downstream water quality. Here, we aim to increase understanding of how nutrient retention may influence nutrient transport to downstream systems to improve long-term water quality management. We analyzed lake ecosystem state, in-lake nutrient retention, and nutrient transport (ratios) for 3482 Chinese lakes using the lake process-based ecosystem model PCLake+. We compared a low climate change and sustainability-, and a high climate change and economy-focused scenario for 2050 against 2012. In both scenarios, the effect of nutrient input reduction outweighs that of temperature rise, resulting in more lakes with good ecological water quality (i.e., macrophyte-dominated) than in 2012. Generally, the sustainability-focused scenario shows a more promising future for water quality than the economy-focused scenario. Nevertheless, most lakes remain phytoplankton-dominated. The shift to more macrophyte-dominated lakes in 2050 is accompanied by higher nutrient retention fractions and less nutrient transport to downstream waterbodies. In-lake nutrient retention also alters the water's TN:TP ratio, depending on the inflow TN:TP ratio and the ecosystem state. In 2050 higher TN:TP ratios are expected in the outflows of lakes than in 2012, especially for the sustainability-focused scenario with strong TP loading reduction. However, the downstream impact of increased TN:TP ratios depends on actual nutrient loadings and the limiting nutrient in the receiving system. We conclude that nutrient input reductions, improved water quality, higher in-lake nutrient retention fractions, and lower nutrient transport to downstream waterbodies go hand in hand. Therefore, water quality management could benefit even more from nutrient pollution reduction than one would expect at first sight.

Eutrophication poses a threat to lake ecosystem services provisioning worldwide. When eutrophic lakes are connected to other water systems, either through water flows, or through organismal movement and dispersal, their excess nutrients affect nearby lakes too. Understanding nutrient transport dynamics in lake meta-ecosystems is not trivial, as it encompasses the complexity of ecosystems themselves (i.e., food web dynamics, nutrient cycling) and the transport between ecosystems. Hitherto, it remains unknown how heterogeneity in lake meta-ecosystems affects their ecological resilience. We argue that scientists and water managers would benefit from the use of meta-ecosystem models while unravelling meta-ecosystem complexity. To this end, we converted lake ecosystem model PCLake+ into lake meta-ecosystem model PCLakeS+. We showed that the spatial configuration of a lake meta-ecosystem influences its ecological dynamics, and that nutrient transport depends heavily on food web processes. We conclude that PCLakeS+ is suitable for exploring meta-ecosystem concepts for science and water management.

Freshwater ecosystems are exceptionally rich in biodiversity and provide essential benefits to people. Yet they are disproportionately threatened compared to terrestrial and marine systems and remain underrepresented in the scenarios and models used for global environmental assessments. The Nature Futures Framework (NFF) has recently been proposed to advance the contribution of scenarios and models for environmental assessments. This framework places the diverse relationships between people and nature at its core, identifying three value perspectives as points of departure: Nature for Nature, Nature for Society, and Nature as Culture. We explore how the NFF may be implemented for improved assessment of freshwater ecosystems. First, we outline how the NFF and its main value perspectives can be translated to freshwater systems and explore what desirable freshwater futures would look like from each of the above perspectives. Second, we review scenario strategies and current models to examine how freshwater modelling can be linked to the NFF in terms of its aims and outcomes. In doing so, we also identify which aspects of the NFF framework are not yet captured in current freshwater models and suggest possible ways to bridge them. Our analysis provides future directions for a more holistic freshwater model and scenario development and demonstrates how society can benefit from freshwater modelling efforts that are integrated with the value-perspectives of the NFF.

Ecology is usually very good in making descriptive explanations of what is observed, but is often unable to make predictions of the response of ecosystems to change. This has implications in a human-dominated world where a suite of anthropogenic stresses are threatening the resilience and functioning of ecosystems that sustain mankind through a range of critical regulating and supporting services. In ecosystems, cause-and-effect relationships are difficult to elucidate because of complex networks of negative and positive feedbacks. Therefore, being able to effectively predict when and where ecosystems could pass into different (and potentially unstable) new states is vitally important under rapid global change. Here, we argue that such better predictions may be reached if we focus on organisms instead of species, because organisms are the principal biotic agents in ecosystems that react directly on changes in their environment. Several studies show that changes in ecosystems may be accurately described as the result of changes in organisms and their interactions. Organism-based theories are available that are simple and derived from first principles, but allow many predictions. Of these we discuss Trait-based Ecology, Agent Based Models, and Maximum Entropy Theory of Ecology and show that together they form a logical sequence of approaches that allow organism-based studies of ecological communities. Combining and extending them makes it possible to predict the spatiotemporal distribution of groups of organisms in terms of how metabolic energy is distributed over areas, time, and resources. We expect that this “Organism-based Ecology” (OE) ultimately will improve our ability to predict ecosystem dynamics.

Nutrients are essential resources for food production but are used inefficiently, and thereby they pollute inland and coastal waters and are lost into the oceans. Nutrient conservation by retention and consecutive reuse would prevent nutrient losses to the atmosphere and downstream ecosystems. We present Smart Nutrient Retention Networks (SNRNs) as a novel management approach to achieve nutrient conservation across networks of connected waterbodies through strategic water quality management. To present the key features of SNRNs, we review existing knowledge of nutrient retention processes in inland waters, water quality management options for nutrient conservation, and nutrient retention models to develop SNRNs. We argue that successful nutrient conservation, even at a local level, through SNRN management strategies requires clearly formulated goals and catchment-wide system understanding. Waterbody characteristics, such as hydraulic residence time and the presence of macrophytes, shape local nutrient retention with potential network-wide cascading effects of improved water quality and are therefore key targets of SNRN management strategies. Nutrient retention models that include the self-reinforcing feedback loop of ecological water quality, nutrient retention, and nutrient loading in networks of inland waters in relation to management options can support the development of SNRNs. We conclude that SNRNs can contribute to sustainable use of nutrients in human food production.

Achieving global sustainability goals requires most people and societies to fundamentally revisit their relationship with nature. New approaches are called for to guide change processes towards sustainable futures that embrace the plurality of people’s desired relationships with nature. This paper presents a novel approach to exploring desirable futures for nature and people that was developed through an application in Nationaal Park Hollandse Duinen in the Netherlands. This new national park is developed bottom-up by a diverse group of actors reshaping their interactions with each other and with nature. Our approach, co-designed with key stakeholders of the national park, engages with a new pluralistic framework for human-nature relationships presented by the IPBES task force on scenarios and models to catalyze the development of nature-centered scenarios. We integrated this Nature Futures Framework with the Three Horizons Framework in a participatory workshop process designed to bring people’s diverse relationships with nature to the fore, and jointly envision desirable futures and the pathways to get there. We present a methodology to analyze and compare the visions and assess their potential contribution to the SDGs. We summarize the results of the application in Nationaal Park Hollandse Duinen and reflect on lessons learned. The approach successfully engaged participants in joint exploration of desirable futures for the national park based on their plural perspectives on human-nature relationships. We see much potential for its applications to support change processes in various social-ecological contexts toward more sustainable futures for nature and people.

Protected areas are the cornerstone of nature conservation, although this approach has not prevented the current biodiversity crisis. In addition, the approach leads to the suggestion that only organisms living within these areas constitute nature. Nature, however, cannot be spatially constrained, and the same holds for human influence on nature. In this essay we develop an area-wide and human-inclusive vision of nature conservation into a new approach for national parks that we call National Park 3.0 (NP 3.0). The concept is rooted in a re-evaluation of human-nature relations sensu the Nature Futures Framework developed under IPBES. Moreover, we note that ‘landscape’ has always been a social-ecological concept since the term was coined by 17th century Dutch painters. Finally, we note that nature and human infrastructure are deeply entangled at multiple spatial scales in modern landscapes. We define NP 3.0 spatially by the contours of a landscape that is recognizable by people and has geomorphological and ecological coherence. We relate NP 3.0 to other initiatives for restoring biodiversity and provide a conceptual design for NP 3.0. Throughout this essay we use Nationaal Park Hollandse Duinen as a case study where NP 3.0 is worked out in practice.

Ongoing anthropogenic and climatic pressures on inland waters have made water quality management a challenge of the 21st century. A holistic catchment-scale approach to water management which includes stakeholder participation will be a key in maintaining lake health. A first step toward community engagement is to bolster environmental literacy on lake management, ecology, and eutrophication concepts of stakeholders now and in future generations. However, communicating with nonwater professionals about effects of pollution on water quality and catchment-scale interactions across space and time can be difficult. Here, we present “Flipping Lakes,” a games-based method for lake professionals to communicate and educate about catchment-level water quality management to diverse audiences. In Flipping Lakes, the players take on the role of water managers in a catchment and are tasked to prevent a lake from “flipping” from a clear to a turbid state. During the game, the catchment slowly becomes polluted by a range of sources of which the effects are exacerbated by societal or climatic scenarios. Players need to implement measures while taking into consideration the intrinsic properties of the catchment in order to keep lakes clean. The game was tested with a diverse range of user groups and was well-received. With its entertaining and accessible content, Flipping Lakes can lower communication barriers and increase understanding of difficult water quality concepts. The game is highly customizable, making it applicable to a variety of settings to support education and engagement of stakeholders and the broader community in order to address local water challenges around the globe.

This study investigates the effect of water temperature on the development rate of eggs and larvae, the duration of the endogenous feeding period and its consequences for recruitment of smelt (Osmerus eperlanus) in Dutch lakes IJsselmeer and Markermeer. This study measured temperature‐dependent egg and larval development rates as well as mortality rates from fertilization till the moment of absorption of the yolk‐sac and from yolk‐sac depletion onwards in temperature‐controlled indoor experiments. Using multinomial modelling the authors found significant differences in development time of egg development stages under different temperature regimes. Based on historic water temperatures, the model predicted that the larval endogenous feeding period has advanced at a rate of about 2.9 days per decade in a more than 50 year period since 1961, yet there was no change in the duration of the endogenous feeding period. As zooplankton is more responsive to daylight than water temperature cues, a mismatch between the peak of the onset of exogenous feeding of smelt and the peak of zooplankton blooms could lead to high mortality and therefore low recruitment of smelt. Such a mismatch might contribute to a decline in the smelt population in Lake IJsselmeer and Lake Markermeer.

Wild vertebrate populations all over the globe are in decline, with poaching being the second-most-important cause. The high poaching rate of rhinoceros may drive these species into extinction within the coming decades. Some stakeholders argue to lift the ban on international rhino horn trade to potentially benefit rhino conservation, as current interventions appear to be insufficient. We reviewed scientific and grey literature to scrutinize the validity of reasoning behind the potential benefit of legal horn trade for wild rhino populations. We identified four mechanisms through which legal trade would impact wild rhino populations, of which only the increased revenue for rhino farmers could potentially benefit rhino conservation. Conversely, the global demand for rhino horn is likely to increase to a level that cannot be met solely by legal supply. Moreover, corruption is omnipresent in countries along the trade routes, which has the potential to negatively affect rhino conservation. Finally, programmes aimed at reducing rhino horn demand will be counteracted through trade legalization by removing the stigma on consuming rhino horn. Combining these insights and comparing them with criteria for sustainable wildlife farming, we conclude that legalizing rhino horn trade will likely negatively impact the remaining wild rhino populations. To preserve rhino species, we suggest to prioritize reducing corruption within rhino horn trade, increasing the rhino population within well-protected 'safe havens' and implementing educational programmes and law enforcement targeted at rhino horn consumers.

Globally, many shallow lakes have shifted from a clear macrophyte-dominated state to a turbid phytoplankton-dominated state due to eutrophication. Such shifts are often accompanied by toxic cyanobacterial blooms, with specialized traits including buoyancy regulation and nitrogen fixation. Previous work has focused on how these traits contribute to cyanobacterial competitiveness. Yet, little is known on how these traits affect the value of nutrient loading thresholds of shallow lakes. These thresholds are defined as the nutrient loading at which lakes shift water quality state. Here, we used a modelling approach to estimate the effects of traits on nutrient loading thresholds. We incorporated cyanobacterial traits in the process-based ecosystem model PCLake+, known for its ability to determine nutrient loading thresholds. Four scenarios were simulated, including cyanobacteria without traits, with buoyancy regulation, with nitrogen fixation, and with both traits. Nutrient loading thresholds were obtained under N-limited, P-limited, and colimited conditions. Results show that cyanobacterial traits can impede lake restoration actions aimed at removing cyanobacterial blooms via nutrient loading reduction. However, these traits hardly affect the nutrient loading thresholds for clear lakes experiencing eutrophication. Our results provide references for nutrient loading thresholds and draw attention to cyanobacterial traits during the remediation of eutrophic water bodies.

The current anthropogenic impacts on nature necessitate more research for nature conservation and restoration purposes. To answer ecological and conservation questions concerning endangered species, individual-based modelling is an obvious choice. Individual-based models can provide reliable results that may be used to predict the effects of different future conservation strategies, once calibrated correctly. Here, we calibrate an individual-based model of Maui dolphin movement, which generates Maui dolphin probability distribution maps. We used sighting data for calibration of the chosen parameter combinations; for each simulation run, collected simulated data was compared to the empirical survey data, resulting in cost (Badness-of-Fit) estimates. Using costs of four different aspects of dolphin behaviour, we estimated the most likely parameter combinations. With optimized parameter values, Maui dolphin probability distribution maps were created, resulting in distributions that fall well outside of the current protection zones where either gillnets or trawling or both are prohibited. With these results, protected areas can be properly adjusted to the estimated distribution of this critically endangered species and so aid in their conservation.

Water bodies in the urban landscape are omnipresent, with many being small, lentic waters such as ponds and lakes. Because of high anthropogenic forcing, these systems have poor water quality, with large consequences for the provisioning of ecosystem services. Understanding of the main pressures on urban water quality is key to successful management. We identify six pressures that we hypothesize to have strong links to anthropogenic forcing including: eutrophication, aquatic invasive species, altered hydrology, altered habitat structure, climate change, and micropollutants. We discuss how these pressures may affect water quality and ecological functioning of urban waters. We describe how these pressures may interact, posing challengers for water management. We identify steps that need to be taken towards sustainable restoration, recognizing the challenges that potentially interacting pressures pose to water managers.

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.

Background: The Planetary Boundaries concept (PBc) has emerged as a key global sustainability concept in international sustainable development arenas. Initially presented as an agenda for global sustainability research, it now shows potential for sustainability governance. We use the fact that it is widely cited in scientific literature (>3500 citations) and an extensively studied concept to analyse how it has been used and developed since its first publication. 
Design: From the literature that cites the PBc, we select those articles that have the terms ‘planetary boundaries’ or ‘safe operating space’ in either title, abstract or keywords. We assume that this literature substantively engages with and develops the PBc.
Results: We find that 6% of the citing literature engages with the concept. Within this fraction of the literature we distinguish commentaries – that discuss the context and challenges to implementing the PBc, articles that develop the core biogeophysical concept and articles that apply the concept by translating to sub-global scales and by adding a human component to it. Applied literature adds to the concept by explicitly including society through perspectives of impacts, needs, aspirations and behaviours. 
Discussion: Literature applying the concept does not yet include the more complex, diverse, cultural and behavioural facet of humanity that is implied in commentary literature. We suggest there is need for a positive framing of sustainability goals – as a Safe Operating Space rather than boundaries. Key scientific challenges include distinguishing generalised from context-specific knowledge, clarifying which processes are generalizable and which are scalable, and explicitly applying complex systems’ knowledge in the application and development of the PBc. We envisage that opportunities to address these challenges will arise when more human social dimensions are integrated, as we learn to feed the global sustainability vision with a plurality of bottom-up realisations of sustainability.

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).

