The simultaneous interaction of lake breeze (LB) flows, complex terrain circulations and urban environments has so far received limited attention in the scientific literature. Here, we use the Weather Research and Forecasting model to investigate the aero- and thermodynamical interaction between Lake Geneva, the Swiss cities of Lausanne and Geneva and their rugged alpine landscape. To better isolate the role of urban areas, we compare results from a set of year-long simulations representing both realistic urban and hypothetical rural landcover scenarios. The results show that the urban areas of Lausanne and Geneva have a negligible effect on the dynamical evolution of LB, mostly consisting of wind deceleration caused by increased surface drag. However, the daytime excess heat over Lausanne results in a shift of the local anabatic wind regime onset time, one hour ahead, and a 1 km spatial displacement northward of the location of opposing flow collision. Urban-induced changes in heat advection can further lead to warmer air temperatures over the lake or cooler urban conditions along the lake shore. Our study shows that, although with due magnitude differences, mid-sized cities may have similar effects on wind and heat dynamics as larger metropolises in different landscapes and climates.

Models are simplified descriptions of reality and are intrinsically limited by the assumptions that have been introduced in their formulation. With the development of automatic calibration toolboxes, finding optimal parameters that suit the environmental system has become more convenient. Here, we explore how optimization toolboxes can be applied innovatively to uncover flaws in the physical formulations of models. We illustrate this approach by evaluating the effect of simplifications embedded in the formulation of a widely used hydro-thermodynamic model. We calibrate a Delft3D model based on temperature profiles for a case study, Lake Morat (Switzerland), through the DYNO-PODS optimization tool. The results show that higher values of the light extinction coefficient can compensate for neglecting the fraction β of short-wave radiation absorbed at the surface of the water. This leads to unrealistic values of the light extinction coefficient, as the optimization pushes its value toward the limit of no transparency, consistent with the need to reproduce a significant absorption at the surface. Although it is well known that β is significantly larger than zero, its absence from the model was never noticed as critical. Automatic calibration tools provide valuable diagnostic insights into the physical robustness of models, enabling more precise evaluation of their structural integrity and performance.

Sun-induced fluorescence (SIF) from phytoplankton has historically been used as a proxy for chlorophyll-a concentration (chl-a) estimates in water bodies using optical Earth observation data. However, the relationship is often affected by spectral features caused by elastic scattering, and by the shifting incidence of different fluorescence quenching mechanisms. This study found that disentangling Photochemical Quenching (PQ) and Non-Photochemical Quenching (NPQ) cases improves SIF-based chl-a estimates. Further, we defined strategies which can distinguish the two quenching mechanisms. We assembled a unique dataset collected between 2018 and 2022 by an autonomous profiler in Lake Geneva (Western Europe). We used NPQ-influenced chl-a estimates from the fluorometer and NPQ-corrected chl-a estimates to distinguish between PQ and NPQ cases. The correlation between SIF yield and chl-a is weak when considering the entire dataset (R² = 0.37; Median Absolute Percentage Difference (MAPD) = 74%). It increases strongly when comparing PQ cases (R² = 0.72, MAPD = 49%) and NPQ cases (R² = 0.48, MAPD = 68%) separately. Analyzing a subset of in situ measurements acquired around Sentinel-3 overpasses (±3 hours) improved the performance metrics for both PQ cases (R² = 0.82, MAPD = 35%) and NPQ cases (R² = 0.43, MAPD = 61%). However, when applying the same approach to Sentinel-3 OLCI data, we found that the errors in remote sensing reflectance products disable such an adaptation. We conclude that enhanced atmospheric correction in the red-NIR region for oligo-mesotrophic lakes is needed to demonstrate the upscaling of our in situ-based results. This will enhance satellite-based SIF yield retrievals and subsequently, obtain SIF-related phytoplankton physiology products.

Freshwater algae exhibit complex dynamics, particularly in meso-oligotrophic lakes with sudden and dramatic increases in algal biomass following long periods of low background concentration. While the fundamental prerequisites for algal blooms, namely light and nutrient availability, are well-known, their specific causation involves an intricate chain of conditions. Here we examine a recent massive Uroglena bloom in Lake Geneva (Switzerland/France). We show that a certain sequence of meteorological conditions triggered this specific algal bloom event: heavy rainfall promoting excessive organic matter and nutrients loading, followed by wind-induced coastal upwelling, and a prolonged period of warm, calm weather. The combination of satellite remote sensing, in-situ measurements, ad-hoc biogeochemical analyses, and three-dimensional modeling proved invaluable in unraveling the complex dynamics of algal blooms highlighting the substantial role of littoral-pelagic connectivities in large low-nutrient lakes. These findings underscore the advantages of state-of-the-art multidisciplinary approaches for an improved understanding of dynamic systems as a whole.

