There is an increasing interest in dynamical food web modeling, and recent advances of computational biology provide new algorithms and tools for modern systems ecology. In this work stochastic individual-based models are used for simulating food web dynamics in two case studies: the Kelian river, in Borneo, Indonesia and a marine ecosystem in Gulf of Guinea. The two cases present effects from human perturbations. In both cases, we constructed food webs, based on real databases. We parameterized the stochastic dynamical model for the system models and performed sensitivity analysis (and community response indicators) in order to quantify the relative importance of system components. The main aims are to understand the importance of functional diversity of aquatic ecosystems and relations between the dynamics of species and the whole community in perturbed ecosystems due to human activities (pollution due to gold mining activity and human settlements in the case of the Kelian river ecosystem and the impact of Fish Aggregation Devices on skipjack tuna communities in the case of the Gulf of Guinea ecosystem). In Kelian river case, our results suggest that invertebrate shredders are indicators of human impact on the river. In downstream sites our results show that the river is more polluted and the relative importance of grazers and shredders decrease. The primary producers disappear downstream as consequence of mine activity and human waste. In the marine system case study, we analyzed the effects of association between tunas and FADs, and compared this to the behavior of free tuna individuals. The results suggest that skipjack tuna is affected by the use of FADs as fishing strategy on them. Some individual species show more sensibility to variation of population size of tuna. These two studies contribute to better understand how functional diversity is related to human impact. This kind of approach may help in shaping systems-based conservation and marine fisheries management strategies. Keywords: food web, aquatic ecosystems, stochastic model, sensitivity analysis

Firstly, I proposed a very simple SIS/SIR model for a general vector-borne disease transmission considering constant population sizes over the season, where contact between the host and the vector responsible of the transmission is assumed to occur only during the summer of each year. I discussed two different types of threshold for pathogen persistence that I explicitly computed: a "short-term threshold" and a "long-term threshold". Later, I took into account the seasonality of the populations involved in the transmission. For a single season, the model consists of system of non linear differential equations considering the various stages of the infection transmission between the vector and the host population. Assuming the overwintering in the mosquito populations, I simulated the model for several years. Finally, I studied the spatial spread of a vector-borne disease throught an impusive reaction-diffusion model and I showed some simulations.

Governments adopt strategies to follow the objective Europe 2020 and focus on the development of Renewable Energy Technologies, RET, to improve the transition of the production of energy from fossil fuels sources to renewable energy sources, RES. More than decades before, the energy transition towards renewable energies emerges as a relevant objective of the European governments. The fluctuating prices of oil and the uncertainty on the future supply of fossil fuels open new challenges for communities to actuate an energy transition towards RES. The RET can afflict deeply the landscape structure and by this point of view the energy transition is one of the most relevant drivers in the landscape change of the last three decades. In several cases energy transition may face opposition from regions and communities because of the change that RET produce in local landscapes and related economic, cultural and ecological functions. This change has been defined as a conflict between the local narrative of the right to the landscape by local communities and the global narrative that aims at a low carbon future. Exploring the relationship between Ecosystem Services (ES) and Renewable Energy (RE), the conflict among a global perspective and a local perspective has been resumed by several authors as a trade-off among provisioning and regulating ES from one side and cultural ES from the other. The overcoming of this conflict can be based on bottom-up processes that enhance the energy transition starting by local organizations of communities that want to reach a self-sufficieny in renewable energy supply. Transition management is possible if we produce innovation at local scale. An ES approach supports the transition management and the envisioning future energy landscapes by offering transparent trade-offs, exposing risks and benefits. If societies produce clean energy it may happen that RET afflict other ES. The main paradigm for the sustainability of a energy landscape is that the introduction of RET should not cause crucial trade-offs among the other ES, this is why this research wants to study this relationship, as several authors have already stressed. By the literature review it is possible to state a general gap of knowledge in integrated approaches in the evaluation of RET, considering diverse RES and ES provided by the landscape and evaluating a trade-off through a participatory process. To fulfill such gap and produce an enhancement of knowledge, this research follows the main objective of introducing a trade-off analysis into a design approach to formulate long-term visions for sustainable energy landscapes. The results we got indicate that it is possible to plan and design with the ES sustainable energy landscape.This process facilitates a sustainable energy transition of communities through a participatory landscape design that reduce the trade-off between the Renewable Energy and the ES supplies.