Many aquatic ecosystems have deteriorated due to human activities and their restoration is often troublesome. It is proposed here that the restoration success of deteriorated lakes critically depends on hitherto largely neglected spatial heterogeneity in nutrient loading and hydrology. A modelling approach is used to study this hypothesis by considering four lake types with contrasting nutrient loading (point versus diffuse) and hydrology (seepage versus drainage). By comparing the longterm effect of common restoration measures (nutrient load reduction, lake flushing or biomanipulation) in these four lake types, we found that restoration through reduction of nutrient loading is effective in all cases. In contrast, biomanipulation only works in seepage lakes with diffuse nutrient inputs, while lake flushing will even be counterproductive in lakes with nutrient point sources. The main conclusion of the presented analysis is that a priori assessment of spatial heterogeneity caused by nutrient loading and hydrology is essential for successful restoration of lake ecosystems.

A long-standing debate in ecology deals with the role of nitrogen and phosphorus in management and restoration of aquatic ecosystems. It has been argued that nutrient reduction strategies to combat blooms of phytoplankton or floating plants should solely focus on phosphorus (P). The underlying argument is that reducing nitrogen (N) inputs is ineffective because N2-fixing species will compensate for N deficits, thus perpetuating P limitation of primary production. A mechanistic understanding of this principle is, however, incomplete. Here, we use resource competition theory, a complex dynamic ecosystem model and a 32-year field data set on eutrophic, floating-plant dominated ecosystems to show that the growth of non-N2-fixing species can become N limited under high P and low N inputs, even in the presence of N2 fixing species. N2-fixers typically require higher P concentrations than non-N2-fixers to persist. Hence, the N2 fixers cannot deplete the P concentration enough for the non-N2-fixing community to become P limited because they would be outcompeted. These findings provide a testable mechanistic basis for the need to consider the reduction of both N and P inputs to most effectively restore nutrient over-enriched aquatic ecosystems. This article is protected by copyright. All rights reserved.

“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.

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.

Worldwide, eutrophication is threatening lake ecosystems. To support lake management numerous eutrophication models have been developed. Diverse research questions in a wide range of lake ecosystems are addressed by these models. The established models are based on three key approaches: the empirical approach that employs field surveys, the theoretical approach in which models based on first principles are tested against lab experiments, and the process-based approach that uses parameters and functions representing detailed biogeochemical processes. These approaches have led to an accumulation of field-, lab- and model-based knowledge, respectively. Linking these sources of knowledge would benefit lake management by exploiting complementary information; however, the development of a simple tool that links these approaches was hampered by their large differences in scale and complexity. Here we propose a Generically Parameterized Lake eutrophication model (GPLake) that links field-, lab- and model-based knowledge and can be used to make a first diagnosis of lake water quality. We derived GPLake from consumer-resource theory by the principle that lacustrine phytoplankton is typically limited by two resources: nutrients and light. These limitations are captured in two generic parameters that shape the nutrient to chlorophyll-a relations. Next, we parameterized GPLake, using knowledge from empirical, theoretical, and process-based approaches. GPLake generic parameters were found to scale in a comparable manner across data sources. Finally, we show that GPLake can be applied as a simple tool that provides lake managers with a first diagnosis of the limiting factor and lake water quality, using only the parameters for lake depth, residence time and current nutrient loading. With this first-order assessment, lake managers can easily assess measures such as reducing nutrient load, decreasing residence time or changing depth before spending money on field-, lab- or model- experiments to support lake management.

Induced bank filtration (IBF) is a water abstraction technology using different natural infiltration systems for groundwater recharge, such as river banks and lake shores. It is a cost-effective pre-treatment method for drinking water production used in many regions worldwide, predominantly in urban areas. Until now, research concerning IBF has almost exclusively focussed on the purification efficiency and infiltration capacity. Consequently, knowledge about the effects on source water bodies is lacking. Yet, IBF interrupts groundwater seepage and affects processes in the sediment potentially resulting in adverse effects on lake or river water quality. Securing sufficient source water quality, however, is important for a sustainable drinking water production by IBF. In this study, we analysed the effects of five predicted mechanisms of IBF on shallow lake ecosystems using the dynamic model PCLake: declining CO2 and nutrient availability, as well as increasing summer water temperatures, sedimentation rates and oxygen penetration into sediments. Shallow lake ecosystems are abundant worldwide and characterised by the occurrence of alternative stable states with either clear water and macrophyte dominance or turbid, phytoplankton-dominated conditions. Our results show that IBF in most scenarios increased phytoplankton abundance and thus had adverse effects on shallow lake water quality. Threshold levels for critical nutrient loading inducing regime shifts from clear to turbid conditions were up to 80% lower with IBF indicating a decreased resilience to eutrophication. The effects were strongest when IBF interrupted the seepage of CO2 rich groundwater resulting in lower macrophyte growth. IBF could also enhance water quality, but only when interrupting the seepage of groundwater with high nutrient concentrations. Higher summer water temperatures increased the share of cyanobacteria in the phytoplankton community and thus the risk of toxin production. In relative terms, the effects of changing sedimentation rates and oxygen penetration were small. Lake depth and size influenced the effect of IBF on critical nutrient loads, which was strongest in shallower and smaller lakes. Our model results stress the need of a more comprehensive ecosystem perspective including an assessment of IBF effects on threshold levels for regime shifts to prevent high phytoplankton abundance in the source water body and secure a sustainable drinking water supply.

Wetlands play an important role in the provision of important ecosystem services like the provision of clean water to the world, adaptation to climate change, and support for biodiversity; although they are sometimes also associated with adverse climate effects. Wetlands are, however, currently grossly underrepresented in global environmental models. In this paper, we explore the required functionality of a generic model of the effects of climate and land-use changes on wetlands ecosystem services worldwide. We briefly review existing models to identify elements which can be combined to compile a generic wetland model. The proposed global wetland model should be integrated into and receive data from existing hydrology and climate models. Wetland delineation can be based on local hydrological and topographical conditions and verified with global wetland databases. We conclude that an integrated approach combining hydrology, biogeochemistry and vegetation for wetlands is not available yet, however, useful building blocks exist that can be combined.

Freshwater shallow lake ecosystems provide valuable ecological services to human beings. However, these systems are subject to severe contamination from anthropogenic sources. Per- and polyfluoroalkyl substances (PFASs), including perfluorooctanoic acid (PFOA) and perfluorooctane sulphonate (PFOS), are among the contaminants that have received substantial attention, primarily due to abundant applications, environment persistence, and potential threats to ecological and human health. Understanding the environmental behavior of these contaminants in shallow freshwater lake environments using a modeling approach is therefore critical. Here, we characterize the fate, transport and transformation of both PFOA and PFOS in the fifth largest freshwater lake in China (Chaohu) during a two-year period (2013–2015) using a fugacity-based multimedia fate model. A reasonable agreement between the measured and modeled concentrations in various compartments confirms the model's reliability. The model successfully quantifies the environmental processes and identifies the major sources and input pathways of PFOA and PFOS to the Chaohu water body. Sensitivity analysis reveals the critical role of nonlinear Freundlich sorption, which contributes to a variable fraction of the model true uncertainty in different compartments (8.1%–93.6%). Through additional model scenario analyses, we further elucidate the importance of nonlinear Freundlich sorption that is essential for the reliable model performance. We also reveal the distinct composition of emission sources for the two contaminants, as the major sources are indirect soil volatilization and direct release from human activities for PFOA and PFOS, respectively. The present study is expected to provide implications for local management of PFASs pollution in Lake Chaohu and to contribute to developing a general model framework for the evaluation of PFASs in shallow lakes.

Submerged macrophytes play a key role in north temperate shallow lakes by stabilising clear-water conditions. Eutrophication has resulted in macrophyte loss and shifts to turbid conditions in many lakes. Considerable efforts have been devoted to shallow lake restoration in many countries, but long-term success depends on a stable recovery of submerged macrophytes. However, recovery patterns vary widely and remain to be fully understood. We hypothesize that reduced external nutrient loading leads to an intermediate recovery state with clear spring and turbid summer conditions similar to the pattern described for eutrophication. In contrast, lake internal restoration measures can result in transient clear-water conditions both in spring and summer and reversals to turbid conditions. Furthermore, we hypothesize that these contrasting restoration measures result in different macrophyte species composition, with added implications for seasonal dynamics due to differences in plant traits. To test these hypotheses, we analysed data on water quality and submerged macrophytes from 49 north temperate shallow lakes that were in a turbid state and subjected to restoration measures. To study the dynamics of macrophytes during nutrient load reduction, we adapted the ecosystem model PCLake. Our survey and model simulations revealed the existence of an intermediate recovery state upon reduced external nutrient loading, characterised by spring clear-water phases and turbid summers, whereas internal lake restoration measures often resulted in clear-water conditions in spring and summer with returns to turbid conditions after some years. External and internal lake restoration measures resulted in different macrophyte communities. The intermediate recovery state following reduced nutrient loading is characterised by a few macrophyte species (mainly pondweeds) that can resist wave action allowing survival in shallow areas, germinate early in spring, have energy-rich vegetative propagules facilitating rapid initial growth and that can complete their life cycle by early summer. Later in the growing season these plants are, according to our simulations, outcompeted by periphyton, leading to late-summer phytoplankton blooms. Internal lake restoration measures often coincide with a rapid but transient colonisation by hornworts, waterweeds or charophytes. Stable clear-water conditions and a diverse macrophyte flora only occurred decades after external nutrient load reduction or when measures were combined.

Many of the world's wetlands may be profoundly affected by climate change over the coming decades. Although wetland managers may have little control over the causes of climate change, they can help to counteract its effects through local measures. This is because direct anthropogenic impacts, such as water extraction and nutrient loading, work in concert with climate change to damage wetlands. Control of these local stressors may therefore ameliorate undesired effects of climate change, such as a shift towards dominance by invasive floating plants, increasingly frequent cyanobacteria blooms, or extinction of key species. Using the iconic Doñana wetlands in Spain as a case study, we illustrate how the concept of creating a “safe operating space” may be implemented to better ensure that ecosystems do not surpass thresholds for collapse during an era of global change.

Ongoing eutrophication frequently causes toxic phytoplankton blooms. This induces huge worldwide challenges for drinking water quality, food security and public health. Of crucial importance in avoiding and reducing blooms is to determine the maximum nutrient load ecosystems can absorb, while remaining in a good ecological state. These so called critical nutrient loads for lakes depend on the shape of the load-response curve. Due to spatial variation within lakes, load-response curves and therefore critical nutrient loads could vary throughout the lake. In this study we determine spatial patterns in critical nutrient loads for Lake Taihu (China) with a novel modelling approach called Spatial Ecosystem Bifurcation Analysis (SEBA). SEBA evaluates the impact of the lake's total external nutrient load on the local lake dynamics, resulting in a map of critical nutrient loads for different locations throughout the lake. Our analysis shows that the largest part of Lake Taihu follows a nonlinear load-response curve without hysteresis. The corresponding critical nutrient loads vary within the lake and depend on management goals, i.e. the maximum allowable chlorophyll concentration. According to our model, total nutrient loads need to be more than halved to reach chlorophyll-a concentrations of 30–40 μg L−1 in most sections of the lake. To prevent phytoplankton blooms with 20 μg L−1 chlorophyll-a throughout Lake Taihu, both phosphorus and nitrogen loads need a nearly 90% reduction. We conclude that our approach is of great value to determine critical nutrient loads of lake ecosystems such as Taihu and likely of spatially heterogeneous ecosystems in general.

Submerged macrophytes play an important role in maintaining good water quality in shallow lakes. Yet extensive stands easily interfere with various services provided by these lakes, and harvesting is increasingly applied as a management measure. Because shallow lakes may possess alternative stable states over a wide range of environmental conditions, designing a successful mowing strategy is challenging, given the important role of macrophytes in stabilizing the clear water state. In this study, the integrated ecosystem model PCLake is used to explore the consequences of mowing, in terms of reducing nuisance and ecosystem stability, for a wide range of external nutrient loadings, mowing intensities and timings. Elodea is used as a model species. Additionally, we use PCLake to estimate how much phosphorus is removed with the harvested biomass, and evaluate the long-term effect of harvesting. Our model indicates that mowing can temporarily reduce nuisance caused by submerged plants in the first weeks after cutting, particularly when external nutrient loading is fairly low. The risk of instigating a regime shift can be tempered by mowing halfway the growing season when the resilience of the system is highest, as our model showed. Up to half of the phosphorus entering the system can potentially be removed along with the harvested biomass. As a result, prolonged mowing can prevent an oligo—to mesotrophic lake from becoming eutrophic to a certain extent, as our model shows that the critical nutrient loading, where the lake shifts to the turbid phytoplankton-dominated state, can be slightly increased.

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 when implementing hydrological regulation for aquatic ecosystems around the globe.

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.

Food web structure dynamics and ecosystem functioning are strongly linked, and both are indispensable in evaluating ecosystem development in lakes under multiple anthropogenic stressors. However, model-based approaches concerning the changes in food web structure and ecosystem functioning in a certain lake during distinct periods are scarce. In this study, we focus on Lake Chaohu, the fifth-largest lake in China, which has undergone drastic changes over the last several decades. Data from the 1950s, 1980s and 2000s were used to create three Ecopath mass-balance models. These Ecopath models were validated by the stable isotope-determined trophic level (TL) for each functional group, which indicated an acceptable model performance. Over time, we observed a collapse of the food web toward a simplified structure and decreasing biodiversity and trophic interactions. The lake ecosystem was approaching an immature but stable status from the 1950s to the 2000s, as indicated by the multiple related indicators and the distribution of energy flows in slow detrital-based and fast primary producer-based channels. We further discuss the potential driving factors and underlying mechanisms, hypothesizing that hydrological regulation may play a significant role in driving all of these changes in Lake Chaohu in addition to eutrophication and intensive fishery. Overall, we strongly advocate the identification of a threshold in abundance of zooplanktivorous fish, an integrated strategy for future ecological restoration in Lake Chaohu, and the consideration of using Ecopath as a new management tool for other lakes, thereby bridging the strategies from both environmental and ecological perspectives.

This study presents FABM-PCLake, a complete redesign of the PCLake aquatic ecosystem model, which we implemented into the Framework for Aquatic Biogeochemical Models (FABM). In contrast to the original model, which was designed for temperate, fully mixed freshwater lakes, the new FABM-PCLake represents an integrated aquatic ecosystem model that enables simulations of hydrodynamics and biogeochemical processes for zero dimensional, one-dimensional as well as three-dimensional heterogeneous environments. FABM-PCLake describes interactions between multiple trophic levels, including piscivorous, zooplanktivorous and benthivorous fish, zooplankton, zoobenthos, three groups of phytoplankton and rooted macrophytes. The model also accounts for oxygen dynamics and nutrient cycling for nitrogen, phosphorus and silicon, both within the pelagic and benthic domains. FABM-PCLake includes a two-way communication between the biogeochemical processes and the physics, where some biogeochemical state variables (e.g., phytoplankton) influence light attenuation and thereby the spatial and temporal distributions of light and heat. At the same time, the physical environment, including water currents, light and temperature influence a wide range of biogeochemical processes. The model enables studies on ecosystem dynamics in physically heterogeneous environments (e.g., stratifying water bodies, and water bodies with horizontal gradient in physical and biogeochemical properties), and through FABM also enables data assimilation and multi-model ensemble simulations. Examples of relevant model applications include climate change impact studies and environmental impact assessment scenarios for lakes and reservoirs worldwide.

