Integrating Information Sources for Inland Waters - A New Global Framework for Lakes Modelling and Monitoring

Like islands, lakes are not only unique geographical features, but also ecological concepts on their own. Their exceptional variability has been studied numerous times, yet no unique framework capable of reproducing the wide range of lake dynamics observed in various regions of the World has been formulated. Increasingly facing external pressures, inland waters adaptation and changes have to be understood and monitored efficiently in order to provide timely, scientifically credible, and policy-relevant environmental information, to ultimately assist stakeholders in evidence-based decision-making and sustainable management. Such monitoring capabilities are of great importance for the management and surveillance of the necessary measures to prevent lakes deterioration, as stated by the EU Water Framework Directive, or the United Nations’ Post 2015 agenda. Those are only two among the numerous recent political actions aiming at sustainably securing the ecosystem services provided by lakes on a regional to global scale, using new approaches for water management tailored to local conditions. Over the last decades, various research communities addressed this problem using different information sources, such as in-situ measurements, remote sensing observations and mathematical models. The challenge of this thesis is to couple those information sources through adapted data assimilation algorithms. The coupling of those three data sources aims at providing a new, reliable, flexible, and global modelling framework for inland waters monitoring across Switzerland, Europe and possibly expanding to other lakes of the World. The development of this framework will consider both hydrodynamic and water quality models with one- and three-dimensional domains. Year-long in-situ campaigns will complement existing field data, including setups on permanent stations. Remote sensing products consist in the approved AVHRR surface temperature dataset and cutting-edge Sentinel-2 chlorophyll observations. In terms of system operations, the framework will be operated in real-time for several Swiss lakes, with short-term forecasting of hydrodynamic and water quality properties, available online, and open to the public. The impacts of such system are expected at public, governmental and scientific levels. For the latter, this project aims at contributing to advances in aquatic research by (i) identifying and studying mesoscale processes such as up- downwellings, horizontal distribution of ecological properties, and (ii) assessing the variability of lake responses to climate change, in terms of warming and ice cover.

From observations to 3D forecasts: Data assimilation for high resolution lakes monitoring

Theo Baracchini

Lake mesoscale processes have no secrets for artists, they have some for scientists and policy-makers. In the introduction to this dissertation, we saw that poets and painters depict the lake with rich variability. This vision conflicts with conventional approaches inferring the lake's bio-physical status from a few in-situ measurements with limited spatio-temporal coverage. Yet it reflects upon true physical processes, capable of disrupting the misleading lentic nature of lakes, the essential ecosystem services they provide, and even citizens' safety. Recent overarching policies now aim at securing those services, using novel approaches like numerical simulations and remote sensing observations. Harnessing the potentiality of in-situ, remote sensing data and model simulations, this thesis developed an end-to-end framework delivering reliable synoptic lake information, at high spatial and temporal resolution. In lakes, three-dimensional hydrodynamic models are the only information source capable of resolving transport and mixing, and forecasting their dynamics. However, they still rely on large observational datasets for their complex parameterizations and for constraining their uncertainties. This thesis addressed such challenges by (i) implementing an automated model calibration framework alleviating the need for expert knowledge, and by (ii) developing a data assimilative scheme capable of reducing and quantifying model uncertainties by incorporating satellite and in-situ data. Both yielded remarkable results: the former returned parametric values diminishing models Root Mean Square Error by up to 47 %, while the latter cut it further down by 54 %. Furthermore, the data assimilation enhanced the spatial coherence and magnitude of imperfectly resolved physical processes, and provided system uncertainties. Finally, this thesis delivered a practical outcome of its findings by developing an online pre-operational three-dimensional lake monitoring and forecasting system: meteolakes.ch. For two years, Meteolakes has been disseminating spatially explicit real-time lake information and data products to more than hundred thousand end-users. This pioneering platform has been featured in numerous media (newspapers, radio, television), public events, museum exhibitions, and benefited scientific, lake professionals, and public communities. A pinnacle of this research has been its early-warning and forecasting capabilities, which anticipated numerous mesoscale physical phenomena in Lake Geneva, such as upwellings, gyres, and strong currents. Two of those events, which impacted public and commercial activities, are illustrated in this dissertation. From observations and models to societal benefit, we created here a long value chain for water management. At the crossroads of scientific, computational and observational advances, this research paves the route for understanding lakes' delicate imbalance. By producing data society can use, it opens novel frontiers for interdisciplinary research on previously elusive lake physical processes, and their implications on the everyday life of people.