River/stream water temperature is one of the master water quality parameters as it controls several key iogeochemical, physical and ecological processes and river ecosystem functioning. Thermal regimes of several rivers have been substantially altered by climate change and other anthropogenic impacts resulting in deleterious impacts on river health. Given its importance, several studies have been conducted to understand the key processes defining water temperature, its controls and drivers of change. Temporal and spatial river temperature changes are a result of complex interactions between climate, hydrology and landscape/basin properties, making it difficult to identify and quantify the effect of individual controls. There is a need to further improve our understanding of the causes of spatiotemporal heterogeneity in river temperatures and the governing processes altering river temperatures. Furthermore, to assess the impacts of changing river temperatures on the river ecosystem, it is crucial to better understand the responses of freshwater biota to simultaneously acting stressors such as changing river temperatures, hydrology and river quality aspects (e.g. dissolved oxygen levels). So far, only a handful of studies have explored the impacts of multiple stressors, including changing river temperature, on river biota and, thus, are not well known. This thesis, thus, analysed the changes in river temperature behaviour at different scales and its effects on freshwater organisms. Firstly, at a regional scale, temporal changes in river temperature within long (25 years) and short time periods (10 years) were quantified and the roles of climatic, hydrological and landscape factors were identified for North German rivers. Secondly, at a reach scale, spatial temperature heterogeneity in a sixth-order lowland river (River Spree) was quantified and the role of landscape factors in inducing such heterogeneity was elucidated. Thirdly, at a site scale, short-term behavioural responses (namely drift) of three benthic invertebrate species to varying levels of water temperature, flow, and dissolved oxygen, and to combinations of those factors were experimentally investigated. Results from this thesis showed that, at a regional scale, the majority of investigated rivers in Germany have undergone significant annual and seasonal warming in the past decades. Air temperature change was found to be the major control of increasing river temperatures and of its temporal variability, with increasing influence for increasing catchment area and lower altitudes (lowland rivers). Strongest river temperature increase was observed in areas with low water availability. Other hydro-climatological variables such as flow, baseflow, NAO, had significant contributions in river temperature variability. Spatial variability in river temperature trend rates was mainly governed by ecoregion, altitude and catchment area via affecting the sensitivity of river temperature to its local climate. At a reach scale as well, air temperature was the major control of the temporal variability in river temperature over a period of nine months within a 200 km lowland river reach. The spatial heterogeneity of river temperature in this reach was most apparent during warm months and was mainly a result of the local landscape settings namely, urban areas and lakes. The influence of urban areas was independent of its distance from the river edge, at least when present within 1 km. Heat advected from upstream reaches determined the base river temperature while climatological controls induced river temperature variations around that base temperature, especially below lakes. Riparian buffers were not found to be effective in substantially moderating river temperature in reaches affected by lake warming due to the dominant advected heat from the upstream lake. Experimental investigation indicated that increasing water temperature had a stronger short-term effect on behavioural responses of benthic invertebrates, than simultaneous changes in flow or dissolved oxygen. Also, increases in water temperature was shown to affect benthic invertebrates more severely if accompanied by concomitant low dissolved oxygen and flow levels, while interactive effects among variables vary much among taxa. These results support findings of other studies that river warming, similar to climate change, might be a global phenomenon. Within Germany, lowland rivers are the most vulnerable to future warming, with reaches affected by urbanization