Shallow lakes have the potential to switch between two alternative stable states: a clear macrophyte-dominated and a turbid phytoplankton-dominated state. Observational and experimental studies show that in some lakes herbivory by birds may severely decrease macrophyte biomass, while in other lakes, the removed biomass by herbivory is compensated by regrowth. These contradictory outcomes might arise because of interplay between top-down control by bird herbivory and bottom-up effects by nutrient loading on macrophytes. Here, we use the ecosystem model PCLake to study top-down and bottom-up control of macrophytes by coots and nutrient loading. Our model predicted that (1) herbivory by birds lowers the critical nutrient loading at which the regime shift occurs; (2) bird impact on macrophyte biomass through herbivory increases with nutrient loading; and (3) improved food quality enhances the impact of birds on macrophytes, thus decreasing the resilience of the clear-water state even further. The fact that bird herbivory can have a large impact on macrophyte biomass and can facilitate a regime shift implies that the presence of waterfowl should be taken into account in the estimation of critical nutrient loadings to be used in water quality management.

Millions of people rely on the ecosystem services provided by coral reefs, but sustaining these benefits requires an understanding of how reefs and their biotic communities are affected by local human-induced disturbances and global climate change. Ecosystem-based management that explicitly considers the indirect and cumulative effects of multiple disturbances has been recommended and adopted in policies in many places around the globe. Ecosystem models give insight into complex reef dynamics and their responses to multiple disturbances and are useful tools to support planning and implementation of ecosystem-based management. We adapted the Atlantis Ecosystem Model to incorporate key dynamics for a coral reef ecosystem around Guam in the tropical western Pacific. We used this model to quantify the effects of predicted climate and ocean changes and current levels of current land-based sources of pollution (LBSP) and fishing. We used the following six ecosystem metrics as indicators of ecosystem state, resilience and harvest potential: 1) ratio of calcifying to non-calcifying benthic groups, 2) trophic level of the community, 3) biomass of apex predators, 4) biomass of herbivorous fishes, 5) total biomass of living groups and 6) the end-to-start ratio of exploited fish groups. Simulation tests of the effects of each of the three drivers separately suggest that by mid-century climate change will have the largest overall effect on this suite of ecosystem metrics due to substantial negative effects on coral cover. The effects of fishing were also important, negatively influencing five out of the six metrics. Moreover, LBSP exacerbates this effect for all metrics but not quite as badly as would be expected under additive assumptions, although the magnitude of the effects of LBSP are sensitive to uncertainty associated with primary productivity. Over longer time spans (i.e., 65 year simulations), climate change impacts have a slight positive interaction with other drivers, generally meaning that declines in ecosystem metrics are not as steep as the sum of individual effects of the drivers. These analyses offer one way to quantify impacts and interactions of particular stressors in an ecosystem context and so provide guidance to managers. For example, the model showed that improving water quality, rather than prohibiting fishing, extended the timescales over which corals can maintain high abundance by at least 5–8 years. This result, in turn, provides more scope for corals to adapt or for resilient species to become established and for local and global management efforts to reduce or reverse stressors.

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.

There is ample evidence that tube-dwelling invertebrates such as chironomids significantly alter multiple important ecosystem functions, particularly in shallow lakes. Chironomids pump large water volumes, and associated suspended and dissolved substances, through the sediment and thereby compete with pelagic filter feeders for particulate organic matter. This can exert a high grazing pressure on phytoplankton, microorganisms, and perhaps small zooplankton and thus strengthen benthic-pelagic coupling. Furthermore, intermittent pumping by tube-dwelling invertebrates oxygenates sediments and creates a dynamic, three-dimensional mosaic of redox conditions. This shapes microbial community composition and spatial distribution, and alters microbe-mediated biogeochemical functions, which often depend on redox potential. As a result, extended hotspots of element cycling occur at the oxic-anoxic interfaces, controlling the fate of organic matter and nutrients as well as fluxes of nutrients between sediments and water. Surprisingly, the mechanisms and magnitude of interactions mediated by these organisms are still poorly understood. To provide a synthesis of the importance of tube-dwelling invertebrates, we review existing research and integrate previously disregarded functional traits into an ecosystem model. Based on existing research and our models, we conclude that tube-dwelling invertebrates play a central role in controlling water column nutrient pools, and hence water quality and trophic state. Furthermore, these tiny ecosystem engineers can influence the thresholds that determine shifts between alternate clear and turbid states of shallow lakes. The large effects stand in contrast to the conventional limnological paradigm emphasizing predominantly pelagic food webs. Given the vast number of shallow lakes worldwide, benthic invertebrates are likely to be relevant drivers of biogeochemical processes at regional and global scales, thereby mediating feedback mechanisms linked to climate change.

Despite the importance of coral reef ecosystems to the social and economic welfare of coastal communities, the condition of these marine ecosystems have generally degraded over the past decades. With an increased knowledge of coral reef ecosystem processes and a rise in computer power, dynamic models are useful tools in assessing the synergistic effects of local and global stressors on ecosystem functions. We review representative approaches for dynamically modeling coral reef ecosystems and categorize them as minimal, intermediate and complex models. The categorization was based on the leading principle for model development and their level of realism and process detail. This review aims to improve the knowledge of concurrent approaches in coral reef ecosystem modeling and highlights the importance of choosing an appropriate approach based on the type of question(s) to be answered. We contend that minimal and intermediate models are generally valuable tools to assess the response of key states to main stressors and, hence, contribute to understanding ecological surprises. As has been shown in freshwater resources management, insight into these conceptual relations profoundly influences how natural resource managers perceive their systems and how they manage ecosystem recovery. We argue that adaptive resource management requires integrated thinking and decision support, which demands a diversity of modeling approaches. Integration can be achieved through complimentary use of models or through integrated models that systemically combine all relevant aspects in one model. Such whole-of-system models can be useful tools for quantitatively evaluating scenarios. These models allow an assessment of the interactive effects of multiple stressors on various, potentially conflicting, management objectives. All models simplify reality and, as such, have their weaknesses. While minimal models lack multidimensionality, system models are likely difficult to interpret as they require many efforts to decipher the numerous interactions and feedback loops. Given the breadth of questions to be tackled when dealing with coral reefs, the best practice approach uses multiple model types and thus benefits from the strength of different models types.

Abstract In this study, we apply an integrated empirical and mechanism approach to estimate a comprehensive long-term (1953–2012) total nitrogen (TN) and total phosphorus (TP) loading budget for the eutrophic Lake Chaohu in China. This budget is subsequently validated, firstly, by comparing with the available measured data in several years, and secondly, by model simulations for long-term nutrient dynamics using both Vollenweider (VW) model and dynamic nonlinear (DyN) model. Results show that the estimated nutrient budget is applicable for further evaluations. Surprisingly, nutrient loading from non-point sources (85% for TN and 77% for TP on average) is higher than expectation, suggesting the importance of nutrient flux from the soil in the basin. In addition, DyN model performs relatively better than VW model, which is attributed to both the additional sediment recycling process and the parameters adjusted by the Bayesian-based Markov Chain Monte Carlo (MCMC) method. DyN model further shows that the TP loading thresholds from the clear to turbid state (631.8 ± 290.16 t y−1) and from the turbid to clear state (546.0 ± 319.80 t y−1) are significantly different (p < 0.01). Nevertheless, the uncertainty ranges of the thresholds are largely overlapped, which is consistent with the results that the eutrophication of Lake Chaohu is more likely to be reversible (74.12%) than hysteretic (25.53%). The ecosystem of Lake Chaohu shifted from the clear to turbid state during late 1970s. For managers, approximately two-thirds of the current TP loading must be reduced for a shift back with substantial improvement in water quality. Because in practice the reduction of loading from a non-point source is very difficult and costly, additional methods beyond nutrient reduction, such as water level regulation, should be considered for the lake restoration.

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.

Abstract Biodiversity in freshwater ecosystems – rivers, lakes and wetlands – is undergoing rapid global decline. Major drivers are land use change, eutrophication, hydrological disturbance, climate change, overexploitation and invasive species. We developed a global model for assessing the dominant human impacts on inland aquatic biodiversity. The system consists of a biodiversity model, named GLOBIO-Aquatic, that is embedded in the IMAGE model framework, i.e. linked to models for demography, economy, land use changes, climate change, nutrient emissions, a global hydrological model and a global map of water bodies. The biodiversity model is based on a recompilation of existing data, thereby scaling-up from local/regional case-studies to global trends. We compared species composition in impacted lakes, rivers and wetlands to that in comparable undisturbed systems. We focussed on broad categories of human-induced pressures that are relevant at the global scale. The drivers currently included are catchment land use changes and nutrient loading affecting water quality, and hydrological disturbance and climate change affecting water quantity. The resulting relative mean abundance of original species is used as indicator for biodiversity intactness. For lakes, we used dominance of harmful algal blooms as an additional indicator. The results show that there is a significant negative relation between biodiversity intactness and these stressors in all types of freshwater ecosystems. In heavily used catchments, standing water bodies would lose about 80% of their biodiversity intactness and running waters about 70%, while severe hydrological disturbance would result in losses of about 80% in running waters and more than 50% in floodplain wetlands. As an illustration, an analysis using the OECD ‘baseline scenario’ shows a considerable decline of the biodiversity intactness in still existing water bodies in 2000, especially in temperate and subtropical regions, and a further decline especially in tropical regions in 2050. Historical loss of wetland areas is not yet included in these results. The model may inform policy makers at the global level in what regions aquatic biodiversity will be affected most and by what causes, and allows for scenario analysis to evaluate policy options.

Dominance of free-floating plants poses a threat to biodiversity in many freshwater ecosystems. Here we propose a theoretical framework to understand this dominance, by modeling the competition for light and nutrients in a layered community of floating and submerged plants. The model shows that at high supply of light and nutrients, floating plants always dominate due to their primacy for light, even when submerged plants have lower minimal resource requirements. The model also shows that floating-plant dominance cannot be an alternative stable state in light-limited environments but only in nutrient-limited environments, depending on the plants’ resource consumption traits. Compared to unlayered communities, the asymmetry in competition for light—coincident with symmetry in competition for nutrients—leads to fundamentally different results: competition outcomes can no longer be predicted from species traits such as minimal resource requirements ( rule) and resource consumption. Also, the same two species can, depending on the environment, coexist or be alternative stable states. When applied to two common plant species in temperate regions, both the model and field data suggest that floating-plant dominance is unlikely to be an alternative stable state.

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.

East Africa’s Lake Victoria provides resources and services to millions of people on the lake’s shores and abroad. In particular, the lake’s fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria’s system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake’s social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks’ vulnerability to exploitation but reduce society’s vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.

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.

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.

Self-organized complexity at multiple spatial scales is a distinctive characteristic of biological systems. Yet, little is known about how different self-organizing processes operating at different spatial scales interact to determine ecosystem functioning. Here we show that the interplay between self-organizing processes at individual and ecosystem level is a key determinant of the functioning and resilience of mussel beds. In mussel beds, self-organization generates spatial patterns at two characteristic spatial scales: small-scale net-shaped patterns due to behavioural aggregation of individuals, and large-scale banded patterns due to the interplay of between-mussel facilitation and resource depletion. Model analysis reveals that the interaction between these behavioural and ecosystem-level mechanisms increases mussel bed resilience, enables persistence under deteriorating conditions and makes them less prone to catastrophic collapse. Our analysis highlights that interactions between different forms of self-organization at multiple spatial scales may enhance the intrinsic ability of ecosystems to withstand both natural and human-induced disturbances.

The current changes in our climate will likely have far reaching consequences for aquatic ecosystems. These changes in the climate, however, do not act alone and are often accompanied by additional stressors such as eutrophication. Both global warming and eutrophication have been shown to affect the timing and magnitude of phytoplankton blooms. Little is known about the combined effects of rising temperatures and eutrophication on the stoichiometry of entire phytoplankton communities. We exposed a natural phytoplankton spring community to different warming and phosphorus loading scenarios using a full-factorial design. Our results demonstrate that rising temperatures promote the growth rate of an entire phytoplankton community. Furthermore, both rising temperatures and phosphorus loading stimulated the maximum biomass built up by the phytoplankton community. Rising temperatures led to higher carbon:nutrient stoichiometry of the phytoplankton community under phosphorus limited conditions. Such a shift towards higher carbon:nutrient ratios, in combination with a higher biomass build-up, suggests a temperature-driven increase in nutrient use efficiency of the phytoplankton community. Importantly, higher carbon:nutrient stoichiometry of phytoplankton is generally of poorer nutritional value for zooplankton. Thus, although warming may result in higher phytoplankton biomass, this may be accompanied by a stoichiometric mismatch between phytoplankton and their grazers, with possible consequences for the entire aquatic food web. Read More: http://www.esajournals.org/doi/abs/10.1890/13-1251.1

Positive and negative interactions within and between species may occur simultaneously, with the net effect depending on population densities. For instance, at low densities plants may ameliorate stress, while competition for resources dominates at higher densities. Here, we propose a simple two-species model in which con- and heterospecifics have a positive effect on per capita growth rate at low densities, while negative interactions dominate at high densities. The model thus includes both Allee effects (intraspecific positive effects) and mutualism (interspecific positive effects), as well as intra- and interspecific competition. Using graphical methods we derive conditions for alternative stable states and species coexistence. We show that mutual non-invasibility (i.e. the inability of each species to invade a population of the other) is more likely when species have a strong positive effect on the own species or a strong negative effect on the other species. Mutual non-invasibility implies alternative stable states, however, there may also be alternative stable states at which species coexist. In the case of species symmetry (i.e. when species are indistinguishable), such alternative coexistence states require that if the positive effect exerted at low densities at the own species is stronger than on the other species, the negative effect at higher densities is also stronger on the own species than on the other species, or, vice versa, if the interspecific positive effects at low densities are stronger than the intraspecific effects, the negative effects at higher densities are also stronger between species than within species. However, the reachability of alternative stable states is restricted by the frequency and density at which species are introduced during community assembly, so that alternative stable states do not always represent alternative endstates of community assembly.

Complex ecological models are used to predict the consequences of anticipated future changes in climate and nutrient loading for lake water quality. These models may, however, suffer from nonuniqueness in that various sets of model parameter values may yield equally satisfactory representations of the system being modeled, but when applied in future scenarios these sets of values may divert considerably in their simulated outcomes. Compilation of an ensemble of model runs allows us to account for simulation variability arising from model parameter estimates. Thus, we propose a new approach for aquatic ecological models creating a more robust prediction of future water quality. We used our ensemble approach in an application of the widely used PCLake model for Danish shallow Lake Arreskov, which during the past two decades has demonstrated frequent shifts between turbid and clear water states. Despite marked variability, the span of our ensemble runs encapsulated 70-90% of the observed variation in lake water quality. The model exercise demonstrates that future warming and increased nutrient loading lead to lower probability of a clear water, vegetation-rich state and greater likelihood of cyanobacteria dominance. In a 6.0 degrees C warming scenario, for instance, the current nutrient loading of nitrogen and phosphorus must be reduced by about 75% to maintain the present ecological state of Lake Arreskov, but even in a near-future 2.0 degrees C warming scenario, a higher probability of a turbid, cyanobacteria-dominated state is predicted. As managers may wish to determine the probability of achieving a certain ecological state, our proposed ensemble approach facilitates new ways of communicating future stressor impacts.

Peatlands are important sinks for atmospheric carbon (C), yet the role of plant functional types (PFTs) for C sequestration under climatic perturbations is still unclear. A plant removal experiment was used to study the importance of vascular PFTs for the net ecosystem CO2 exchange (NEE) during (i.e. resistance) and after (i.e. recovery) an experimental drought. The removal of PFTs caused a decrease of NEE, but the rate differed between microhabitats (i.e. hummocks and lawns) and the type of PFTs. Ericoid removal had a large effect on NEE in hummocks, while in the lawns the graminoids played a major role. The removal of PFTs did not affect the resistance or the recovery after the experimental drought. We argue that the response of Sphagnum mosses (the only PFT present in all treatments) to drought is dominant over that of coexisting PFTs. However, we observed that the moment in which the system switched from C sink to C source during the drought was controlled by the vascular PFTs. In the light of climate change, the shifts in species composition or even the loss of certain PFTs are expected to strongly affect the future C dynamics in response to environmental stress.