EPFL2019

Biogeoinformatics for the management of Farm Animal Genetic Resources (FAnGR)

Solange Catherine Gaillard

In the context of both severe selection in farm animals and potential effects of climate change, it is crucial to implement a sustainable management of the breeding practice, supported by a judicious use of geographic information technologies. Based on this observation, this thesis advocates the use of biogeoinformatics (the combined use of biology, geographic information and informatics) to cope with the challenges encountered by the livestock sector. Indeed, although biogeoinformatics can provide key insights for FAnGR (Farm Animal Genetic Resources) management, the variety and complexity of tasks involved hinders a wider usage of this type of analyses. The thesis shows how novel dedicated tools are likely to facilitate the adoption of biogeoinformatics by animals scientists and by stakeholders in the livestock sector, while investigating three main challenges related to FAnGR management, namely i) erosion of genetic diversity, ii) effects of climate change on the breeding activity, and iii) pressure on typical cultural breeding practices such as high alpine grazing. On this basis, the thesis is organised around three axes:

Preserving locally adapted breeds In order to prevent the erosion of genetic diversity, locally adapted breeds should be monitored to prevent their extinction. To this end, we developed the open source GENMON WebGIS platform, able to monitor FAnGR and to evaluate the degree of endangerment of livestock breeds. The system integrates various sources of information that are linked with the help of geographic information: pedigree and introgression, geographical concentration of animals, cryo-conservation and sustainability of breeding activities. The score can be visualised on a map and allows a fast and regional identification of breeds in danger.
Preserving locally adapted genetic variations Considering the pace at which genetic diversity is being eroded, it has become urgent to identify and then preserve important genetic variations linked to locally adapted phenotypes. In this context, the recent SamÎ²ada software was designed to search for signatures of local adaptation through the study of genomeâenvironment association. However, preâ and postprocessing of data for this analysis can be labourâintensive, and, we therefore developed the R.SamBada R package providing a pipeline for landscape genomic analyses. Based on SamÎ²ada, it spans from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, it grants access to biogeoinformatic analyses to researchers with no skills in geography.
Preserving a traditional farming technique suited for local breeds The preservation of locally adapted breeds is also strongly linked with the conservation of traditional farming techniques, which in Switzerland, include the grazing of high alpine pastures during summer. One major effect of this transhumance on cows is that milk production declines due to food shortage and climatic stress. Here, we developed a new mathematical model to fit a lactation curve for mountain-pastured cows, and tested the influence of environmental, physiological, and morphological factors on the production using five million monthly milk records from Braunvieh cows. When compared to physiological factors, environmental variables show a limited impact on milk production at alpine pastures, precipitation in spring being the most important.

EPFL2020

Density currents driven by differential cooling in lakes: occurrence, dynamics and implications for littoral-pelagic exchange

Tomy Doda

Cross-shore flows exchange water laterally in lakes, with ecological implications for the ecosystem. One example is the convective circulation induced by differential cooling, also known as the thermal siphon. This lateral flow forms when the sloping sides of lakes experience surface cooling. Shallow areas cool faster, which generates lateral density gradients and drives a cold downslope gravity current and an onshore surface flow. The role of this two-layer-circulation in lateral exchange in lakes is poorly understood, due to the lack of long-term and high-resolution measurements of thermal siphons. This thesis aims at filling this gap by investigating the occurrence and dynamics of thermal siphons from extensive in situ observations in a wind-sheltered Swiss lake (Rotsee).We first quantified the seasonality of thermal siphons from one-year-long observations in Rotsee. Thermal siphons occurred on a daily basis from late summer to winter and flushed the littoral region in ~ 10 h. Their duration increased but their intensity decreased over the same period. We linked this seasonality to the change in forcing conditions by testing scaling relationships from theoretical and laboratory-based studies.We then focused on the short-term temporal variability of the transport by quantifying the dynamics of thermal siphons over a diurnal cycle and their interaction with convective plumes. Our results reveal that convective plumes penetrated into the gravity current at night and eroded its upper interface. This vertical mixing generated vertical interface fluctuations and reduced the lateral transport at night. The maximal transport was delayed to daylight conditions when radiative heating weakened penetrative convection.After having quantified the physical water transport, we assessed the role of thermal siphons in the lateral exchange of dissolved gases. We found that both branches of the circulation were capable of transporting gases laterally. The downslope current brought littoral gases to the base of the mixed layer in the stratified region whereas the surface flow transported gases towards the shore. We quantified this exchange for oxygen and methane.Finally, we generalized our observations to other lakes with different bathymetry and forcing conditions. The frequent occurrence of thermal siphons observed in six lakes confirmed that this lateral transport process is ubiquitous in lakes with shallow littoral regions. We showed that our results from Rotsee were applicable to other systems, where the same scaling relationships predicted the formation and intensity of thermal siphons. Based on these results, we proposed a procedure to predict the contribution of thermal siphons for lateral transport in any lake.This thesis provides a comprehensive understanding of the formation and dynamics of thermal siphons and paves the route for integrating this lateral transport process in lake ecosystem research.

EPFL2022