and shallow lentic structures being more vulnerable and, therefore, requiring urgent attention. Furthermore, river biota in lowland rivers is particularly susceptible to short-term increases in river temperature such as heat waves. Plantation of riparian buffers, a widely recognized practice to manage climate change effects, in the headwater reaches can be suggested to mitigate and prevent future warming of lowland rivers in general and also throughout river basins, as river temperature response in lowland catchments is a culmination of local and upstream conditions. However, further river temperature increase in lowland river reaches within or close to urban areas and shallow lentic structures will be more difficult to mitigate only via riparian shading and would require additional measures

Freshwater ecosystems are severely undergoing degradation due to the presence of multiple stressors that are undermining their biodiversity. In this sense, quantifying these effects on Alpine regions is challenging, due to the lack of tailored field measurements of hydrological, biological and chemical variables. This work aims to touch some of these aspects, with particular attention to hydrological dynamics and their effects on macroinvertebrates. Field activities have been conducted within the Adige catchment which has been selected as a case study in the FP7 project GLOBAQUA. Collected data have been analyzed by means of statistical tools and results showed a seasonal and spatial variability of biological communities related to hydrological and chemical variables. In particular, it has been observed that richness, diversity and relative composition of macroinvertebrates community are chiefly affected by hydrological alteration and urban pollution. Available literature confirmed that hydrological alteration is one of the most important factors affecting riverine ecosystems. In Alpine regions, most of the hydrological alterations observed are due to hydropower that represents the major source of energy in the Trentino-Alto Adige region. Since the introduction of the free energy market in Italy, hydropower production shows large fluctuations at the daily and larger temporal scales, as the managers aim at producing when the energy price is high. This increased the variability of streamflow downstream the restitution of the power plants. Changing climate is an additional stressor that can enhance the effects of these anthropogenic influences. Thereby, in this work hydrological alterations have been distinguished between those forced by climate change and those caused by the presence of hydropower plants and have been analysed in detail. The former have been analysed downstream of the Careser glacier, which has long-term observations of climatic variables, mass balances and streamflow. The main purpose of this study was finding a direct relationship linking biological indicators to streamflow variations related mainly to hydropower operations. Quantifying these effects is challenging due to the fact that the behaviour by which macroinvertebrates respond remains largely unexplained. However, analyses of similarities and independence, performed at the basin scale with data provided by the local Environmental Protection Agencies, showed evident differences in the biological communities between impacted and non-impacted sites. These results bring us to believe that a relationship between biological data and hydrological alteration is expected to exist, but that is not clearly explicated by simple correlations. Giving a quantitative interpretation of this correlation could help hydropower manager to improve and optimize the energy production with a more realistic scenario of the effects on the biological community, with also a perspective of the combined effects caused by the presence of multiple reservoirs within the basin.