Submerged macrophytes can stabilise clear water conditions in shallow lakes. However, many existing models for deep lakes neglect their impact. Here, we tested the hypothesis that submerged macrophytes can affect the water clarity in deep lakes. A one-dimensional, vertically resolved macrophyte model was developed based on PCLake and coupled to SALMO-1D and GOTM hydrophysics and validated against field data. Validation showed good coherence in dynamic growth patterns and colonisation depths. In our simulations the presence of submerged macrophytes resulted in up to 50% less phytoplankton biomass in the shallowest simulated lake (11 m) and still 15% less phytoplankton was predicted in 100 m deep oligotrophic lakes. Nutrient loading, lake depth, and lake shape had a strong influence on macrophyte effects. Nutrient competition was found to be the strongest biological interaction. Despite a number of limitations, the derived dynamic lake model suggests significant effects of submerged macrophytes on deep lake water quality. (C) 2014 Elsevier Ltd. All rights reserved.

Algal blooms have caused severe problems in Lake Taihu, China. Early warning of phytoplankton accumulation can support decision-making against harmful algal bloom events. To investigate the performance of different models in forecasting high phytoplankton biomass, we developed a mechanistic, a regression and three artificial neural network (ANN) models to predict short-term (3 days) changes of phytoplankton biomass (expressed as chlorophyll-a concentration) in Gonghu Bay of Lake Taihu. We determined the input variables of the ANN models with a sensitivity analysis, and optimized their parameters with a trial-and-error approach. The sensitivity analysis revealed the effects of the input variables on phytoplankton biomass. To calibrate and validate the models, we collected two data sets of Lake Taihu in 2009: hourly-averaged data collected by an automatic monitoring system and field data with a sampling interval of twice a week. Although the sensitivity analysis results vary among the five models, there is a general consensus that phytoplankton changes are significantly affected by water temperature in Gonghu Bay. The ANN models obtained good model fit indicating their practical values in predicting non-linear phytoplankton dynamics for water management purpose. The mechanistic model predicted the phytoplanIcton distribution dynamically and described the variable interactions explicitly. The regression model is characterized by its easy development. This comparison study assists the modelers in selecting an approximate model for their specific purposes.

A global trend of increasing health hazards associated with proliferation of toxin-producing cyanobacteria makes the ability to project phytoplankton dynamics of paramount importance. Whilst ensemble (multi-)modelling approaches have been used for a number of years to improve the robustness of weather forecasts this approach has until now never been adopted for ecosystem modelling. We show that the average simulated phytoplankton biomass derived from three different aquatic ecosystem models is generally superior to any of the three individual models in describing observed phytoplankton biomass in a typical temperate lake ecosystem, and we simulate a series of climate change projections. While this is the first multi-model ensemble approach applied for some of the most complex aquatic ecosystem models available, we consider it sets a precedent for what will become commonplace methodology in the future, as it enables increased robustness of model projections, and scenario uncertainty estimation due to differences in model structures. (C) 2014 Elsevier Ltd. All rights reserved.

We developed the individual-based model PHYLLOSIM to explain observed variation in the size of bacterial clusters on plant leaf surfaces (the phyllosphere). Specifically, we tested how different ‘waterscapes’ impacted the diffusion of nutrients from the leaf interior to the surface and the growth of individual bacteria on these nutrients. In the ‘null’ model or more complex ‘patchy’ models, the surface was covered with a continuous water film or with water drops of equal or different volumes, respectively. While these models predicted the growth of individual bacterial immigrants into clusters of variable sizes, they were unable to reproduce experimentally derived, previously published patterns of dispersion which were characterized by a much larger variation in cluster sizes and a disproportionate occurrence of clusters consisting of only one or two bacteria. The fit of model predictions to experimental data was about equally poor (

1. A collapse of Nile perch stocks of Lake Victoria could affect up to 30million people. Furthermore, changes in Nile perch population size-structure and stocks make the threat of collapse imminent. However, whether eutrophication or fishing will be the bane of Nile perch is still debated. 2. Here, we attempt to unravel how changes in food resources, a side effect of eutrophication, and fishing mortality determine fish population growth and size structures. We parameterised a physiologically structured model to Nile perch, analysed the influence of ontogenetic diet shifts and relative resource abundances on existence boundaries of Nile perch and described the populations on either side of these boundaries. 3. Our results showed that ignoring ontogenetic diet shifts can lead to over-estimating the maximum sustainable mortality of a fish population. Size distributions can be indicators of processes driving population dynamics. However, the vulnerability of stocks to fishing mortality is dependent on its environment and is not always reflected in size distributions. 4. We suggest that the ecosystem, instead of populations, should be used to monitor long-term effects of human impact. [KEYWORDS: diet shift existence boundaries Nile perch population growth sustainable fishing lates-niloticus l size-structured populations life-history traits haplochromine cichlids east-africa mwanza gulf nyanza-gulf competition predation dynamics]

1.In our recent contribution to the special issue on plankton dynamics in a fast-changing world, we outlined some general predictions of plankton dynamics in different climate regions now and in future, building on the Plankton Ecology Group (PEG) model (de Senerpont Domis et al., 2013). 2.We proposed a stylised version of plankton dynamics in Fig. 3 of our article and stated that these patterns need to be further elaborated. Our figure displays annual plankton dynamics now and in future in oligotrophic, mesotrophic and eutrophic lakes in arctic, temperate and tropical climate zones. 3.We fully agree with Sarmento, Amado & Descy (2013) that more data on tropical regions are needed, and we are looking forward to the emergence of published data from tropical regions to extend our still-limited understanding of plankton dynamics in these regions. 4.Sarmento et al. (2013) did not agree with our predictions on plankton dynamics for hydrology-driven water systems in the tropics. Unfortunately, however, Sarmento et al. (2013) did not substantiate their statements with the much-needed data on plankton dynamics in the tropics. Moreover, they merely provide an overview of precipitation patterns in the tropics, not an alternative hypothesis for our predictions.

1. Despite the strong impact parasites can have, only few models of phytoplankton ecology or aquatic food webs have specifically included parasitism. 2. Here, we provide a susceptible-infected model for a diatom-chytrid host–parasite system that explicitly includes nutrients, infected and uninfected hosts, reproduction of the parasite on the hosts and free-living infective stages. 3. A distinguishing feature of the model is that parasite reproduction on host increases with nutrient availability to the infected host, as has been observed for many parasites and viruses. 4. It follows from this assumption that the parasite’s basic reproduction number, R0, increases with nutrient concentration, because at higher nutrient concentrations, infected hosts consume more nutrients that are used for the reproduction of the parasite. 5. Another important result is that there may be two alternative states to which population densities can converge: one with only the host and one with host and parasite co-existing. In the latter, the parasite can invade a host population only if it is introduced above a threshold density. 6. Furthermore, the model shows a strong tendency for host–parasite cycles, which may be chaotic. Nutrient enrichment leads to increasing amplitude of these cycles, which may cause host or parasite population extinction caused by stochastic fluctuations during periods of low population density, which is the Paradox of Enrichment. 7. Finally, if alternative states and cycles co-occur, increased population cycle amplitude may drive the parasite below its threshold density for successful invasion, causing parasite extinction in a ‘deterministic Paradox of Enrichment’. Published results confirm that host–parasite cycles and collapse of host–parasite systems may occur in real plankton communities. 8. Our results underline that ecological detail in host–parasite models may have consequences for disease dynamics that may be overlooked when ecological interactions between environment, host and parasite are not explicitly taken into account.

Research on the role of top–down (predation) and bottom–up (food) effects in food webs has led to the understanding that the variability of these effects in space and time is a fundamental feature of natural systems. Consequently, our measurement tools must allow us to evaluate the effects from a dynamical perspective. A population-dynamics approach may be appropriate to the task. More specifically, because food and predators both affect birth rate, birth rate dynamics may be a key to understanding their impact on the population of interest. Based on the Edmondson–Paloheimo model for birth rate, we propose a new population metric to assess the relative strength of top–down vs bottom–up effects. The metric is the ratio of contributions of changes in proportion of adults and fecundity to change in birth rate. Proportion of adults reflects a top–down effect (predators are assumed to be size-selective), fecundity reflects a bottom–up effect, and birth rate appears as a common currency with which to compare the former and the latter. Using microcosm experiments and computer simulations on the cladoceran Daphnia, we calibrate the metric and show that, in both types of tests, the ratio of contributions is typically 0.5–0.7 under a strong bottom–up effect and 2.0–2.2 under a strong top–down effect. This provides experimental evidence that the ratio of contributions may allow one to distinguish a strong top–down effect from a strong bottom–up effect.

1.Different components of the climate system have been shown to affect temporal dynamics in natural plankton communities on scales varying from days to years. The seasonal dynamics in temperate lake plankton communities, with emphasis on both physical and biological forcing factors, were captured in the 1980s in a conceptual framework, the Plankton Ecology Group (PEG) model. 2.Taking the PEG model as our starting point, we discuss anticipated changes in seasonal and long-term plankton dynamics and extend this model to other climate regions, particularly polar and tropical latitudes. Based on our improved post-PEG understanding of plankton dynamics, we also evaluate the role of microbial plankton, parasites and fish in governing plankton dynamics and distribution. 3.In polar lakes, there is usually just a single peak in plankton biomass in summer. Lengthening of the growing season under warmer conditions may lead to higher and more prolonged phytoplankton productivity. Climate-induced increases in nutrient loading in these oligotrophic waters may contribute to higher phytoplankton biomass and subsequent higher zooplankton and fish productivity. 4.In temperate lakes, a seasonal pattern with two plankton biomass peaks – in spring and summer – can shift to one with a single but longer and larger biomass peak as nutrient loading increases, with associated higher populations of zooplanktivorous fish. Climate change will exacerbate these trends by increasing nutrient loading through increased internal nutrient inputs (due to warming) and increased catchment inputs (in the case of more precipitation). 5.In tropical systems, temporal variability in precipitation can be an important driver of the seasonal development of plankton. Increases in precipitation intensity may reset the seasonal dynamics of plankton communities and favour species adapted to highly variable environments. The existing intense predation by fish on larger zooplankters may increase further, resulting in a perennially low zooplankton biomass. 6.Bacteria were not included in the original PEG model. Seasonally, bacteria vary less than the phytoplankton but often follow its patterns, particularly in colder lakes. In warmer lakes, and with future warming, a greater influx of allochthonous carbon may obscure this pattern. 7.Our analyses indicate that the consequences of climate change for plankton dynamics are, to a large extent, system specific, depending on characteristics such as food-web structure and nutrient loading. Indirect effects through nutrient loading may be more important than direct effects of temperature increase, especially for phytoplankton. However, with warming a general picture emerges of increases in bacterivory, greater cyanobacterial dominance and smaller-bodied zooplankton that are more heavily impacted by fish predation.

Nile perch (Lates niloticus) suddenly invaded Lake Victoria between 1979 and 1987, 25 years after its introduction in the Ugandan side of the lake. Nile perch then replaced the native fish diversity and irreversibly altered the ecosystem and its role to lakeshore societies: it is now a prised export product that supports millions of livelihoods. The delay in the Nile perch boom led to a hunt for triggers of the sudden boom and generated several hypotheses regarding its growth at low abundances – all hypotheses having important implications for the management of Nile perch stocks. We use logistic growth as a parsimonious null model to predict when the Nile perch invasion should have been expected, given its growth rate, initial stock size and introduction year. We find the first exponential growth phase can explain the timing of the perch boom at the scale of Lake Victoria, suggesting that complex mechanisms are not necessary to explain the Nile perch invasion or its timing. However, the boom started in Kenya before Uganda, indicating perhaps that Allee effects act at smaller scales than that of the whole Lake. The Nile perch invasion of other lakes indicates that habitat differences may also have an effect on invasion success. Our results suggest there is probably no single management strategy applicable to the whole lake that would lead to both efficient and sustainable exploitation of its resources.

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.

In the past decade, much work has been done on integrating different lake models using general frameworks to overcome model incompatibilities. However, a framework may not be flexible enough to support applications in different fields. To overcome this problem, we used Python to integrate three lake models into a Phytoplankton Prediction System for Lake Taihu (Taihu PPS). The system predicts the short-term (1–4 days) distribution of phytoplankton biomass in this large eutrophic lake in China. The object-oriented scripting language Python is used as the so-called ‘glue language’ (a programming language used for connecting software components). The distinguishing features of Python include rich extension libraries for spatial and temporal modelling, modular software architecture, free licensing and a high performance resulting in short execution time. These features facilitate efficient integration of the three models into Taihu PPS. Advanced tools (e.g. tools for statistics, 3D visualization and model calibration) could be developed in the future with the aid of the continuously updated Python libraries. Taihu PPS simulated phytoplankton biomass well and has already been applied to support decision making.

Marine and freshwater phytoplankton populations often show large clonal diversity, which is in disagreement with clonal selection of the most vigorous genotype(s). Temporal fluctuation in selection pressures in variable environments is a leading explanation for maintenance of such genetic diversity. To test the influence of temperature as a selection force in continually (seasonally) changing aquatic systems we carried out reaction norms experiments on co-occurring clonal genotypes of a ubiquitous diatom species, Asterionella formosa Hassall, across an environmentally relevant range of temperatures. We report within population genetic diversity and extensive diversity in genotype-specific reaction norms in growth rates and cell size traits. Our results showed genotype by environment interactions, indicating that no genotype could outgrow all others across all temperature environments. Subsequently, we constructed a model to simulate the relative proportion of each genotype in a hypothetical population based on genotype and temperature-specific population growth rates. This model was run with different seasonal temperature patterns. Our modeling exercise showed a succession of two to several genotypes becoming numerically dominant depending on the underlying temperature pattern. The results suggest that (temperature) context dependent fitness may contribute to the maintenance of genetic diversity in isolated populations of clonally reproducing microorganisms in temporally variable environments.

The seasonal succession of plankton is an annually repeated process of community assembly during which all major external factors and internal interactions shaping communities can be studied. A quarter of a century ago, the state of this understanding was described by the verbal plankton ecology group (PEG) model. It emphasized the role of physical factors, grazing and nutrient limitation for phytoplankton, and the role of food limitation and fish predation for zooplankton. Although originally targeted at lake ecosystems, it became also adopted by marine plankton ecologists. Since then, a suite of ecological interactions previously underestimated in importance have become research foci: overwintering of key organisms, the microbial food web, parasitism, and food quality as a limiting factor and an extended role of higher order predators. A review of the impact of these novel interactions on plankton seasonal succession reveals limited effects on gross seasonal biomass patterns, but strong effects on species replacements.

In the light of ongoing land use changes, it is important to understand how multitrophic communities perform at different land use intensities. The paradox of enrichment predicts that fertilization leads to destabilization and extinction of predator-prey systems. We tested this prediction for a land use intensity gradient from natural to highly fertilized agricultural ecosystems. We included multiple aboveground and belowground trophic levels and land use-dependent searching efficiencies of insects. To overcome logistic constraints of field experiments, we used a successfully validated simulation model to investigate plant responses to removal of herbivores and their enemies. Consistent with our predictions, instability measured by herbivore-induced plant mortality increased with increasing land use intensity. Simultaneously, the balance between herbivores and natural enemies turned increasingly towards herbivore dominance and natural enemy failure. Under natural conditions, there were more frequently significant effects of belowground herbivores and their natural enemies on plant performance, whereas there were more aboveground effects in agroecosystems. This result was partly due to the “boom-bust” behavior of the shoot herbivore population. Plant responses to herbivore or natural enemy removal were much more abrupt than the imposed smooth land use intensity gradient. This may be due to the presence of multiple trophic levels aboveground and belowground. Our model suggests that destabilization and extinction are more likely to occur in agroecosystems than in natural communities, but the shape of the relationship is nonlinear under the influence of multiple trophic interactions.

