Lakes emit substantial amounts of carbon dioxide (CO 2 ) into the atmosphere, but why they do remains debated. The long-standing vision of lakes as solely respirators of the organic matter leaking from the soils has been challenged by evidence that inorganic carbon produced by weathering of the catchment bedrock could also support lake CO 2 emissions. How inorganic carbon inputs ultimately generate lake CO 2 outgassing remains a blind spot. We develop and introduce a calcite module in a coupled one-dimensional physical-biogeochemical model that we use to simulate the carbon cycle of the large Lake Geneva over the past 40 years. We mechanistically demonstrate how the so-far neglected process of calcite precipitation boosts net CO 2 emissions at the annual scale. Far from being anecdotal, we show that calcite precipitation could explain CO 2 outgassing across various lakes globally, including some of the largest lakes in the world.

Abstract In alkaline freshwater systems, the apparent absence of carbon limitation to gross primary production (GPP) at low CO2 concentrations suggests that bicarbonates can support GPP. However, the contribution of bicarbonates to GPP has never been quantified in lakes along the seasons. To detect the origin of the inorganic carbon maintaining GPP, we analyze the daily stoichiometric ratios of CO2–O2 and alkalinity–O2 in a deep hardwater lake. Results show that aquatic primary production withdraws bicarbonate from the alkalinity pool for two‐thirds of the year. Alkalinity rather than CO2 is the dominant inorganic carbon source for GPP throughout the stratified period in both the littoral and pelagic environments. This study sheds light on the neglected role of alkalinity in the freshwater carbon cycle throughout an annual cycle.

In ice-covered lakes, near-bottom oxygen concentration decreases for most of the wintertime, sometimes down to the point that bottom waters become hypoxic. Studies insofar have reached divergent conclusions on whether climate change limits or reinforces the extent and duration of hypoxia under ice, raising the need for a comprehensive understanding of the drivers of the dissolved oxygen (DO) dynamics under lake ice. Using high-temporal resolution time series of DO concentration and temperature across 14 mountain lakes, we showed that the duration of bottom hypoxia under ice varies from 0 to 236 d within lakes and among years. The variability of hypoxia duration was primarily explained by changes in the decay rate of DO above the lake bottom rather than by differences in DO concentration at the ice onset or in the ice-cover duration. We observed that the DO decay rate was primarily linked to physical controls (i.e., deep-water warming) rather than biogeochemical drivers (i.e., proxies for lake or catchment productivity). Using a simple numerical model, we provided a proof-of-concept that the near-bed stratification can be the mechanism tying the DO decay rate to the sediment heat release under the ice. We ultimately showed that the DO decay rate and hypoxia duration are driven by the summer light climate, with faster oxygen decline found under the ice of clearer cryostratified alpine lakes. We derived a framework theorizing how the hypoxia duration might change under the ice of alpine lakes in a warmer climate.

In hardwater lakes, calcite precipitation is an important yet poorly understood process in the lacustrine carbon cycle, in which catchment-derived alkalinity (Alk) is both transformed and translocated. While the physico-chemical conditions supporting the supersaturation of water with respect to calcite are theoretically well described, the magnitude and conditions underlying calcite precipitation at fine temporal and spatial scales are poorly constrained. In this study, we used high frequency, depth-resolved (0-30 m) data collected over 18 months (June 2019 - November 2020) in the deeper basin of Lake Geneva to describe the dynamics of calcite precipitation fluxes at a fine temporal resolution (day to season) and to scale them to carbon fixation by primary production. Calcite precipitation occurred during the warm stratified periods when surface water CO2 concentrations were below atmospheric equilibrium. Seasonally, the extent of Alk loss due to calcite precipitation (i.e., [30-42] g C m-2) depended upon the level of Alk in surface waters. Moreover, interannual variability in seasonal calcite precipitation depended on the duration of stratification, which determined the volume of the water layer susceptible to calcite precipitation. At finer timescales, calcite precipitation was characterized by marked daily variability with dynamics strongly related to that of planktonic autotrophic metabolism. Increasing daily calcite precipitation rates (i.e., maximum values 9 mmol C m-3 d-1) coincided with increasing net ecosystem production (NEP) during periods of enhanced water column stability. In these conditions, calcite precipitation could remove as much inorganic carbon from the productive layers as NEP. This study provides mechanistic insights into the conditions driving pelagic calcite precipitation, and quantifies its essential contribution to the coupling of organic and inorganic carbon cycling in lakes.