The development of algorithms for remote sensing of water quality (RSWQ) requires a large amount of in situ data to account for the bio-geo-optical diversity of inland and coastal waters. The GLObal Reflectance community dataset for Imaging and optical sensing of Aquatic environments (GLORIA) includes 7,572 curated hyperspectral remote sensing reflectance measurements at 1 nm intervals within the 350 to 900 nm wavelength range. In addition, at least one co-located water quality measurement of chlorophyll a, total suspended solids, absorption by dissolved substances, and Secchi depth, is provided. The data were contributed by researchers affiliated with 59 institutions worldwide and come from 450 different water bodies, making GLORIA the de-facto state of knowledge of in situ coastal and inland aquatic optical diversity. Each measurement is documented with comprehensive methodological details, allowing users to evaluate fitness-for-purpose, and providing a reference for practitioners planning similar measurements. We provide open and free access to this dataset with the goal of enabling scientific and technological advancement towards operational regional and global RSWQ monitoring.

Quantum yield of fluorescence (ϕ_F) is key to interpret remote measurements of sun-induced fluorescence (SIF), and whether the SIF signal is governed by photochemical quenching (PQ) or non-photochemical quenching (NPQ). Disentangling PQ from NPQ allows using SIF estimates in various applications in aquatic optics. However, obtaining ϕ_F is challenging due to its high temporal and physiological variability, and the combined measurements needed to enclose all relevant optical paths. In inland waters, this type of data is scarce and information on diurnal and seasonal ϕ_F dynamics are almost unknown. Using an autonomous hyperspectral Thetis profiler in Lake Geneva, we demonstrate how to estimate ϕ_F using an ensemble of in-situ measurements acquired between 2018 to 2021. We use vertical and temporal changes in retrieved ϕ_F to determine NPQ and PQ conditions. We observed NPQ in 36% of the total daytime profiles used in the ϕ_F analysis. While downwelling irradiance is a significant contributor to ϕ_F, its role cannot be easily interpreted. Other factors such as phytoplankton photoregulation and assemblages also likely play significant roles in quenching mechanisms. We conclude that an adapted approach exploiting in-situ data is suitable to determine diurnal and seasonal NPQ occurrence, and helps develop future remote sensing algorithms.

Water inherent optical properties (IOPs) contain integrative information on the optical constituents of surface waters. In lakes, IOP measurements have not been traditionally collected. This study describes how high-frequency IOP profiles can be used to document short-term physical and biogeochemical processes that ultimately influence the long-term trajectory of lake ecosystems. Between October 2018 and May 2020, we collected 1373 high-resolution hyperspectral IOP profiles in the uppermost 50 m of the large mesotrophic Lake Geneva (Switzerland-France), using an autonomous profiler. A data set of this size and content does not exist for any other lake. Results showed seasonal variations in the IOPs, following the expected dynamic of phytoplankton. We found systematic diel patterns in the IOPs. Phases of these diel cycles were consistent year-round, and amplitudes correlated to the diurnal variations of dissolved oxygen, clarifying the link between IOPs and phytoplankton metabolism. Diel amplitudes were largest in spring and summer under low wind condition. Wind-driven changes in thermal stratification impacted the dynamic of the IOPs, illustrating the potential of high-frequency profiles of water optical properties to increase our understanding of carbon cycling in lake ecosystems.

We present an optical closure exercise using in situ hyperspectral radiometry and Inherent Optical Property (IOP) measurements acquired in Lake Geneva, (Switzerland/France). The dataset includes 294 high-resolution profiles for the period between 10/2018 and 5/2020. Hydrolight was used to simulate remote sensing reflectance (Rrs) from measured IOPs. The comparison with measured Rrs was carried out under six different scenarios: (i) a temporally constant backscattering ratio (Bp=0.0183) without scattering correction, (ii) temporally variable Bp estimated from measured IOPs without scattering correction, and (iii-vi) temporally variable Bp estimated from measured IOPs and using four different scattering correction methods. The results indicate that both a reasonable estimation of Bp and scattering correction of IOPs are crucial for optical closure. We did not find a significant difference in the performance of the different scattering correction methods. Our results suggest that automated optical profiling is an alternative for ground-truthing water-leaving reflectance.