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.

Diversity is expected to increase the resilience of ecosystems. Nevertheless, highly diverse ecosystems have collapsed, as did Lake Victoria's ecosystem of cichlids or Caribbean coral reefs. We try to gain insight to this paradox, by analyzing a simple model of a diverse community where each competing species inflicts a small mortality pressure on an introduced predator. High diversity strengthens this feedback and prevents invasion of the introduced predator. After a gradual loss of native species, the introduced predator can escape control and the system collapses into a contrasting, invaded, low-diversity state. Importantly, we find that a diverse system that has high complementarity gains in resilience, whereas a diverse system with high functional redundancy gains in resistance. Loss of resilience can display early-warning signals of a collapse, but loss of resistance not. Our results emphasize the need for multiple approaches to studying the functioning of ecosystems, as managing an ecosystem requires understanding not only the threats it is vulnerable to but also pressures it appears resistant to. [KEYWORDS: LAKE VICTORIA STABLE STATES

Photoinhibition is characterised by a decreasing rate of photosynthesis with increasing light. It occurs in many photosynthetic organisms and is especially apparent in phytoplankton species sensitive to high light. Yet, the population and community level consequences of photoinhibition are not well understood. Here, we present a resource competition model that includes photoinhibition. The model shows that, in strong light, photoinhibition leads to an increase of the specific growth rate with increasing population density due to self-shading. This so-called Allee effect can be either weak or strong. In monoculture, a strong Allee effect results in two alternative stable states. A low population density does not provide sufficient shade to protect itself against photoinhibition, such that the population goes extinct. Conversely, above a threshold population density the population may create sufficiently turbid conditions to suppress photoinhibition, so that the population can establish itself. When several species compete for light, a species which cannot establish itself due to photoinhibition can be facilitated by other species less sensitive to photoinhibition. If such facilitators are absent, photoinhibition may cause alternative stable states in community composition. Since each alternative stable state is dominated by a single species, photoinhibition does not favour species coexistence. The model predictions are consistent with published competition experiments, and illustrate the complex effects of photoinhibition on community assembly.

1. We describe the dynamics of host–parasite interactions over a period of more than 30 years between the freshwater diatom Asterionella formosa and two highly virulent chytrid parasites (Rhizophydium planktonicum and Zygorhizidium planktonicum) in Lake Maarsseveen, The Netherlands. This period is characterised by a significant warming trend which is strongest in spring. 2. The key spring event in lakes, the diatom bloom, was in many years dominated by Asterionella. We examine whether and how climate warming has affected the prevalence of infection in Asterionella by chytrids. 3. In years with cold winters/early springs, a dense Asterionella bloom is followed by epidemic development of disease as high Asterionella densities greatly facilitate transmission of chytrid zoospores. This sequence of events is absent in milder winters. 4. Earlier experimental studies have shown that the parasite is almost non-infective at water temperatures below 3 °C, offering a disease-free window of opportunity for growth of Asterionella. Climate warming has reduced periods in which water temperature remains

1.We studied the effect of size-selective predation on the outcome of competition between two differently sized prey species in a homogenous environment. 2. Using a physiologically structured population model, we calculated equilibrium food concentrations for a range of predation scenarios defined by varying maximum predation intensity and size-selectivity, the latter being characterized by the neutral selection length (NSL), where negative selection of small prey size-classes turns into positive selection of larger prey. We parameterized the model according to the well-studied example of fish predation on two differently sized cladoceran species, Daphnia pulicaria and Daphnia galeata. 3.Although the larger D. pulicaria was principally the better competitor for food, competitive superiority shifted to the smaller D. galeata under certain predation scenarios. The lowest predation intensity needed to induce a shift from D. pulicaria to D. galeata was found at NSL values in between the sizes at maturity of both species. 4.Analysing the per capita mortality rates as a result of the underlying parameters of the mortality model, NSL and maximum predation intensity, revealed that the tolerable mortality rate of daphnids decreased as NSL increases towards values close to the size at maturity. This effect was most pronounced in D. pulicaria, thus explaining a higher vulnerability of the larger species to size-selective predation. 5.A reduction of the size at maturity in the smaller species (D. galeata) as a phenotypic response to the presence of fish resulted not only in an increased capability to withstand predation, but also in competitive dominance shifts over the larger D. pulicaria at lower predation intensities and a much wider range of NSL as a trait-mediated indirect effect. 6.Overall, our results demonstrate that shifts in dominance of differently sized herbivores under size-selective predation regimes may be facilitated by the demonstrated alteration in competitive capacities and thus might not be exclusively caused by direct predation effects.

In meromictic lakes such as Lake Shira, horizontal inhomogeneity is small in comparison with vertical gradients. To determine the vertical distribution of temperature, salinity, and density of water in a deep zone of a Lake Shira, or other saline lakes, a one-dimensional (in vertical direction) mathematical model is presented. A special feature of this model is that it takes into account the process of ice formation. The model of ice formation is based on the one-phase Stefan problem with the linear temperature distribution in the solid phase. A convective mixed layer is formed under an ice cover due to salt extraction in the ice formation process. To obtain analytical solutions for the vertical distribution of temperature, salinity, and density of water, we use a scheme of vertical structure in the form of several layers. In spring, the ice melts as top and bottom. These processes are taken into account in the model. The calculated profiles of salinity and temperature of Shira Lake are in good agreement with field measurement data for each season. Additionally, we focussed on the redox zone, which is the zone in which the aerobic layers of a water column meet the anaerobic ones. Hyperactivity of plankton communities is observed in this zone in lakes with hydrogen sulphide monimolimnion, and Lake Shira is among them. The location of the redox zone in the lake, which is estimated from field measurements, coincides with a sharp increase in density (the pycnocline) during autumn and winter. During spring and summer, the redox zone is deeper than the pycnocline. The location of pycnocline calculated with the hydro physical model is in good agreement with field measurement data.

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 on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.

A one-dimensional numerical model and a two-dimensional numerical model of the hydrodynamic and thermal structure of Lake Shira during summer have been developed, with several original physical and numerical features. These models are well suited to simulate the formation and dynamics of vertical stratification and provide a basis for an ecological water-quality model of the lake. They allow for the quantification of the vertical mixing processes that govern not only the thermal structure but also the nutrient exchange, and more generally, the exchange of dissolved and particulate matter between different parts of the lake. The outcome of the calculations has been compared with the field data on vertical temperature and salinity distributions in Lake Shira. Lake Shira is meromictic and exhibits very stable annual stratification. The stratification is so stable because of the high salinity of the water. If the water in Lake Shira were fresh and other parameters (depth, volume, and meteorology) were the same, as now, the lake would be mixed in autumn. Using the newly developed models and using common meteorological parameters, we conclude that Lake Shira will remain stratified in autumn as long as the average salinity is higher than 3‰.

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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 addition to vertical inhomogeneities of both physicochemical parameters, biological and physical factors also play a role in maintaining these inhomogeneities. We conclude that the stratified distributions of the major food web components will have several implications for ecosystem structure and dynamics. Trophic interactions as well as mass and energy flows can be significantly impacted by such heterogeneous distributions. Species spatially separated even by relatively short distances, say a few centimetres will not directly compete. Importantly, we demonstrate that not only bacteria, phytoflagellates and ciliate tend to concentrate in thin layers but also larger-sized species such Gammarus (amphipods) can also under certain environmental conditions have stratified distribution with maxima in relatively thin layer. As the vertical structure of the lake ecosystem is rather complex in such stratified lakes as ours, the strategy of research, including sampling techniques, should consider potentially variable and non-homogeneous distributions.

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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.

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.

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.

Addressing complex ecological research questions often requires complex empirical experiments. However, due to the logistic constraints of empirical studies there is a trade-off between the complexity of experimental designs and sample size. Here, we explore if the simulation of complex ecological experiments including stochasticity-induced variation can aid in alleviating the sample size limitation of empirical studies. One area where sample size limitations constrain empirical approaches is in studies of the above- and belowground controls of trophic structure. Based on a rule- and individual-based simulation model on the effect of above- and belowground herbivores and their enemies on plant biomass, we evaluate the reliability of biomass estimates, the probability of experimental failure in terms of missing values, and the statistical power of biomass comparisons for a range of sample sizes. As expected, we observed superior performance of setups with sample sizes typical of simulations (n = 1000) as compared to empirical experiments (n = 10). At low sample sizes, simulated standard errors were smaller than expected from statistical theory, indicating that stochastic simulation models may be required in those cases where it is not possible to perform pilot studies for determining sample sizes. To avoid experimental failure, a sample size of n = 30 was required. In conclusion, we propose that the standard tool box of any ecologist should comprise a combination of simulation and empirical approaches to benefit from the realism of empirical experiments as well as the statistical power of simulations.

When does community assembly lead to a predictable species composition and when does this process depend on chance events, such as the timing of species arrivals? We studied the combined effects of enrichment and predation on the occurrence of priority effects, i.e. dependency on the timing of arrival, using a model of a small food web consisting of a predator, two competing prey and interference through allelopathy. Our analysis shows the conditions under which priority effects can occur. In the system we studied, the interfering species has to be the weaker resource exploiter of the two consumers, or it has to be more susceptible to predation. When it is the weaker resource exploiter, a minimum level of nutrient input is required for interference to be strong enough to cause a priority effect. When the interfering species is more susceptible to predation, a priority effect actually requires predation, which in itself also requires a minimum level of nutrient inflow. However, the priority effect disappears when predation pressure rises above a threshold value, also when the two competitors are equally preferred by the predator. This is so because predation reduces population densities and thereby the strength of interference. Our analyses make clear how the effects of resources and predation can combine to result in the absence or presence of priority effects during community assembly.

Modeling studies examining the effect of lakes on regional and global climate, as well as studies on the influence of climate variability and change on aquatic ecosystems, are surveyed. Fully coupled atmosphere–land surface–lake climate models that could be used for both of these types of study simultaneously do not presently exist, though there are many applications that would benefit from such models. It is argued here that current understanding of physical and biogeochemical processes in freshwater systems is sufficient to begin to construct such models, and a path forward is proposed. The largest impediment to fully representing lakes in the climate system lies in the handling of lakes that are too small to be explicitly resolved by the climate model, and that make up the majority of the lake-covered area at the resolutions currently used by global and regional climate models. Ongoing development within the hydrological sciences community and continual improvements in model resolution should help ameliorate this issue.

Growing empirical evidence suggests that aboveground and belowground multitrophic communities interact. However, investigations that comprehensively explore the impacts of above- and belowground third and higher trophic level organisms on plant and herbivore performance are thus far lacking. We tested the hypotheses that above- and belowground higher trophic level organisms as well as decomposers affect plant and herbivore performance and that these effects cross the soil–surface boundary. We used a well-validated simulation model that is individual-based for aboveground trophic levels such as shoot herbivores, parasitoids, and hyperparasitoids while considering belowground herbivores and their antagonists at the population level. We simulated greenhouse experiments by removing trophic levels and decomposers from the simulations in a factorial design. Decomposers and above- and belowground third trophic levels affected plant and herbivore mortality, root biomass, and to a lesser extent shoot biomass. We also tested the effect of gradual modifications of the interactions between different trophic level organisms with a sensitivity analysis. Shoot and root biomass were highly sensitive to the impact of the fourth trophic level. We found effects that cross the soil surface, such as aboveground herbivores and parasitoids affecting root biomass and belowground herbivores influencing aboveground herbivore mortality. We conclude that higher trophic level organisms and decomposers can strongly influence plant and herbivore performance. We propose that our modelling framework can be used in future applications to quantitatively explore the possible outcomes of complex above- and belowground multitrophic interactions under a range of environmental conditions and species compositions.

The effects of inducible defenses and constitutive defenses on population dynamics were investigated in a freshwater plankton system with rotifers as predators and different algal strains as prey. We made predictions for these systems using a chemostat predator–prey model and focused on population stability and predator persistence as a function of flow-through rate. The model exhibits three major types of behavior at a high nutrient concentration: (1) at high dilution rates, only algae exist; (2) at intermediate dilution rates, algae and rotifers show stable coexistence; (3) at low dilution rates, large population fluctuations occur, with low minimum densities entailing a risk of stochastic rotifer extinctions. The size and location of the corresponding areas in parameter space critically depend on the type of algal defense strategy. In an 83-day high-nutrient chemostat experiment we changed the dilution rate every 3 weeks, from 0.7 to 0.5 to 0.3 to 0.1 per day. Within this range of dilution rates, rotifers and algae coexisted, and population fluctuations of algae clearly increased as dilution rates decreased. The CV of herbivore densities was highest at the end of the experiment, when the dilution rate was low. On day 80, herbivorous rotifers had become undetectable in all three chemostats with permanently defended algae (where rotifer densities had already been low) and in two out of three chemostats where rotifers had been feeding on algae with inducible defenses (that represented more edible food). We interpret our results in relation to the paradox of enrichment.

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.

We followed adaptation of the chytrid parasite Zygorhizidium planktonicum during 200 generations of growth on its host, the freshwater diatom Asterionella formosa, in a serial passage experiment. Evolution of parasite fitness was assessed both on a homogenous and heterogeneous host population, consisting of respectively a single new and ten different new host strains. These 10 host strains were genetically different and also varied in their initial susceptibility to the parasite. Parasite fitness increased significantly and rapidly on the new, genetically homogenous host population, but remained unaltered during 200 generations of growth on the heterogeneous host population. Enhanced parasite fitness was the result of faster and more efficient transmission, resulting in higher values of R0 (number of secondary infections). Consequently, parasites that evolved within the uniclonal host population infected significantly more of these hosts than did their ancestors. We thus provide experimental evidence for the widely held view that host genetic diversity restricts evolution of parasites and moderates their harmful effects. Genetically uniform host populations are not only at increased risk from fungal epidemics because they all share the same susceptibility, but also because new parasite strains are able to adapt quickly to new host environments and to improve their fitness.

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.

We studied costs and benefits of life history shifts of water fleas (genus Daphnia) in response to infochemicals from planktivorous fish. We applied a dynamic energy budget model to investigate the resource allocation patterns underlying the observed life history shifts and their adaptive value under size selective predation in one coherent analysis. Using a published data set of life history shifts in response to fish infochemicals we show that Daphnia invests less energy in somatic growth in the fish treatment. This observation complies with theoretical predictions on optimal resource allocation. However, the observed patterns of phenotypic plasticity cannot be explained by changes in resource allocation patterns alone because our model-based analysis of the empirical data clearly identified additional bioenergetic costs in the fish treatments. Consequently, the response to fish kairomone only becomes adaptive if the intensity of size selective predation surpasses a certain critical level. We believe that this is the first study that puts resource allocation, energetic costs, and adaptive value of predator induced life-history shifts – using empirical data – into one theoretical framework.

The Intergovernmental Panel on Climate Change (IPCC) predicts increases in global average surface temperature from 1.1 to 6.4 °C for the year 2100. Here, we focus on the impact of climate warming on eutrophic shallow lakes in the Netherlands, using three representative lakes that cover the full range of lake sizes and depths. In these lakes, temperature has been shown to be the main determinant of hatching and growth of young-of-the-year fish. Because records of water temperature of our study lakes are incomplete, we applied an existing model to predict water temperatures from air temperatures for shallow, wind exposed and holomictic water bodies. To evaluate the implications of our results for marine systems, we also analyzed water temperature data of Marsdiep, a tidal inlet to the Waddensea. The lake water temperature model fitted equally well to all four water bodies. Applying the water temperature model to the period 1961–2006 showed an annual increase of 0.042 °C irrespective of lake size and depth. We extrapolated the consequences of lake warming for the onset of growth of larval bream and the size of young-of-the-year bream at the end of the year using an existing fish hatching and growth model. Both models were tested against data from Lake Tjeukemeer, which is intermediate in size compared to Lake Zwemlust and Lake IJsselmeer. The main conclusions of this study are that 1) there is a very tight coupling between air and water temperatures in Dutch shallow lakes, irrespective of their size, resulting in highly similar patterns of lake temperature and a direct translation of climate warming into lake warming; 2) on average water temperature has increased by 2 °C in the period 1961–2006; 3) temperature patterns in the tidal inlet showed a surprising resemblance with the lake temperature patterns, the coastal marine system essentially behaving like an extremely large lake; 4) there are, however, strong seasonal patterns in the extent of warming in a given period of the year; 5) lake warming leads to ca. 3 weeks earlier onset of growth and 20 mm larger sizes in bream during 1971–2006 under the assumption of temperature limited growth in these eutrophic ecosystems.