This thesis provides a contribution to the knowledge on the effects of deglaciation on alpine stream ecosystems, taking into account also the hydroecological influence of thawing permafrost and paraglacial features. With a focus on the European Alps, a review is provided on the climate changes and shifts in the cryosphere (snow, glaciers, permafrost), the related changes in hydrology, geomorphic processes and the physical and chemical habitat of alpine river networks, and the consequent shifts in stream communities and food webs. A conceptual model is provided to summarize the complex interactions and the cascading effects triggered by deglaciation on hydrology, habitat and biota of alpine streams, that can be useful for educational purposes and to help the scientific community to contextualize these issues to other alpine areas. Deglaciation induces homogenisation of river networks, loss of biodiversity, and shifts in primary and secondary production, functional diversity and food webs. The scarce published studies on streams influenced by permafrost provide hints on the role of thawing rock glaciers (i.e. evident form of mountain permafrost) in shaping the ecology of freshwaters, and reveal important research gaps. To increase the knowledge on this topic, different alpine streams fed by waters of different origin were selected in two subcatchments (Zay, Solda) of a deglaciating area of the Central Italian Alps (Solda Valley), and their habitat conditions and benthic invertebrate communities were investigated over a two-year period. Rock glacier-fed streams could be distinguished from those fed by glaciers, groundwater and those of mixed origin because of their constantly clear and very cold waters, stable channels, and high concentrations of ions and trace elements that increased as summer progressed. Furthermore, the Zay rock glacier strongly influenced the glacier-fed stream through an intense export of solutes, which become progressively more relevant towards the end of summer. This influence was also due to the contribution of a proglacial lake and a moraine body, that both strongly decreased the glacial influence along the glacier-fed stream before its confluence with the rock glacier outflow. The wide range of habitat conditions revealed to strongly influence the benthic invertebrate communities in the study area. Channels with groundwater (krenal) and mixed (glacio-rhithral) exhibited a higher taxa richness and diversity. Peaks of abundance and biomass in the catchment were recorded just downstream the talus body, in the upper glacio-rhithral channel. Chironomidae from the cold-adapted genus Diamesa were dominant in the proglacial sections (upper kryal) of the glacier-fed streams. The proglacial lake, the moraine body and the rock glacial tributary at Zay contributed to the amelioration of the environmental features of the glacier-fed stream (lower kryal), boosting high invertebrate biomass and abundance and causing shifts in the community composition (e.g. increased Orthocladiinae and other Diamesinae chironomids, abundant Trichoptera). The two rock glacial communities differed considerably between each other. In fact, the community of the Zay rock glacial stream was partially influenced by the seepage of glacier waters, and resembled those of the surrounding lower kryal. On the contrary, the Solda rock glacial stream, detached from any glacier influence, hosted a rich and diverse community which resembled those of glacio-rhithral and krenal, even though with a higher abundance of Diamesa. Overall, the results of this thesis showed that in the advanced phases of glacier retreat, paraglacial landforms and permafrost can increasingly contribute to the riverscape diversity and shape the ecology of river networks. Because of their unique environmental settings, rock glacial streams should be considered a distinct alpine stream habitat, acting in deglaciating catchments as stepping stones that enhance the upstream colonisation of non-glacial communities following glacier retreat. At the same time, they might represent cold refugia for cold-stenothermal and/or typically glacial taxa when glaciers will be disappeared, because of the slower thawing rate of rock glacier ice. In this context, the presence of Diamesa kryal specialist species in rock glacial streams deserves further investigation, in order to understand the potential conservation value that these habitats may have in buffering the β-diversity reduction which is predicted in alpine areas as a consequence of glacier loss.

This thesis treats mathematical models for host-parasitoid interactions. It is composed of three parts. In the first part, a class of such models is analyzed theoretically. It focuses on the phenomena of multiple coexistence equilibria of competing parasitoid species. The second part is about a model for determining how a parasitoid release should be timed to optimally control the invasive fruit fly Drosophila suzukii. The third part analyzes an experiment for releasing parasitoids in a greenhouse which is infested by D.suzukii. The models presented are used to discuss how to improve such biological control strategies.