Even low productive, high-altitude lakes experience deep water hypoxia under ice-cover. While the changing ice phenology is expected to ripple on the magnitude of under-ice hypoxia, the lack of a mechanistic framework linking the physical impact of ice loss to biogeochemical properties has led to seemingly contradictory conclusions. Biogeochemical and physical processes constrain the Dissolved Oxygen (DO) dynamic at the sediment-water interface under lake ice. On the one hand, the biogeochemical hypothesis envisions a primary control of DO decay under the ice by sediment oxygen uptake, which arises from benthic microbial respiration and the release of reduced compounds. On the other hand, the physical hypothesis assumes a greater DO decay when sediment heat release reinforces the inverse stratification; the stronger is the sediment heat release, the more the bottom layer, from which oxygen is consumed, gets isolated from potential diffusive resupply from the upper layers. The outcome of a shorter ice-cover on the under-ice DO dynamics depends on the dominance of either biogeochemical or physical processes. Based on in-situ observations of DO and temperature, we assessed the relative share of biogeochemical and physical processes on decay under the ice of 14 high-altitude lakes in the French Alps. We found highly variable DO decay rates across the different lakes and years, with exponential coefficients ranging from 1.10-3 to 6.10-2 d-1. The under-ice DO decay rates increased, within years and lakes, with sediment heat release, while biogeochemical factors played only a marginal role. We tested through a reaction-diffusion model on an archetypal, testbed lake the individual effects of biogeochemical versus physical processes on DO decay. We confirmed that the sediment heat flux at ice-on is a major driver of DO decay under the ice, explaining one mechanism by which shallower or more transparent lakes experience greater DO decay under the ice.

The influence of human activities on the role of inland waters in the global carbon (C) cycle is poorly constrained. In this study, we investigated the impact of human land use on the sources and biodegradation of dissolved organic matter (DOM) and its potential impact on bacterial respiration in 10 independent catchments of the Lake Geneva basin. Sites were selected along a gradient of human disturbance (agriculture and urbanization) and were visited twice during the winter high-flow period. Bacterial respiration and DOM bioavailability were measured in the laboratory through standardized dark bioassays, and the influence of human land uses on DOM sources, composition and reactivity was assessed from fluorescence spectroscopy. Bacterial respiration was higher in agro-urban streams but was related to a short-term bioreactive pool (0–6 d of incubation) of autochthonous origin, whose relative contribution to the total DOM pool increased with the degree of human disturbance. On the other hand, the degradation of a long-term (6–28 d) bioreactive pool related to terrestrial DOM was independent from the catchment land use and did not contribute substantially to aquatic bacterial respiration. From a greenhouse gas emission perspective, our results suggest that human activities may have a limited impact on the net C exchanges between inland waters and the atmosphere, as most CO2 fixed by aquatic producers in agro-urban streams is cycled back to the atmosphere after biomineralization. Although seasonal and longitudinal changes in DOM sources must be considered, the implications of our results likely apply more widely as a greater proportion of autochthonous-DOM signature is a common feature in human-impacted catchments. Yet, on a global scale, the influence of human activities remains to be determined given the large diversity of effects of agriculture and urbanization on freshwater DOM depending on the local environmental context.