Ecologists have long debated the role of predation in mediating the coexistence of prey species. Theory has mainly taken a bitrophic perspective that excludes the effects of inducible defenses at different trophic levels. However, inducible defenses could either limit or enhance the effects of predation on coexistence, by means of effects on bottom-up control and population stability. Our aim was to investigate how inducible defenses at different trophic levels affect the possibilities for predator-mediated coexistence, as opposed to competitive exclusion, in replicated experimental plankton communities. In particular, we analyzed how the presence or absence of inducible defenses in algal basal prey affected the outcome of competition between an inducible defended and an undefended herbivore, in the presence or absence of a carnivore. We found the undefended herbivore to be a superior competitor in the absence of predation. This outcome was reversed in the presence of a shared carnivore: populations of the undefended herbivore then strongly declined. The extent of this population decline differed between food webs based on undefended as opposed to inducible defended algal prey. In the former the undefended herbivore became undetectable for most of the duration of the experiment. In the latter the undefended herbivore also crashed to low densities, but it could still be detected during most of the experiment. In food webs based on inducible defended algae, the carnivore failed to reach high densities and exerted weaker top–down control on the two competing herbivores. We conclude that the inducible defense in one of our two competing herbivores allowed the outcome of competition to be reversed when a shared carnivore was added. Inducible defenses in algae did not change this outcome, but they significantly delayed extinction of the undefended herbivore. Predation itself did not promote coexistence in these experimental plankton communities.

Spatial self-organization is the main theoretical explanation for the global occurrence of regular or otherwise coherent spatial patterns in ecosystems. Using mussel beds as a model ecosystem, we provide an experimental demonstration of spatial self-organization. Under homogeneous laboratory conditions, mussels developed regular patterns, similar to those in the field. An individual-based model derived from our experiments showed that interactions between individuals explained the observed patterns. Furthermore, a field study showed that pattern formation affected ecosystem-level processes in terms of improved growth and resistance to wave action. Our results imply that spatial self-organization is an important determinant of the structure and functioning of ecosystems, and it needs to be considered in their conservation.

We studied how chemicals obtained as filtrates from algal monocultures (algal chemicals) and from rotifer cultures with or without algae (rotifer chemicals) affected feeding rates of the rotifer Brachionus calyciflorus on its food algae, both directly and indirectly (through chemical-induced changes in algal morphology). Algal chemicals had a strong stimulating effect on the feeding rate of B. calyciflorus, but these effects were counteracted by rotifer chemicals. In functional response experiments, rotifer chemicals lowered maximum ingestion rates and had strong effects on assimilation rates and assimilation efficiencies of B. calyciflorus, probably due to the release of unspecific (auto)toxic metabolites. Furthermore, rotifer chemicals induced colony formation in the food alga Scenedesmus obliquus. Above the optimum particle size for ingestion by B. calyciflorus, larger algal colony sizes increased the food-handling time, thus lowering ingestion and assimilation rates. Through their effects on trophic interactions, infochemicals may play a role in structuring and the functioning of aquatic food webs.

Theoretical studies have predicted that inducible defenses affect food chain dynamics and persistence. Here we review and evaluate laboratory experiments that tested hypotheses developed from these theoretical studies. This review specifically focuses on the effects of inducible defenses in phytoplankton-rotifer food chain dynamics. First, we describe the occurrence of colony formation within different strains of green algae (Scenedesmaceae) in response to infochemicals released during grazing by the herbivorous rotifer Brachionus calyciflorus. Then we examined the effects of inducible defenses on the population dynamics of this planktonic system in which algal strains that differed in their defense strategies were used. Simple food chains were composed of green algae (Scenedesmaceae), herbivorous rotifers (Brachionus calyciflorus) and carnivorous rotifers (Asplanchna brightwellii). In this system B. calyciflorus exhibits an inducible defense against predation by developing long postero-lateral spines. Experimental studies showed that inducible defenses, as opposed to their absence, could prevent high-amplitude population fluctuations. We discuss the dual effects of induced defenses on extinction probabilities and consider the fit of a theoretical model to experimental data to understand the mechanisms that underlie the observed dynamics.

Climate change is likely to have far-reaching effects on biotic interactions in aquatic ecosystems. We investigated the effect of different spring warming scenarios on the succession of three algal groups (cyanobacteria, diatoms and green algae) in 10-l microcosms. We fitted these microcosm data to a simple mechanistic model to estimate the effect of different climate warming scenarios on the population dynamics of these algal functional groups. Experimental and model results indicate that the different algal functional groups respond differently to climate warming under phosphorus-limited conditions. Whereas the successional sequence, from diatoms to green algae to cyanobacteria, was not affected by the different climate warming scenarios, cyanobacteria showed a stronger response to the different climate warming scenarios than diatoms or green algae. Both the growth rates and peak abundances of cyanobacteria were significantly higher in the average and warm spring scenarios than in the cold spring scenario. Our findings illustrate that integration of models and microcosm experiments are a useful approach in predicting the impacts of rising temperatures on the dynamics of phytoplankton communities.

Inducible defenses are dynamic traits that modulate the strength of both plant–herbivore and herbivore–carnivore interactions. Surprisingly few studies have considered the relative contributions of induced plant and herbivore defenses to the overall balance of bottom-up and top-down control. Here we compare trophic cascade strengths using replicated two-level and three-level plankton communities in which we systematically varied the presence or absence of induced defenses at the plant and/or herbivore levels. Our results show that a trophic cascade, i.e., significantly higher plant biomass in three-level than in two-level food chains, occurred whenever herbivores were undefended against carnivores. Trophic cascades did not occur when herbivores exhibited an induced defense. This pattern was obtained irrespective of the presence or absence of induced defenses at the plant level. We thus found that herbivore defenses, not plant defenses, had an overriding effect on cascade strength. We discuss these results in relation to variation in cascade strengths in natural communities.

We describe the limnological changes between 1989 and 2006 in an urban, shallow lake, Laguna Alalay, located in the Andean valley of Cochabamba (Bolivia). Until 1960, water diversion to the lake was used to lower the inundation risk of Cochabamba city. In the 1980s and 1990s, the high waterfowl diversity and recreational services provided by the lake increased its conservation value. However, the population increase and the discharge of wastewater rich in nutrients increased eutrophication, and the lake became characterized by an annual alternation of submerged macrophytes and phytoplankton. The main aim of the present study is to analyze the response of the lake to manipulations implemented by local authorities: (a) sediment removal and accidental introduction of the exotic fish species Odontesthes bonariensis in 1997 and (b) manual mass removal of floating macrophytes during 2004–2006. The sediment removal and species introduction had several unpredictable consequences for the functioning of the lake, namely the transition to a permanent turbid water state and the persistent dominance of floating macrophytes. A general conclusion of our study is that any lake recovery measures in Bolivia should consider not only ecological, but also socio-economic and political aspects. Taking these into account, restoration of the submerged macrophyte-dominated state may not be that universally desirable as is widely held.

Mismatches between predator and prey due to climate change have now been documented for a number of systems. Ultimately, a mismatch may have far-reaching consequences for ecosystem functioning as decoupling of trophic relationships results in trophic cascades. Here, we examine the potential for climate change induced mismatches between zooplankton and algae during spring succession, with a focus on Daphnia and its algal food. Whereas the development of an overwintering population of daphnids may parallel shifts in phytoplankton phenology due to climate warming, changes in the photoperiod–temperature interaction may cause the emerging population of daphnids to hatch too late and mismatch their phytoplankton prey. A decoupling of the trophic relationship between the keystone herbivore Daphnia and its algal prey can result in the absence of a spring clear water phase. We extended an existing minimal model of seasonal dynamics of Daphnia and algae and varied the way the Daphnia population is started in spring, i.e., from free swimming individuals or from hatching resting eggs. Our model results show that temperature affects the timing of peak abundance in Daphnia and algae, and subsequently the timing of the clear water phase. When a population is started from a small inoculum of hatching resting eggs, extreme climate warming (+6°C) results in a decoupling of trophic relationships and the clear water phase fails to occur. In the other scenarios, the trophic relationships between Daphnia and its algal food source remain intact. Analysis of 36 temperate lakes showed that shallow lakes have a higher potential for climate induced match–mismatches, as the probability of active overwintering daphnids decreases with lake depth. Future research should point out whether lake depth is a direct causal factor in determining the presence of active overwintering daphnids or merely indicative for underlying causal factors such as fish predation and macrophyte cover.

Global average surface temperatures are expected to rise by about 1.4–5.8°C from the present until the year 2100. This temperature increase will affect all ecosystems on earth. For shallow lakes—which can be either in a clear water or a turbid state—this climate change will expectedly negatively affect water transparency though the prediction is far from conclusive and experimental investigations elucidating the potential climatic effects on shallow lakes are still rare. The aim of this study was to further shape and sharpens hypotheses on the impact of climate change on shallow lakes by applying an existing and well-calibrated ecosystem model, PCLake. We focused on asymptotic model behaviour for a range of temperature and loading scenarios in a factorial design. We conclude that climate change will likely lead to decreased critical nutrient loadings. Combined with an expected increase in the external nutrient loading, this will increase the probability of a shift from a clear to a turbid state. As the model predicts a higher summer chlorophyll-a concentration, a stronger dominance of cyanobacteria during summer and a reduced zooplankton abundance due to climate change, the turbid state itself is likely to become even more severe.

Here we consider how information transfer shapes interactions in aquatic and terrestrial food webs. All organisms, whether they are dead or alive, release certain chemicals into their environment. These can be used as infochemicals by any other individual in the food web that has the biological machinery to sense and process such information. Such machinery has evolved in bacteria, plants and animals and has thus become an inextricable part of the mechanisms that underlie feeding relations in food webs. Organisms live in environments suffused with infochemicals and this information network can be tapped into by both predators and their prey. However, it also opens doors to confusion in the face of a bewildering abundance and complexity of information. Infochemical mixing, masking, crypsis and mimicry could cause such confusion, especially in species-rich communities. We provide a point of entry into this field of enquiry by identifying seminal papers and major reviews and by discussing research lines that might enhance our mechanistic understanding of interactions in food webs. We highlight empirical work on the ways in which individuals use infochemicals and discuss model results on how this mediates patterns of population dynamics. We consider implications for ecosystem management and indicate how classical models and novel approaches from ecological infor [KEYWORDS: Biodiversity ; Biological control ; Climate ; Dimethyl sulphide ; Global warming ; Individual based models ; Information networks in ecosystems ; Integration of laboratory and field data ; Learning ; Linking levels of ecological organization ; Lake restoration ; Phenotypic plasticity ; Trait-mediated interactions]

Learning animals are predicted to use a flexible patch-leaving threshold (PLT) while foraging in a depletable environment under exploitative competition. This prediction was tested in flock-feeding Bewick's swans (Cygnus columbianus bewickii) depleting hidden tubers of fennel pondweed (Potamogeton pectinatus) in a two-dimensional, continuous environment. The swans' patch residence time was measured by combining recordings of the foraging behaviour and movement paths. The tuber biomass density was measured before and after the period of exploitation, using the presumable foraging window of the swans as the scale of measurement. Swan foraging was simulated in order to predict the effects of flexible and fixed PLTs, respectively, on the patch residence time and the spatial heterogeneity of the tuber biomass density. Flexible PLTs were predicted to lead to short and decreasing patch residence times and a decrease in the coefficient of variation in tuber biomass densities, whereas the reverse was generally the case for fixed PLTs. Observed patch residence times did not decrease with time and were intermediate between those predicted for swans with flexible and fixed PLTs. Furthermore, an increase of the coefficient of variation in the tuber biomass density was observed. Given the observed giving-up biomass densities the most likely model was one with swans with a fixed rather than a flexible PLT. These results point at factors that may affect the spacing behaviour or constrain the use of a flexible PLT in swans.

1. Theoretical studies have shown that inducible defences have the potential to affect population stability and persistence in bi- and tritrophic food chains. Experimental studies on such effects of prey defence strategies on the dynamics of predator–prey systems are still rare. We performed replicated population dynamics experiments using the herbivorous rotifer Brachionus calyciflorus and four strains of closely related algae that show different defence responses to this herbivore. 2. We observed herbivore populations to fluctuate at a higher frequency when feeding on small undefended algae. During these fluctuations minimum rotifer densities remained sufficiently high to ensure population persistence in all the replicates. The initial growth of rotifer populations in this treatment coincided with a sharp drop in algal density. Such a suppression of algae by herbivores was not observed in the other treatments, where algae were larger due to induced or permanent defences. I 3. A variety of alternative mechanisms could explain differential herbivore persistence in the different defence treatments. Our analysis showed the density and fraction of highly edible algal particles to better explain herbivore persistence and extinctions than total algal density, the fraction of highly inedible food particles or the accumulation of herbivore waste products or autotoxins. 4. We argue that the rotifers require a minimum fraction and density of edible food particles for maintenance and reproduction. We conjecture that induced defences in algae may thus favour larger zooplankton species such as Daphnia spp. that are less sensitive to shifts in their food size spectrum, relative to smaller zooplankton species, such as rotifers and in this way contributes to the structuring of planktonic communities. [KEYWORDS: consumer–resource interactions ; inducible defences ; phenotypic plasticity ; Scenedesmus ; trait-mediated interactions.]

Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers.

Laboratory experiments were conducted to elucidate the allelopathic effects of exudates from the aquatic macrophyte Stratiotes aloides on the growth and morphology of the green alga Scenedesmus obliquus. Both water originating from a S. aloides culture and water that had not been in contact with S. aloides was simultaneously inoculated with S. obliquus cells. In all experiments we observed a highly significant inhibitory effect of Stratiotes water on the green alga. The duration of the lag phase as well as the initial biovolume doubling time of S. obliquus were extended. The growth rate of S. obliquus was only significantly inhibited by the younger Stratiotes plants. Furthermore, the mean particle volume (MPV) of Scenedesmus increased significantly in the presence of Stratiotes water in all three experiments. Microscopic analyses confirmed that S. obliquus forms more colonies in the presence of water from a S. aloides culture. Colonies of phytoplankton have higher sinking rates than single phytoplankton cells of the same species and disappear faster from the upper water layers, reducing the competition for light between algae and macrophytes. [KEYWORDS: Colony formation ; Growth inhibition ; Infochemical ; Macrophytes ; Sedimentation]

Individual-based models (IBMs) allow the explicit inclusion of individual variation in greater detail than do classical differential and difference equation models. Inclusion of such variation is important for continued progress in ecological and evolutionary theory. We provide a conceptual basis for IBMs by describing five major types of individual variation in IBMs: spatial, ontogenetic, phenotypic, cognitive, and genetic. IBMs are now used in almost all subfields of ecology and evolutionary biology. We map those subfields and look more closely at selected key papers on fish recruitment, forest dynamics, sympatric speciation, metapopulation dynamics, maintenance of diversity, and species conservation. Theorists are currently divided on whether IBMs represent only a practical tool for extending classical theory to more complex situations, or whether individual-based theory represents a radically new research program. We feel that the tension between these two poles of thinking can be a source of creativity in ecology and evolutionary theory.