In the current era of the Anthropocene, human activities are powerful forces that affect the geosphere, atmosphere, and biosphere – globally, fundamentally, and in most cases irreversibly. In freshwaters, land use change, chemical pollution, decline in biodiversity, spread of invasive species, climate change, and shifts in the hydrological regime are among the key drivers of changes. In the 21st century, major water engineering projects such as large dams and water diversion schemes will fundamentally alter the natural hydrological regime of entire landscapes and even continents. At the same time, the hydrological regime is the governing variable for biodiversity, ecosystem functions and services in river networks. Indeed, there will be an increasing conflict between managing water as a resource for human use and waters as highly valuable ecosystems. Therefore, research needs to unravel the challenges that the freshwaters are facing, understand their potential drivers and impacts, and develop sustainable management practices – for the benefit of humans and ecosystems alike. The present thesis focuses on three currently understudied alterations in flow and material dynamics within river networks, namely (i) on the dynamics of floating organic matter (FOM) and its modification in dammed rivers, (ii) on river intermittency and its effects on nutrient and organic matter (OM) dynamics, and (iii) on major future water transfer schemes. Massive construction and operation of dams cause modification of water flow and material fluxes in rivers, such as of FOM. FOM serves as an essential component of river integrity, but a comprehensive understanding of its dynamics is still lacking. River damming, climate change and water extraction for human needs lead to a rapid expansion in number and extent of intermittent rivers worldwide, with major biogeochemical consequences on both regional and global scales. Increased intermittency of river networks also forces people to implement engineering solutions, such as water transfer schemes, which help to supply water to places of demand. Water transfer projects introduce artificial links among freshwater bodies modifying the hydrological balance. Impacts of abovementioned activities on freshwaters have been assessed in single case studies. However, the current knowledge does not allow a generalization of their globally applicable meaning for ecosystems. Furthermore, mostly neglected aspects of these alterations, such as the potential consequences of FOM extraction from rivers, the biogeochemical role of intermittent rivers upon rewetting, and the current scale of water transfers require better understanding before bold conclusions could be made. By combining research methods such as extensive literature reviews, laboratory experiments and quantitative analyses including spatial analyses with Geographic Information Systems, I investigated (1) the natural cycle, functions, and amounts of FOM in rivers fragmented by dams, (2) effects of rewetting events on the pulsed release of nutrients and OM in intermittent rivers and ephemeral streams (IRES), and (3) the potential extent of water transfer megaprojects (WTMP) that are currently under construction or in the planning phase and their role in modifying the global freshwater landscape. In all three cases, I provide a global perspective. The role of FOM in rivers as a geomorphological agent, a resource, a dispersal vector and a biogeochemical component was investigated based on an extensive literature review. Collected information allowed for conceptualizing its natural cycle and dynamics, applicable to a wide range of rivers. Data on FOM accumulations at 31 dams located within catchments of 13 rivers showed that damming leads to FOM entrapment (partly or completely) and modifies its natural cycling. The results of a spatial analysis considering environmental properties revealed that catchment characteristics can explain around 57% in the variation of amounts of trapped FOM. Effects of rewetting events on the release of nutrients and OM from bed sediments and course particulate organic materials (CPOM) accumulated in IRES was studied in laboratory experiments. Using a large set of samples collected from 205 rivers, located in 27 countries and distributed across five major climate zones, I determined the concentrations and qualitative characteristics of nutrients and OM released from sediments and CPOM. I also assessed how these characteristics can be predicted based on environmental variables within sampled IRES. In addition, I calculated area-specific fluxes of nutrients and OM from dry river beds. I found that the characteristics of released substances are climate specific. In the Continental zone I found the highest concentrations of released nutrients, but the lowest quality of OM in terms of its potential bioavailability. In contrast, in the Arid zone the concentrations of released nutrients were the lowest, but the quality of OM the highest. The effect of environmental variables on the concentrations of nutrients and the quality of OM was better predicted for sediments than for other substrates with the highest share of explained variance in the Continental and Tropical zones. On the global scale, dissolved organic carbon, phenolics, and nitrate dominate fluxes released during rewetting events. Overall, this study emphasized that on the global scale rewetting events in IRES represent biogeochemical “hot moments†, but characteristics of released nutrients and OM differ greatly among climate zones. The present thesis fills also a major knowledge gap on the global distribution of large water transfer schemes (referred to as “megaprojects†) that are actually planned or under construction. To provide an inventory of WTMP, I collected data from various literature sources, ranging from published academic studies, the official web-sites of water transfer projects, environmental impact assessments, reports of non-governmental organizations, and information available in on-line newspapers. In total, 60 WTMP were identified. Information on spatial location, distances and volumes of water transfer, costs, and purposes of WTMP was collected and compared with those of existing schemes. The results showed that North America, Asia and Africa will be the most affected by future WTMP having the highest densities of projects and the largest water transfer distances and volumes. If all projects were completed by 2050, the total water transfer distances would reach 77,063 km transferring more than 1,249 km3 per year, which corresponds to about 20 times the annual flow of the river Rhine. The outcomes of the thesis provide major implications for environmental management. Natural FOM is an important component for sustaining the ecological and geomorphic integrity of rivers and, therefore, should be managed appropriately. Intermittent rivers must be considered in models quantifying nutrient and OM fluxes in river networks. First flush events in particular release huge amounts of nutrients and OM, which may cause dramatic metabolic effects on downstream receiving waters. Finally, the future WTMP alter the hydrological balance of entire river basins and continents. They require multiple assessments before construction and careful management practices for sustainable operation in order to consider both freshwater as a resource as well as freshwaters as pivotal ecosystems.