Dissolved inorganic carbon (DIC) is rarely regarded as a limiting factor of gross primary production (GPP) because atmospheric CO2 invasion is expected to compensate for the DIC demands at high GPP levels. However, from May to August, the CO2 concentrations in the surface waters of Lake Geneva, a large and deep hardwater lake, can be as low as 100 ppm, i.e. threshold values for carbon limitation of gross primary production (GPP). Because GPP values remain high during summer in Lake Geneva, we questioned whether CO2 invasion was sufficient to supply GPP in inorganic carbon, or whether additional inorganic carbon was supplied by alkalinity, through CO2 released by the background calcite precipitation. Using the paired O2–CO2 departure from the atmospheric equilibrium coupled to alkalinity data in littoral and pelagic environments, we investigated the sources of the inorganic carbon fixed by primary production, along three hypotheses. The first hypothesis (H1) is that atmospheric CO2 invasion is sufficient to compensate for the CO2 demand. The second hypothesis (H2) builds on H1 while including the chemical enhancement of CO2 influxes. The third hypothesis (H3) consists in adding to H2 CO2 released by calcite precipitation. We find first that daily molar changes in DO are unrelated to daily molar changes in CO2, but to molar changes in alkalinity for most of the warm season. For days for which we could compute GPP, we found that for GPP < 30 µmol C L–1 d–1, H1 and H2 are sufficient to maintain the CO2 demand, in both the littoral and pelagic habitats. Above 30 µmol C L–1 d–1, even chemically enhanced CO2 invasion cannot compensate for GPP, and CO2 demand can only be meet adding CO2 supplied by alkalinity through calcite precipitation. In Lake Geneva, alkalinity could thus supply inorganic carbon to high GPP up to ~ 40% during the stratified season for littoral and pelagic primary producers.

Whiting events, i.e., sudden and massive calcite precipitation turning lake waters to a milky turquoise colour, are unpredictable in space and time. This lack of understanding arises from the transitory nature of whiting events and their variable spatial extent, which are not well captured by traditional monitoring. We use a multi-spectral remote sensing approach to reconstruct the occurrence, timing, and spatial extent of whiting events in Lake Geneva from 2013 to 2021. Landsat-8 and Sentinel-2 multispectral sensors were combined and intercalibrated to derive the AreaBGR index and identify whiting events over the studied period. Then, intercalibrated remote sensing was used to estimate spatial extents and temporal occurrences of whiting events in Lake Geneva. Principal Component Analysis (PCA) identified environmental drivers of typical features of whiting events (such as meteorological, Rhône River and lake physical conditions). KNN (K-nearest neighbours) was used to reconstruct the full time-series of whiting events over the last 50 years. Ongoing results show that the combination of multi-spectral sensors is suitable for monitoring whiting events in Lake Geneva, based on the description of their spatial and temporal occurrences.

Whiting events are massive calcite precipitation events turning hardwater lake waters to a milky turquoise color. Herein, we use a multispectral remote sensing approach to describe the spatial and temporal occurrences of whitings in Lake Geneva from 2013 to 2021. Landsat-8, Sentinel-2, and Sentinel-3 sensors are combined to derive the AreaBGR index and identify whitings using appropriate filters. 95% of the detected whitings are located in the northeastern part of the lake and occur in a highly reproducible environmental setting. An extended time series of whitings in the last 60 years is reconstructed from a random forest algorithm and analyzed through a Bayesian decomposition for annual and seasonal trends. The annual number of whiting days between 1958 and 2021 does not follow any particular monotonic trend. The inter-annual changes of whiting occurrences significantly correlate to the Western Mediterranean Oscillation Index. Spring whitings have increased since 2000 and significantly follow the Atlantic Multidecadal Oscillation index. Future climate change in the Mediterranean Sea and the Atlantic Ocean could induce more variable and earlier whiting events in Lake Geneva.