Climate change will alter freshwater ecosystems but specific effects will vary among regions and the type of water body. Here, we give an integrative review of the observed and predicted impacts of climate change on shallow lakes in the Netherlands and put these impacts in an international perspective. Most of these lakes are man-made and have preset water levels and poorly developed littoral zones. Relevant climatic factors for these ecosystems are temperature, ice-cover and wind. Secondary factors affected by climate include nutrient loading, residence time and water levels. We reviewed the relevant literature in order to assess the impact of climate change on these lakes. We focussed on six management objectives as bioindicators for the functioning of these ecosystems: target species, nuisance species, invading species, transparency, carrying capacity and biodiversity. We conclude that climate change will likely (i) reduce the numbers of several target species of birds; (ii) favour and stabilize cyanobacterial dominance in phytoplankton communities; (iii) cause more serious incidents of botulism among waterfowl and enhance the spreading of mosquito borne diseases; (iv) benefit invaders originating from the Ponto-Caspian region; (v) stabilize turbid, phytoplankton-dominated systems, thus counteracting restoration measures; (vi) destabilize macrophyte-dominated clear-water lakes; (vii) increase the carrying capacity of primary producers, especially phytoplankton, thus mimicking eutrophication; (viii) affect higher trophic levels as a result of enhanced primary production; (ix) have a negative impact on biodiversity which is linked to the clear water state; (x) affect biodiversity by changing the disturbance regime. Water managers can counteract these developments by reduction of nutrient loading, development of the littoral zone, compartmentalization of lakes and fisheries management. [KEYWORDS: Biodiversity ; Carrying capacity ; Invading species ; Nuisance species ; Temperature ; Transparency]

According to the size-efficiency hypothesis (SEH) larger bodied cladocerans are better competitors for food than small bodied species. In environments with fish, however, the higher losses of the large bodied species due to size-selective predation may shift the balance in favor of the small bodied species. Here we present a theoretical framework for the analysis of the competitive abilities of zooplankton species that takes both competition and predation into account in one coherent analysis. By applying the conceptually well-understood framework of physiologically structured population models we were able to predict the relative difference in predation rates necessary to cause a shift in dominance of the large-bodied species (Daphnia pulicaria) to the small-bodied species (D. galeata). These predictions depend only on seven easily interpretable parameters per species: size at birth, size at maturity and maximum size, age at maturity, maximal clutch size, egg development time and finally the half-saturation constant for food. The critical equilibrium mortality of D. pulicaria was 0.16 d1 at food concentrations close to the critical food concentration of D. galeata, i.e. D. pulicaria will win the competition as long as its mortality rate is below 0.16 d1. At higher food concentrations the differential mortality curve (plotting equilibrium mortalities of both species against each other) approached a linear function with a slope of one and an intercept equal to the difference in maximal population birth rates. The prediction of critical predation rates was independent of the ingestion rate of the cladocerans and the algal carrying capacity and food regeneration rate of the environment although the mechanism works through competition for a shared algal food resource. We interpret these findings in terms of the relative predation risk large and small-bodied cladocerans will face in various freshwater ecosystems.

The allelopathic potential of exudates from the aquatic macrophyte Stratiotes aloides on the growth of phytoplankton was investigated. A selection of phytoplankton species, occurring in habitats similar to that of Stratiotes, was used: two cyanobacterial strains (toxic and non-toxic Microcystis aeruginosa), one green alga (Scenedesmus obliquus) and one eustigmatophyte (Nannochloropsis limnetica). The results indicate allelopathic effects of Stratiotes on phytoplankton in six of the eight cases, expressed in an extended duration of the initial biovolume doubling time. The overall inhibitory effect (8–51%) was strain-specific for the two cyanobacteria. We also studied the effect of irradiance on the allelopathic potential of exudates from Stratiotes. Irradiance influenced the response of Scenedesmus only. The inhibitory effect of Stratiotes exudates on the growth of this green alga was stronger at 35 µmol m-2 s-1 than at 105 µmol m-2 s-1. We conclude that Stratiotes has allelopathic effects on phytoplankton, and that irradiance can, but does not always determine the extent of the allelopathic inhibition. In our experiments, the sensitivity of cyanobacteria to Stratiotes exudates was not higher than for other phytoplankton strains, but within cyanobacteria, the toxic strain was more sensitive than the non-toxic one. [KEYWORDS: Allelopathy ; Exudate ; Growth inhibition ; Initial biovolume doubling time ; Irradiance ; Lag phase]

Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern-oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity.

We developed a dynamic model to investigate the effect of atmospheric carbon dioxide (CO2) increase on plant growth in freshwater ecosystems. Steady-state simulations were performed to analyze the response of phytoplankton and submerged macrophytes to atmospheric CO2 elevation from 350 to 700 ppm. We studied various conditions that may affect this response, such as alkalinity, the air–water exchange rate of CO2, the community respiration rate, and the phosphorus (P) supply rate. The increase in atmospheric CO2 could affect submerged plant growth only under relatively eutrophic conditions and at a low community respiration rate. Alkalinity had little effect on the response of the different species. When the air–water exchange was low, the proportional effect of the CO2 increase on plant growth was higher. Under eutrophic conditions, algae and macrophytes using CO2 and HCO3 – may double their growth rate due to atmospheric CO2 elevation, while the growth of macrophytes restricted to CO2 assimilation may be threefold. The differences in response of the species under various conditions indicate that the elevation of atmospheric CO2 may induce drastic changes in the productivity and species dominance in freshwater systems. [KEYWORDS: climate change - phytoplankton - carbon dioxide - nutrients - air–water exchange - bicarbonate - alkalinity - phosphorus - macrophytes]

In order to evaluate the effects of inducible defences on community stability and persistence, we analyzed models of bitrophic and tritrophic food chains that incorporate consumer-induced polymorphisms. These models predict that intra-specific heterogeneity in defence levels resolves the paradox of enrichment for a range of top-down effects that affect consumer death rates and for all possible levels of primary productivity. We show analytically that this stability can be understood in terms of differences in handling times on the different prey types. Our predictions still hold when defences also affect consumer attack rates. The predicted stability occurs in both bitrophic and tritrophic food chains. Inducible defences may promote population persistence in tritrophic food chains. Here the minimum densities of cycling populations remain bound away from zero, thus decreasing the risk of population extinctions. However, the reverse can be true for the equivalent bitrophic predator-prey model. This shows that theoretical extrapolations from simple to complex communities should be made with caution. Our results show that inducible defences are among the ecological factors that promote stability i

Diel vertical migration (DVM) is a dynamic behavioral pattern found extensively in the world's oceans and lakes, yet the role of food and temperature distribution on DVM is still unclear. While DVM has been mostly studied in systems with surface food maxima, deep-water food maxima are quite common in lakes and oceans. In such ecosystems, optimal conditions of temperature and food are uncoupled. In a Swiss high-mountain lake (Oberer Arosasee) with a deep-water food maximum, we found that Daphnia galeata adults and juveniles exhibit DVM behavior almost throughout the year and migrated upwards, out of food-rich environments, at night. In a large indoor mesocosm experiment, we were able to show that Daphnia respond to fish-mediated cues by migrating into deeper water layers. In the presence of fish and using natural vertical food and temperature distributions in the mesocosms, we could reproduce the vertical distribution of adult Daphnia observed in the field. The indoor experiments show that food and temperature modulate the actual depth at which the animals stop migrating, whereas fish and ultraviolet radiation likely determine the timing of migration (its synchronization with dawn and dusk). Overall, our results show that the nighttime movement into the surface waters contributes to the fitness of Daphnia, given the costs and benefits associated with the trade-off between food and temperature. [KEYWORDS: deep-water chlorophyll maximum; diel vertical migration; enclosure experiment; fish kairomones; fish stocking; food–temperature trade-off; high-mountain lakes; phototaxis; plankton towers; zooplankton]

Resource edibility is a crucial factor in ecological theory on the relative importance of bottom-up and top-down control. Current theory explains trophic structure in terms of the relative abundance and succession of edible and inedible species across gradients of primary productivity. We argue that this explanation is incomplete owing to its focus on inedibility and the assumption that plants and herbivores have fixed defense levels. Consumer-induced defenses are an important source of variation in the vulnerability of prey and are prevalent in natural communities. Such induced defenses decrease per capita consumption rates of consumers but hardly ever result in complete inedibility. When defenses are inducible a prey population may consist of both undefended and defended individuals. Here we use food chain models with realistic parameter values to show that variation in consumption rates on different prey types causes a gradual instead of stepwise increase in the biomass of all trophic levels in response to enrichment. Such all-level responses have been observed in both aquatic and terrestrial ecosystems and in microbial food chains in the laboratory. We stress that, in addition to the known food web effects of interspecific variation in edibility, intraspecific variation in edibility is another form of within-trophic-level heterogeneity that also has such effects. We conclude that inducible defenses increase the relative importance of bottom-up control. [KEYWORDS: biomass responses; bottom-up control; edibility; enrichment; food chain; food web; infochemicals; multitrophic interactions; primary productivity; top-down control]

Everglades restoration will alter the hydrology of South Florida, affecting both water depth and salinity levels in the southern fringes of the Everglades, the habitat of the endangered American crocodile (Crocodylus acutus). A key question is what the effects of these hydrologic changes will be on the crocodile population. Reliable predictions of the viability of endangered species under a variety of management scenarios are of vital importance in conservation ecology. Juvenile American crocodiles are thought to be sensitive to high salinity levels, suffering reduced mass, and potentially reduced survivorship and recruitment. This could negatively impact the population recovery. We addressed the management issue of how the crocodile population will respond to alterations in hydrology with a spatially explicit individual-based model. The model is designed to relate water levels, salinities, and dominant vegetation to crocodile distribution, abundance, population growth, individual growth, survival, nesting effort, and nesting success. Our analysis shows that Everglades restoration, through its effects on water flow to estuaries, may benefit crocodile populations if increased freshwater flow reduces the chance that regional salinity levels exceed levels where small individuals lose mass. In addition, we conclude that conservation priority should be placed on reducing anthropogenic sources of mortality on large individuals, such as road mortality. Finally, research should focus on estimates of annual survivorship for large individuals. [KEYWORDS: Everglades restoration; Simulation model; American crocodile; Uncertainty analysis; Individual-based model]

Life history shifts in daphnids in response to fish infochemicals are generally interpreted as an adaptive response to positive size-selective predation. This interpretation does, however, not hold for larval and small juvenile planktivorous fish, which due to gape limitation, feed on small and medium sized prey. In a life table experiment we show that daphnids exposed to infochemicals excreted by small gape-limited perch and larger perch changed their life history in the same direction, irrespective of the contrasting size-selection of the fish. However, responses to fish infochemicals were strongly influenced by food conditions for daphnids. In the high food treatments size at maturity was in the presence of fish infochemicals, whereas age at maturity remained unchanged. Under low food conditions, size at maturity was generally smaller compared with the high food situation, but unaffected by fish infochemicals. By contrast, age at maturity, which was increased at low food levels, was significantly lower in fish treatments compared with the control. We conclude that life history responses of daphnids to gape-limited fish can indeed be maladaptive, but only in situations of high food availability. This combination of factors is, however, rather unlikely because gape-limited fish usually occur in late spring during the clear water phase when daphnids are severely food limited. We thus hypothesize that the costs of this maladaptive response under negative size-selective predation will be low under field conditions and the selective advantage under positive size-selective predation later in the season will outweigh these costs.

Uncertainty in estimates of survival of dispersing animals is a vexing difficulty in conservation biology. The current notion is that this uncertainty decreases the usefulness of spatially explicit population models in particular. We examined this problem by comparing dispersal models of three levels of complexity: (1) an event-based binomial model that considers only the occurrence of mortality or arrival, (2) a temporally explicit exponential model that employs mortality and arrival rates, and (3) a spatially explicit grid-walk model that simulates the movement of animals through an artificial landscape. Each model was fitted to the same set of field data. A first objective of the paper is to illustrate how the maximum-likelihood method can be used in all three cases to estimate the means and confidence limits for the relevant model parameters, given a particular set of data on dispersal survival. Using this framework we show that the structure of the uncertainty for all three models is strikingly similar. In fact, the results of our unified approach imply that spatially explicit dispersal models, which take advantage of information on landscape details, suffer less from uncertainly than do simpler models. Moreover, we show that the proposed strategy of model development safeguards one from error propagation in these more complex models. Finally, our approach shows that all models related to animal dispersal, ranging from simple to complex, can be related in a hierarchical fashion, so that the various approaches to modeling such dispersal can be viewed from a unified perspective [KEYWORDS: dispersal models, uncertainty; dispersal mortality; dispersal success; individual-based modeling; landscape details; likelihood, maximum; managing endangered species; model complexity; population models; random grid-walk models; spatially explicit modeling; suitable habitat]

Surface waterblooms of toxic cyanobacteria (scums) interfere with the use of lakes, for instance in the production of drinking water or for recreation. Routine monitoring data are not sufficient for early warning due to the large temporal and spatial variability in the occurrence of surface waterblooms, and the time lag between the formation of the scum and the availability of relevant information for risk management. We combined a “traditional” dynamic simulation model based upon differential equations with fuzzy logic to describe the three main conditions governing surface waterbloom formation: (1) a preexisting population of cyanobacteria, (2) buoyancy of the cells, and (3) stability of the water column. The attributes and membership functions of the fuzzy model were based on earlier field studies of diel changes in buoyancy and vertical distribution of cyanobacteria. The model was applied without further calibration to the large lake IJsselmeer (1200 km2) in the Netherlands, and we validated the model output using 12 years of NOAA-AVHRR (National Oceanic and Atmospheric Administration–Advanced Very High Resolution Radiometers) satellite images on which surface blooms are discernible as an enhanced vegetation index or increased surface water temperature. Existing surface blooms were predicted with high accuracy, but additional blooms were also predicted. A statistical test (Cohen's Kappa) showed that correct predictions of the absence or presence of surface blooms were highly unlikely to have occurred by chance only. The model can be used to predict the occurrence of surface waterblooms in advance on the basis of the long-term weather forecast, leaving time for appropriate management of the problem. The lake management has expressed interest in converting the present model into a fully operational–online–early warning system [KEYWORDS: algal blooms; early warning; blue-green algae; cyanobacteria; ecological models; eutrophication; fuzzy logic; Microcystis; remote sensing; scums; water management]

Various approaches to modeling the population dynamics and demography of Daphnia have been published. These methods range from the simple egg-ratio method, to mathematically complex models based on partial differential equations and numerically complex individual-based Daphnia population models. The usefulness of these models in unraveling the population dynamics and demography of Daphnia under natural conditions is discussed. Next to this, an extended version of an existing individual-based Daphnia model is documented (Cladosim) and its application to a typical field data set collected in 1995 in Lake Volkerak is shown. To answer the question which factor was limiting Daphnia numbers during the course of the season food level and temperature in the model were varied and results were compared with those obtained for the observed food level and temperature. These analysis showed that in April temperature was limiting while during May–July and September–October food was limiting. In August neither temperature nor food was limiting. Analysis with a set of size-selective mortality scenarios showed that on average the Daphnia population in Lake Volkerak experienced a mild positive size-selective mortality during the year that was analyzed. Birth rates derived with the detailed individual-based model were compared with those derived with the much simpler egg-ratio method. For the conditions as observed in Lake Volkerak in 1995, both methods gave very comparable results, despite sampling intervals of up to four weeks. The same holds under the environmental scenarios. Using the size-selective mortality scenarios it could be shown, however, that under strong mortality of the smaller daphnids, the egg-ratio method severely underestimates the birth rate. The vices and virtues of the new model and potential extensions are discussed [KEYWORDS: individual-based model, egg-ratio method, birth rate, size-selective mortality, food, temperature, Lake Volkerak]

