Highlights  The General Lake Model (GLM) is stress tested against 32 globally distributed lakes.  There was low correlation between input data uncertainty and model performance.  Model performance related to lake-morphometry, light extinction and flow regime; deep, clear lakes with high residence times had the lowest model error.

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Over the past decade, neutral theory has gained attention and recognition for its capacity to explain bacterial community structure (BCS) in addition to deterministic processes. However, no clear consensus has been drawn so far on their relative importance. In a metacommunity analysis, we explored at the regional and local scale the effects of these processes on the bacterial community assembly within the water column of 49 freshwater lakes. The BCS was assessed using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA genes. At the regional scales, results indicated that the neutral community model well predicted the spatial community structure (R(2) mean = 76%) compared with the deterministic factors - which explained only a small fraction of the BCS total variance (less than 14%). This suggests that the bacterial compartment was notably driven by stochastic processes, through loss and gain of taxa. At the local scale, the bacterial community appeared to be spatially structured by stochastic processes (R(2) mean = 65%) and temporally governed by the water temperature, a deterministic factor, even if some bacterial taxa were driven by neutral dynamics. Therefore, at both regional and local scales the neutral community model appeared to be relevant in explaining the bacterial assemblage structure.

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River inflows have a major influence on lake water quality due to their input of sediments, nutrients and contaminants. After leaving the river channel, river waters form a plume and interact with ambient lake waters. Strong hydrodynamic changes take place in the nearfield. To determine the nearfield hydro-sedimentary dynamics of the negatively-buoyant Rhône River plume in thermally stratified Lake Geneva, field campaigns were carried out at high and intermediate river discharge. High-resolution full-depth Acoustic Doppler Current Profiler (ADCP) transects were taken at 400, 800, 1,200, and 1,500 m from the river mouth, combined with profiles of temperature, turbidity and particle size distribution. These measurements provided, for the first time in a lake, detailed velocity fields across the full-plume cross-section in each transect. Furthermore, the unique combination of measurement techniques allowed the quantification of entrainment, Suspended Particulate Matter (SPM) concentrations and fluxes. They revealed that the negatively buoyant river inflow intruded into the metalimnion as a laterally unconfined interflow and continued flowing straight out in the streamwise direction, since currents in the lake were weak. At the same time, it mainly spread laterally due to entrainment of ambient water. The size of the interflow core and its velocity progressively decreased with distance from the mouth, as did SPM concentrations and volumes of particles (by a factor of 2–3 within 1,500 m), due to sediment settling and entrainment. The interflow momentum flux remained constant along the pathway, but interflow cross sections and discharge increased 2–3 times (within 1,500 m). The entrainment coefficient was >2 at 400 m and further increased non-linearly along the pathway. These values are much higher than those reported for laterally confined laboratory studies. The particle size distribution in the interflow was dominated by fine particles (<32 μm), which were transported up to 1,500 m from the mouth and most likely beyond, whereas larger particles (>62 μm) almost completely settled out before reaching that distance. The above processes occurred independent of river discharge; their intensity, however, changed with discharge.

Based on field investigations carried out in Lake Geneva during summer stratification in 2019, this study documents, for the first time, the rapid change of negatively buoyant river inflow dynamics caused by the passing of a coastal upwelling. Under calm conditions, the negatively buoyant Rhône River, entering at the eastern end of the lake, interacts with the lake density profile such that the river intrusion moves as an interflow in the thermocline layer straight out into the lake. A strong, large-scale spatially homogeneous wind that lasts for several days causes a downward thermocline tilt at the western end of the lake, coastal downwelling on the northern shore, and coastal upwelling on the southern shore. This cold-water upwelling progresses like a Kelvin wave around the lake after wind forcing ceases. When it arrives at the river inflow area, it homogenizes the lake water temperatures, and the river inflow transforms into an intrusion that spreads over the whole water column. Trapped by strong alongshore currents generated by the progressing coastal upwelling, the river plume is sharply deviated and flows along the shore in the nearshore zone, potentially bringing nutrients directly into the phototrophic near-surface layer. Following the passage of the coastal upwelling, the river inflow transforms back into an interflow. This change in inflow dynamics, which is documented for five strong wind events between June and September by combining in situ measurements, remote sensing, and numerical simulation, can be expected to occur in other large lakes with comparable wind-induced large-scale thermocline displacement.

Lake biological parameters show important spatio-temporal heterogeneities. This is why explaining the spatial patchiness of phytoplankton abundance has been a recurrent ecological issue and is an essential prerequisite for objectively assessing, protecting and restoring freshwater ecosystems. The drivers of these heterogeneities can be identified by modeling their dynamics. This approach is useful for theoretical and applied limnology. In this study, a 3D hydrodynamic model of Lake Geneva (France/Switzerland) was created. It is based on the Delft3D suite software and includes the main tributary (Rhône River) and two-dimensional high-resolution meteorological forcing. It provides 3D maps of water temperature and current velocities with a 1 h time step on a 1 km horizontal grid size and with a vertical resolution of 1 m near the surface to 7 m at the bottom of the lake. The dynamics and the drivers of phytoplankton heterogeneities were assessed by combining the outputs of the model and chlorophyll-a concentration (Chl-a) data from MERIS satellite images between 2008 and 2012. Results highlight physical mechanisms responsible for the occurrence of seasonal hot-spots in phytoplankton abundance in the lake. At the beginning of spring, Chl-a heterogeneities are usually caused by an earlier onset of phytoplankton growth in the shallowest and more sheltered areas; spatial differences in the timing of phytoplankton growth can be explained by spatial variability in thermal stratification dynamics. In summer, transient and locally higher phytoplankton abundances are observed in relation to the impact of basin-scale upwelling.

Predicting phytoplankton succession and variability in natural systems remains to be a grand challenge in aquatic ecosystems research. In this study, we identi ed six major plankton groups in Lake Bourget (France), based on cell size, taxonomic properties, food-web interactions and occurrence patterns: cyanobacterium Planktothrix rubescens, small and large phytoplankton, mixotrophs, herbivorous and carnivorous zooplankton. We then developed a deterministic dynamic model that describes the dynamics of these groups in terms of carbon and phosphorus uxes, as well as of particulate organic phosphorus and dissolved inorganic provide evidence for the hypothesis that the abundance of this species before the onset of strati cation is critical for its success later in the growing season, pointing thereby to a priority e ect.