Whiting events are transient phenomena commonly occurring in hardwater lakes and manifesting as a turquoise coloration of surface waters during massive calcium carbonate precipitation. While biological and physico‐chemical drivers of carbonate precipitation are known, their relative contributions in controlling whiting events' timing and spatial extent remain poorly understood. Coupling spatially resolved data obtained for two sampling surveys using multiple analytical techniques and geochemical modeling, this study investigated the mechanisms underlying a whiting event during the early summer of 2019 in Lake Geneva. Satellite observations showed that the phenomenon started during a snowmelt period in the catchment at the Rhône River delta before spreading along the lake's northern shore and covering vast areas of its deeper basin. Authigenic calcite precipitated at the river mouth during mixing of warmer calcite super‐saturated lake surface waters with colder snowmelt‐diluted, sediment‐rich river water containing detrital carbonates as potential nucleation sites. The development of the whiting event depended upon the thermal stratification of the water column and the existence of a physically stable metalimnion, within which a river interflow transported finer particles across the lake. During transport, the whiting plume enriched in authigenic carbonates by settling of coarser detrital particles and additional precipitation likely both on the fine‐grained carbonate fraction and through biologically induced mechanisms in the superficial layers of the lake. This study provides novel mechanistic insights on the conditions controlling whiting events in lakes, highlighting a tight coupling of their dynamics with processes acting at the catchment scale.

The gas transfer velocity (k) is a major source of uncertainty when assessing the magnitude of lake gas exchange with the atmosphere. For the diversity of existing empirical and process-based k models, the transfer velocity increases with the level of turbulence near the air–water interface. However, predictions for k can vary by a factor of 2 among different models. Near-surface turbulence results from the action of wind shear, surface waves, and buoyancy-driven convection. Wind shear has long been identified as a key driver, but recent lake studies have shifted the focus towards the role of convection, particularly in small lakes. In large lakes, wind fetch can, however, be long enough to generate surface waves and contribute to enhance gas transfer, as widely recognised in oceanographic studies. Here, field values for gas transfer velocity were computed in a large hard-water lake, Lake Geneva, from CO2 fluxes measured with an automated (forced diffusion) flux chamber and CO2 partial pressure measured with high-frequency sensors. k estimates were compared to a set of reference limnological and oceanic k models. Our analysis reveals that accounting for surface waves generated during windy events significantly improves the accuracy of k estimates in this large lake. The improved k model is then used to compute k over a 1-year time period. Results show that episodic extreme events with surface waves (6 % occurrence, significant wave height > 0.4 m) can generate more than 20 % of annual cumulative k and more than 25 % of annual net CO2 fluxes in Lake Geneva. We conclude that for lakes whose fetch can exceed 15 km, k models need to integrate the effect of surface waves.

Abstract. The influence of human activities on the role of inland waters in the global carbon (C) cycle is poorly constrained. In this study, we investigated the impact of human land use on the degradation of terrestrial dissolved organic matter (DOM) and its potential impact on bacterial respiration in ten independent catchments of the Lake Geneva Basin. Sites were selected along a gradient of human disturbance (agriculture and urbanization), and we monitored bacterial respiration in parallel to DOM bioavailability. Fluorescence spectroscopy was used to determine the influence of human land uses on DOM sources and composition as well as the dynamic of degradation or production of the fluorophores identified in our study sites. Higher bacterial respiration measured in agro-urban streams related to a short-term bioreactive pool (0–6 days of incubation) from autochthonous origin, whose the size increased with human disturbance. On the other hand, the degradation of terrestrial DOM was not impacted by human activities and was not found to contribute substantially to aquatic bacterial respiration. Although human land uses controlled DOM sources, composition and bioavailability at the basin scale, our results showed that human activities in the Lake Geneva Basin had a limited impact on the net C exchanges between inland waters and the atmosphere related to DOM mineralization. Considering that greater proportion of autochthonous-DOM signature is a common feature in human-impacted catchments, the implications of our results likely apply more widely. Yet, on a global scale, the influence of human activities remains to be determine given the large diversity of effects of agriculture and urbanization on freshwater DOM depending on the local environmental context.