We investigated the relative importance of a behavioural defence (refuge use through diel vertical migration) and a life history change (a reduced size at first reproduction) that are used by daphnids to decrease the risk of predation by visually hunting fish. We used an individual based model of a Daphnia population in a stratified lake to quantify the effects of these inducible defences on Daphnia predation-mortality and the resulting Daphnia population dynamics. Our analysis shows that diel vertical migration (DVM) confers a much stronger protection against fish predation than a reduced size at first reproduction (SFR). DVM allows daphnids to withstand a higher predation pressure in the epilimnion and it decelerates a Daphnia population decline more strongly than a reduced SFR. DVM effectively reduces the (P/B) flow of carbon from daphnids to fish. Many theoretical studies have only considered the fitness benefits of DVM above ‘staying up’ in the epilimnion of a lake. Our results suggest that ‘staying down’ in the hypolimnion would confer an even stronger fitness benefit to Daphnia than DVM at times of peak predation risk. Daphnids that remain in the hypolimnion avoid the predation suffered by migrating daphnids around dusk and dawn. Staying down could prevent a Daphnia population decline, while DVM and a reduced SFR can only decelerate th

SUMMARY1. The development of bream populations, water transparency, chlorophyll-a concentration, extent of submerged vegetation and densities of the zebra mussel, Dreissena polymorpha, were analysed in three shallow eutrophic lake systems subject to different fish management. 2. In Lake Veluwemeer, the bream population was reduced from c. 100 to 20 kg ha1 after 5 years of fishing. The mortality caused by the fishery was estimated at 38% of bream >15 cm in addition to a 13% natural mortality of bream >17 cm. The decline was followed by an expansion of the Chara beds present in the shallow parts, an increase in water transparency in the open-water zone, an increase in the density of zebra mussels and a decrease in chlorophyll-a concentrations. 3. The newly created Lake Volkerak showed trends opposite to those in Lake Veluwemeer. Bream colonised the lake in 1988 and reached a biomass of c. 140 kg ha1 in 1998. The water transparency decreased from a maximum of 3 m to c. 1 m and the chlorophyll-a concentration increased from 5 to 45 g L1. Submerged vegetation colonised up to 20% of the total lake area in the first 5 years after creation of the lake in 1987 but decreased to 10% as turbidity increased. 4. Seine fishery in the Frisian lake system did not appear to affect the bream population despite annual catches as high as 40-50 kg ha1. The estimated natural mortality of fish >15 cm was 15% and mortality by fishery was 26%. The high loss was apparently compensated by good recruitment and high growth rates resulting from a c. 1 °C higher water temperature during the years when bream were removed by fishing. There was only a slight decrease in chlorophyll-a concentrations and a slight increase 5. The results of this study suggest that the effects of bream exploitation in eutrophic lakes can vary depending on the efficiency of the fishery, recruitment success and temperature regime. In the absence of fishery, bream dominated the fish community in the study lakes and apparently prevented D. polymorpha and submerged vegetation from establishing because of physical disturbance, enhanced internal P-loading and resettling of resuspended sediments.

The paper aims at exploring the viability of the Florida snail kite population under various drought regimes in its wetland habitat. The population dynamics of snail kites are strongly linked with the hydrology of the system due to the dependence of this bird species on one exclusive prey species, the apple snail, which is negatively affected by a drying out of habitat. Based on empirical evidence, it has been hypothesised that the viability of the snail kite population critically depends not only on the time interval between droughts, but also on the spatial extent of these droughts. A system wide drought is likely to result in reduced reproduction and increased mortality, whereas the birds can respond to local droughts by moving to sites where conditions are still favourable. This paper explores the implications of this hypothesis by means of a spatially-explicit individual-based model. The specific aim of the model is to study in a factorial design the dynamics of the kite population in relation to two scale parameters, the temporal interval between droughts and the spatial correlation between droughts. In the model high drought frequencies led to reduced numbers of kites. Also, habitat degradation due to prolonged periods of inundation led to lower predicted numbers of kites. Another main result was that when the spatial correlation between droughts was low, the model showed little variability in the predicted numbers of kites. But when droughts occurred mostly on a system wide level, environmental stochasticity strongly increased the stochasticity in kite numbers and in the worst case the viability of the kite population was seriously threatened. [KEYWORDS: Conservation; Everglades; Rostrhamus sociabilis; Spatially explicit individual based model; Habitat quality; Hydrology; Inundation; Succession]

1. Tundra swans forage on below-ground pondweed tubers that are heterogeneously distributed in space. The swans have no visual cues to delineate patches. It was tested whether swans employ an area-restricted search tactic. Theory predicts that swans should alternate between an intensive (low-speed, sinuous) search mode in high tuber density areas and an extensive (high-speed, directed) search mode between these areas. 2. A quantitative analysis of movement paths recorded over short time frames (15 min) revealed that the sequential step lengths were strongly autocorrelated. After partitioning the data in low-speed paths and high-speed paths, this autocorrelation was very much reduced. 3. Movement paths with low speed were non-directional and could well be described as random walks. In contrast, high-speed paths were directed forward, and were better described as correlated (i.e. directional) random walks. 4. Movement paths recorded over longer time frames (1-4 h) provided empirical evidence that an alternation of low-speed, sinuous and high-speed, directed searches occurred. 5. There was a spatial autocorrelation in tuber biomass density, being significantly positively correlated until c. 10 m distance. The scale of the food clump size and step length of high-speed paths matched, suggesting that they were causally linked. 6. Computer simulations confirmed that swans using the observed search tactic achieved a higher energy gain than swans using only an intensive search mode, provided that the tuber biomass density occurred in clumps. They also achieved a higher gain than swans that alternated between intensive and extensive search mode, but always moved in a random direction.

In contradiction with field observations, theory predicts that the number of coexisting plankton species at equilibrium cannot exceed the number of limiting resources, which is called the "paradox of the plankton". Recently, Huisman & Weissing (1999, 2000) showed, in a model study, that the number of coexisting species may exceed the number of limiting resources when internal system feedback induces oscillations or chaos. In this paper, we use the term "supersaturated coexistence" for this phenomenon. On the basis of these findings, they claimed that the paradox of the plankton is solved. We investigated the prerequisites for supersaturated coexistence in the same model. Our results indicate that supersaturated coexistence is a rare phenomenon in parameter space, requires a very precise parameterization of the community members and is sensitive to the introduction of new species and the removal of the present species. This raises the question of whether supersaturated coexistence is likely to occur in nature. We conclude that the claim by Huisman & Weissing (1999, 2000) is premature. [KEYWORDS: biodiversity; chemostat; chaos; model;multiple resource competition; oscillations; persistence phytoplankton; supersaturated coexistence Phytoplankton; biodiversity; competition]

A relatively simple approach is presented for statistical analysis and comparison of fish growth patterns inferred from size-at-age data. It can be used for any growth model and small sample sizes. Bootstrapping is used to generate confidence regions for the model parameters and for size and growth rate at age. Significance of differences between growth patterns is tested with a likelihood ratio test, the validity of which was confirmed by Monte Carlo simulations. As an illustration of the applicability of this approach, we analyzed a set of length-at- age data on female (N = 57) and male (N = 27) Eurasian perch Perca fluviatilis from a shallow, eutrophic Dutch lake, Tjeukemeer. We used the von Bertalanffy growth curve to model length at age for both sexes separately. This analysis showed a significant difference in length between males and females between age 2 and age 6, with females being larger. At older ages the confidence regions became too wide to detect sexual dimorphism. The applicability of our approach was furthermore shown by comparing the results for Tjeukemeer with existing data for two other lakes. Eurasian perch in IJsselmeer (The Netherlands) showed comparable maximum lengths and dimorphism among sexes, but significant lower initial growth rates. Eurasian perch in Lake Windermere (UK) showed significantly lower maximum lengths; initial growth rates showed a wide range, with maximum values equal to those of Tjeukemeer. Because we used nonparametric tests (randomization techniques), which only assume independence of the model deviations, our conclusions are statistically well founded, despite the small size of the samples on which they are based. [KEYWORDS: Eutrophic lake-tjeukemeer; individual variability; vonbertalanffy; parameters; model; size; equation; fluviatilis; temperature; food]

Correlations between the biomass of phytoplankton and the biomass of bacteria and, between the biomass of bacteria and the biomass of protozoans suggest that there is coupling between these compartments of the "microbial loop." To investigate this coupling on the species level, bacteria and protozoans from untreated lake water inocula were allowed to grow on detritus of the green alga Ankistrodesmus falcatus or the cyanobacterium Oscillatoria limnetica in continuous-flow systems for 1 month. Denaturing gradient gel electrophoresis (DGGE) of the 16S and 18S rRNA genes was used. to monitor the development of the bacterial community structure and the eukaryotic community structure, respectively. Nonmetric multidimensional scaling of the DGGE profiles revealed the changes in the microbial community structure. This analysis showed that significantly different bacterial communities developed on the green algal detritus and on the cyanobacterial detritus. Although similar results were obtained for the eukaryotic communities,the differences were not significant. Hence, our findings indicate that the origin of detritus can affect the structure of at least the bacterial community. A phylogenetic analysis of 20 18S ribosomal DNA clones that were isolated from the continuous cultures revealed that many sequences were related to the sequences of bacterivorous protozoans (members:of the Ciliophora, Rhizopoda, Amoeba, and Kinetoplastida). One clone grouped in a recently established clade whose previously described members are all parasites. The affiliations of about 20% of the clones could not be determined. [KEYWORDS: ALGAL EXTRACELLULAR PRODUCTS; DISSOLVED ORGANIC-CARBON; FRESH-WATER; BACTERIAL UTILIZATION; PHYTOPLANKTON; MARINE; BACTERIOPLANKTON; DECOMPOSITION; POPULATIONS; METABOLISM]

The somatic growth rate of 0+ fish of the six major species in Dutch shallow eutrophic lakes, bream (Abramis brama), roach (Rutilus rutilus), pikeperch (Stizostedion lucioperca) (planktivorous and piscivorous), perch (Perca fluviatilis), ruffe (Gymnocephalus cernuus), and smelt (Osmerus eperlanus), was analysed by using a differential equation. This equation models the instantaneous growth rate of a fish as a temperature-dependent power function of body weight. Two of the model parameters were calibrated by optimising the prediction of the growth rate of the fish. Using a new method, which included a parametric bootstrap procedure, confidence limits were estimated for these two calibrated parameters and were used to test the significance of differences between species in growth performance under natural conditions. These tests revealed four groups of species: (A) smelt, (B) roach and bream, (C) ruffe and perch, and (D) piscivorous pikeperch. Growth performance of planktivorous pikeperch mainly overlapped with roach and bream (B) but showed some overlap with ruffe and perch (C). Differences and similarities are explained from the food type (D Versus A, B, and C) and the phylogenetic constraints (A versus B versus C) of each species. [KEYWORDS: Shallow eutrophic lake; rutilus-rutilus; salmo-trutta; brown trout; body-size; tjeukemeer; patterns; bream; roach; life]

To assess the impact of predation by young-of-the-year (0+) fish on the population dynamics of Daphnia species, we made independent estimations of the mortality of Daphnia species during the year, and of the predation pressure exerted by the juvenile fish. Mortality of daphnids was computed using a model that allowed us to differentiate between different size- classes, while total fish consumption was estimated from the temperature-dependent daily weight increase and the population development of the 0+ fish. The predation pressure on the different size-classes of Daphnia species was estimated by combining the total fish consumption with estimates of the selective feeding behaviour of the fish. To make the estimates of fish consumption independent of our current (1989-1991) zooplankton data set, we estimated fish species-specific and fish length-dependent selectivity indices on zooplankton using a different data set (1976-1977). Daphnia population densities usually increased in spring and decreased rapidly in early summer. Predation by 0+ fish was not severe enough to explain the large mortality that caused the summer decline; later in the year most of the mortality in the larger size-classes of the daphnids (>1.0 mm) could be explained by fish predation. [KEYWORDS: Young yellow perch; clear-water phase; body size; planktivorous fish; leptodora-kindti; neusiedler-see; eutrophic lake; hyalina leydig; birth-rate; zooplankton]

Variations in abundance and survival of larvae of the major fish species, bream, roach, pikeperch, perch and smelt were studied in shallow eutrophic lake Tjeukemeer (1986-1988). Except for smelt, the size of the spawning stock and the abundance of larvae were not related. Both the timing of appearance of larvae and their growth rate were determined by water temperature as was shown by a growth model developed earlier for Tjeukemeer fishes. In cyprinids and percids the survival of the larvae was hypothesized to be negatively related to the duration of the earliest stages. Except in cyprinids, the abundance of 0+ juvenile fish could be explained by the number of larvae. In cyprinids 0+ juvenile abundance at the end of the year was not related to the number of larvae in May and June. The cyprinid juvenile survival rates are hypothesized to be related to the size of the main cyprinid predator, 0+ pikeperch. [KEYWORDS: recruitment; spawning stock; 0+ juvenile fish; temperature; 0+ growth model; mortality; predation; starvation; cyprinids; percids Population-dynamics; rutilus-rutilus; cyclopoid redation; daphnia-hyalina; abramis-brama; south bay; growth; temperature; size; recruitment]

Formation of year-class strength of bream Abramis brama, the most abundant fish in shallow eutrophic Lake Tjeukemeer, was studied during a 14-year period. Although the size of the spawning stock of bream was rather stable during this period, analysis of length-frequency distributions indicates that it comprised only a few year-classes. The strength of a year-class was determined at a fork length of about ii cm, at the end of the second summer. Mortality rates of fish larger than 11 cm were low (

A general framework for the implementation of ecological models directed towards the falsification of knowledge, as opposed to models directed at making predictions, is proposed. The framework is constructed by defining a set of classes, with their interrelationships, in an object-oriented programming language. The classes represent the major levels of the so- called levels-of-integration hierarchy: individual, population and system. The abiotic physical and chemical environment is implemented by the classes condition and resource, respectively. Class habitat is used to represent the spatial structure of an ecosystem. The simulation is controlled by a class called analyser. The simulation mechanism is implemented by deriving all these real-life objects from a more abstract class simobject. The engine of the simulation is formed by a dynamic list of references to simobjects, sorted according to the time each simobject should be activated next, The data of each object are implemented in class dataobject, from which simobject is derived. The applicability of this framework, called OSIRIS (object-oriented simulation framework for individual-based simulations), is shown for a population dynamical study on daphnids, The effects of variation among individual daphnids on the growth rate and structure of a population of daphnids are studied by comparing the results of the individual-based model with those of a life table. Moreover, variation in population growth rate over time, which parameter cannot be derived from a life table, is calculated. Finally, the sensitivity of the model for the number of modelled individuals and the sampling interval is analysed. [KEYWORDS: model; falsification versus prediction; levels of integration individuals versus ecosystem Shallow eutrophic lake; models; fish; system; growth;variability; temperature; tjeukemeer; cucullata; hybrid]

For more than 20 years scientists of the ‘Food-chain studies’ Group of the former Limnological Institute have been studying interactions within the pelagic food web. Purpose of research was to explain the structure and dynamics of the zooplankton and fish communities in lakes and reservoirs in relation to biotic and abiotic environmental factors. A so-called multi-species approach was used, in which all common and abundant species within a specific ecosystem were studied on the individual and population level with the same degree of detail. The recent results and the scientific approach used are evaluated and the main gaps in knowledge about food-web dynamics in shallow eutrophic lakes are identified and discussed. It is concluded that instead of the purely functional approach used so far, future studies should also include evolutionary aspects which determine the success of an organism in a given environment and that more attention should be paid to central questions in ‘community ecology’.