About three quarters of human emerging infectious diseases are caused by zoonotic pathogens, and many of them are spread by vectors such as mosquitoes. Mathematical models nowadays represent very powerful tools to make investigations and predictions for biological dynamical systems, providing helpful insights that can be extremely valuable for several aims. In this thesis, we will focus on a particular mosquito-borne zoonosis, West Nile virus (WNV), a flavivirus of emerging public health relevance in Europe and North America, and its main European vector, Culex pipiens mosquitoes. As the transmission of mosquito-borne diseases is largely driven by the abundance of the vector, to design appropriate control strategies it is crucial to understand the population dynamics of existing vector populations and evaluate how it depends on biotic and environmental factors. This thesis presents some new mathematical models that provide insights on several aspects of mosquito population dynamics by using different statistical and computational approaches, including for instance Linear Models and Markov chain Monte Carlo technique. Specifically, they aim to study the effect of biotic and abiotic factors on Cx. pipiens dynamics by using adult mosquito trapping data, gathered over several years in Northern Italy, to feed theoretical models. Furthermore, the effects of host competition and vector feeding preferences on the dynamics of a vector-borne infection (such as WNV) are investigated through a more theoretical study.

Freshwater lakes are among the most important ecosystems for both human and other biological communities. They account for about 87% of surface freshwater in the planet, thus constituting a major source of drinking water. They also provide a wide range of ecosystem services that go from the sustenance of a rich biodiversity to the regulation of hydrological extremes; from the provision of a means for recreation to the support of local economies, e.g., through tourism and fisheries, just to cite a few. Lakes are now also widely recognised as natural early warning systems, their responses potentially being effective indicators of local, regional and global scale phenomena such as acidification and climate change, respectively. This is because of their high sensitivity to environmental factors of the most diverse nature that can rapidly alter the course of their evolution. Examples of this are the observed abrupt shifts between alternative stable states in shallow lakes, which led them to become the archetype, go-to example in alternative stable state theory. Therefore, attaining a good scientific understanding of the many processes that take place within these ecosystems is fundamental for their adequate management. Among the tools that serve this purpose, ecological models are particularly powerful ones. Since their introduction in the 1960s, the development of mechanistic ecological models has been driven by their wide spectrum of potential applications. Nevertheless, these models often fall into one of the two following categories: overly simplistic representations of isolated processes, with limited potential to explain real-world observations as they fail to see the bigger picture; or overly complex and over-parameterised models that can hardly improve scientific understanding, their results being too difficult to analyse in terms of fundamental processes and controls. Moreover, it is now well known that an increased complexity in the mechanistic description of ecological processes, does not necessarily improve model accuracy, predictive capability or overall simulation results. To the contrary, a simpler representation allows for the inclusion of more links between model components, feedbacks which are usually overlooked in highly-complex models that partially couple a hydro-thermodynamic module to a biogeochemical one. However, ecological processes are now known to have the potential to significantly alter the physical response of aquatic ecosystems to environmental forcing. For example, steadily increasing concentrations of coloured dissolved organic carbon, a process known as brownification (also browning), as well as the intense phytoplankton blooms that characterise lakes undergoing severe nutrient enrichment, a process known as eutrophication, have been shown to have the potential to alter the duration of the stratified period, thermal structure and mixing regime of some lakes. In this thesis, with the aim of addressing the limitation of partially-coupled models to account for such feedbacks, we further develop a process-based model