The rates of gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP) provide quantitative information about the cycling of carbon and energy in aquatic ecosystems. In lakes, metabolic rates are often diagnosed from diel oxygen fluctuations recorded with high‐resolution sondes. This requires that the imprint of ecosystem metabolism can be separated from that of physical processes. Here, we quantified the vertical and temporal variability of the metabolic rates of a deep, large, mesotrophic lake (Lake Geneva, Switzerland–France) by using a 6‐month record (April–October 2019) of high‐frequency, depth‐resolved (0–30 m) dissolved oxygen measurements. Two new alternative methods (in the time and frequency domain) were used to filter low‐frequency basin‐scale internal motions from the oxygen signal. Both methods proved successful and yielded consistent metabolic estimates showing net autotrophy (NEP = GPP − R = 55 mmol m−2 day−1) over the sampling period and depth interval, with GPP (235 mmol m−2 day−1) exceeding R (180 mmol m−2 day−1). They also revealed significant temporal variability, with at least two short‐lived blooms occurring during calm periods, and a vertical partitioning of metabolism, with stronger diel cycles and positive NEP in the upper ∼10 m and negative NEP below, where the diel oxygen signal was dominated by internal motions. The proposed methods expand the range of applicability of the diel oxygen technique to large lakes hosting energetic, low‐frequency internal motions, offering new possibilities for unveiling the rich spatiotemporal metabolism dynamics in these systems.

11 The influence of human activities on the role of inland waters in the global carbon (C) 12 cycle is poorly constrained. In this study, we investigated the impact of human land use on the 13 degradation of terrestrial dissolved organic matter (DOM) and its potential impact on bacterial 14 respiration in ten independent catchments of the Lake Geneva Basin. Sites were selected 15 along a gradient of human disturbance (agriculture and urbanization), and we monitored 16 bacterial respiration in parallel to DOM bioavailability. Fluorescence spectroscopy was used to 17 determine the influence of human land uses on DOM sources and composition as well as the 18 dynamic of degradation or production of the fluorophores identified in our study sites. Higher 19 bacterial respiration measured in agro-urban streams related to a short-term bioreactive pool 20 (0-6 days of incubation) from autochthonous origin, whose the size increased with human 21 disturbance. On the other hand, the degradation of terrestrial DOM was not impacted by 22 human activities and was not found to contribute substantially to aquatic bacterial respiration. 23 Although human land uses controlled DOM sources, composition and bioavailability at the 24 basin scale, our results showed that human activities in the Lake Geneva Basin had a limited 25 impact on the net C exchanges between inland waters and the atmosphere related to DOM 26 mineralization. Considering that greater proportion of autochthonous-DOM signature is a 27 common feature in human-impacted catchments, the implications of our results likely apply 28 more widely. Yet, on a global scale, the influence of human activities remains to be determine 29 given the large diversity of effects of agriculture and urbanization on freshwater DOM 30 depending on the local environmental context. 31

Sediment export from glaciated basins involves complex interactions between ice flow, basal erosion and sediment transfer in subglacial and proglacial streams. In particular, we know very little about the processes associated with sediment transfer by subglacial streams. The Haut Glacier d'Arolla (VS, Switzerland) was investigated during the summer melt season of 2015. LiDAR survey revealed positive surface changes in the ablation zone, indicating glacier uplift, at the end of the morning during the period of peak ablation. Instream measures of sediment transport showed that suspended load and bedload responded differently to diurnal flow variability. Suspended load depended on the availability of fine material whereas bedload depended mainly on the competence of the flow. Interpretation of these results allowed development of a conceptual model of subglacial sediment transport dynamics. It is based upon the mechanisms of clogging (deposition) and flushing (transport/erosion) in sub-glacial channels as forced by diurnal flow variability. Through the melt season, the glacier hydrological response evolves from being buffered by glacier snow cover with a poorly developed subglacial drainage system to being dominated by more rapid ice melt with a more hydraulically efficient subglacial channel system. The resultant changes in the shape of diurnal discharge hydrographs, and notably higher peak flows and lower base flows, causes sediment transport to become discontinuous, with overnight clogging and late morning flushing of subglacial channels. Overnight clogging may be sufficient to reduce subglacial channel size, creating temporarily pressurized flow and lateral transfer of water away from the subglacial channels, leading to the late morning glacier surface uplift. However, without further data, we cannot exclude other hypotheses for the uplift. (c) 2018 John Wiley & Sons, Ltd.