previously reported in scientific literature. Subsequent studies have already built upon this model in the last few years. In Chapter 2, we do so too by integrating hydro-thermodynamics and biogeochemistry in a reduced complexity framework, i.e., customising the model so that each version only includes the fundamental processes that, brought together, sufficiently describe the studied phenomena. Two case studies served the purpose of testing the adaptability and applicability of the developed model under different configurations and requirements. Limnological data for these two studies were measured at high spatial and temporal resolutions by means of an automated profiling system and recorded as part of two large-scale mesocosm experiments conducted in 2015 and 2016 at the IGB LakeLab in Lake Stechlin, Brandenburg, Germany. Meteorological datasets were also made available to us for both periods by the German Federal Environment Agency. The scope of the first experiment, which we describe in Chapter 3, was that of detecting any changes attributable to eutrophication and browning, in the competition for nutrients and light between four different groups of lake primary producers. These four groups are phytoplankton, periphyton, epiphyton and macrophytes. The model version for this study, therefore, includes equations for all four groups. By tailoring the model to these very specific needs with relative ease, we demonstrate its versatility and hint at its potential. The second experiment, described in Chapter 4, sought to shed light on the largely unknown effects of an increase in the diffuse luminance of the night sky that is due to artificial light at night (artificial skyglow) on lake metabolic rates, i.e., gross primary productivity, ecosystem respiration and net ecosystem productivity (the difference between the first two). For this purpose, an empirical equation for dissolved oxygen concentration was included, the parameters of which were estimated by means of a Markov Chain Monte Carlo sampling method within a Bayesian statistical framework, showing the compatibility, with these statistical methods, of our otherwise fully deterministic model. In Chapter 5, we present a theoretical study on the ecological controls of light and thermal patterns in lake ecosystems. A series of simulations were performed to determine in which cases ecological processes such as eutrophication and brownification may have an observable effect on the physical response of lakes to environmental forcing, which we assessed along a latitudinal gradient. Results show that, in general, across all examined latitudes, and consistent with previous studies, accounting for phytoplankton biomass results in higher surface temperatures during the warm-up phase, slightly lower water temperatures during the cool-down phase, and a shallower thermocline throughout the entire stratified period. This effect is relatively more important in eutrophic lakes where intense blooms are likely. This importance, however, decreases as lakes get browner. Finally, in line with the overall scope of the SMART EMJD, in Chapter 6 we illustrate the case of Ypacaraí Lake, the most important lake in landlocked Paraguay, hoping to provide an example of how interdisciplinary research and international intersectoral collaboration can help bridge the gap between science and management of freshwater ecosystems. This lake presents very special hydro-ecological conditions, such as very high turbidity that can impair phytoplankton growth despite its nutrient-based trophic state indices having consistently fallen within the hyper-eutrophic range in recent years. A strong interest in its complex functioning, through modelling, was taken early on. This led to a collaborative research line being established among several public and private institutions in Italy, Germany and Paraguay. Results so far include: • three concluded UniTN Master theses in Environmental Engineering, partly developed in Paraguay, the first two in collaboration with the “Nuestra Señora de la Asunción” Catholic University (UCNSA) and the third one with the National University of Asunción (UNA); • a collaborative UCNSA-UniTN research proposal submitted for consideration to receive funding through the PROCIENCIA Programme of the National Council of Science and Technology of Paraguay (CONACYT); and • the first multidisciplinary review that has ever been published about the case of Ypacaraí Lake, which highlights the importance of such a collaborative and integrative approach to further advance scientific knowledge and effectively manage this ecosystem.