Mesoscale eddies drive complex, large-scale three-dimensional biochemical variability in the mixed layer of a large lake (Lake Geneva)

Mesoscale eddies drive complex, large-scale three-dimensional biochemical variability in the mixed layer of a large lake (Lake Geneva) | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Mesoscale eddies drive complex, large-scale three-dimensional biochemical variability in the mixed layer of a large lake (Lake Geneva) Seyed Mahmood Hamze-Ziabari, Ulrich Lemmin, David Andrew Barry This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8156830/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 11 You are reading this latest preprint version Abstract The influence of three-dimensional (3D) hydrodynamic processes, in particular that of mesoscale cyclonic (CEs) and anticyclonic eddies (ACEs), on water quality in lakes is largely unexplored. In this study, high-resolution field measurements based on 3D forecasting simulations allowed examination of how mesoscale eddies modulate the spatial distribution of key water quality parameters such as dissolved oxygen (DO), conductivity, and thermal stratification in Lake Geneva. The analysis focuses on periods of strong (summer) and weak (fall) thermal stratification. Results reveal that the interplay between simultaneously occurring CEs and ACEs (diameters ~ 10 km) causes lateral variability in water quality by regulating the strength, the extent, and the shape of the metalimnion, a critical stratification interface. Compared to profiles taken at a station outside these eddies, CEs are characterized by higher DO concentrations, a shallower mixed layer, and a thicker metalimnion, whereas ACEs exhibit opposite trends. Within the mixed layer and metalimnion, DO production in summer and consumption in the fall occur across a wider depth range in the thicker metalimnion induced by CEs, whereas ACEs compress the metalimnion and limit vertical exchange. It is demonstrated that, depending on the season, extreme values of vertical DO gradients are primarily controlled by CEs or ACEs, which influence the depth distribution and intensity of biological processes, with potential implications for lake ecosystem dynamics. Earth and environmental sciences/Climate sciences Earth and environmental sciences/Environmental sciences Earth and environmental sciences/Hydrology Earth and environmental sciences/Ocean sciences Mesoscale eddies Cyclonic and anticyclonic circulations Mixed layer dynamics Thermal stratification Dissolved oxygen gradients Biogeochemical cycling Large lakes Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Introduction In oceans, Coriolis force-generated cyclonic (counterclockwise rotating in the Northern Hemisphere) and anticyclonic (clockwise rotating) circulations, such as gyres and eddies, are recognized as principal mesoscale processes that transport mass, momentum, heat and biogeochemical parameters 1 , 2 , 3 ; thus they can affect physical and biochemical dynamics horizontally and vertically 4 , 5 . Pelagic upwelling/downwelling associated with cyclonic/anticyclonic circulation can increase/decrease nutrient supply to the euphotic zone by raising/lowering the nutricline, which in turn enhances/weakens primary production 6 , 7 , 8 , 9 , 10 and thereby changes, for example, Dissolved Oxygen (DO) levels 11 , 12 , 13 . At present, comparable information relating to large lakes is scarce. Lateral variability of hydrodynamic processes and water quality parameters in marine ecosystems or large lakes, which is caused by the presence of large scale eddies, is often assessed by remote sensing 14 , 15 , 16 , 17 , 18 , 19 , 20 and Autonomous Underwater Vehicle (AUV) surveys 21 , 22 , 23 , 24 . Remote sensing offers exceptional lateral resolution, but is restricted to the near-surface layers and can be biased by cloud cover 25 , 26 ; the use of AUVs in lakes is limited 27 . To effectively manage lake water quality, it is essential to understand how lateral variability due to mesoscale eddy interplay affects the interaction of physical and biochemical processes. In this study, mesoscale eddies are defined as coherent structures whose dimensions are determined by the size of the lake basin; in Lake Geneva, they are limited by the width of the basin and have a typical diameter of ~ 10 km. They have fixed locations 28 . Submesoscale eddies are smaller in diameter (~ 3 to 5 km) and move between mesoscale eddies 19 . Their impact on water quality parameters is poorly understood, primarily due to the scarcity of spatially distributed, high-resolution biochemical observations in the water-column. In many lakes, assessment of biological, chemical, and physical processes is traditionally conducted using single station monitoring data 29 . Following such an approach in large lakes, however, fails to take into consideration circulation-induced lateral variability caused by Coriolis force. Surveys employing Conductivity-Temperature-Depth (CTD) and Acoustic Doppler Current Profiler (ADCP) instruments can collect data at high spatial and vertical resolution. In the past, the challenge was to predict when and where to sample effectively to capture the spatial variability caused by mesoscale eddies. However, recent advances in high-resolution hydrodynamic models 30 , 31 , 32 , when coupled with enhanced statistical analysis techniques, remote sensing and numerical weather forecasting models, now allow the spatial distribution of mesoscale processes in large lakes to be accurately predicted 19 , 28 . As a result, field campaigns can be efficiently planned in advance to obtain biological-chemical-physical data with high spatial and vertical resolution and thus quantify the 3D effect of mesoscale circulations. This field study in Lake Geneva examines for the first time the intricate interplay between mesoscale circulations and the resultant lateral variability of water quality parameters in a lake environment. Based on predictions generated by high-resolution, 3D hydrodynamic simulations, field measurement campaigns were designed to capture data sets to address the following questions: Does the interplay of mesoscale eddies influence the thermal structure, conductivity, and Dissolved Oxygen (DO) levels within the epilimnion and metalimnion? Does this pattern vary with seasonal stratification conditions? Are routine monitoring programs affected by the presence/absence of mesoscale eddies? Our findings reveal the critical role that mesoscale eddies play in thermal dynamics, and in governing biochemical distributions in a stratified lake. This knowledge, presently lacking, improves the predictive capabilities for quantifying ecological responses to physical processes in large lake systems. The Supporting Information (SI) section provides additional clarifications/details on certain topics mentioned in the text. Results and Discussion The two dominant winds over Lake Geneva—the northeast Bise and the southwest Vent —drive basin-scale circulations and govern stratification and vertical mixing (Fig. 1 b,c) 33 . Their interaction with the lake’s complex bathymetry organizes the flow into mesoscale eddies, filaments, and frontal structures 28 , 34 (Fig. 1 d,e). To quantify how these mesoscale features modulate physical and biogeochemical fields, we conducted four model-informed field campaigns with transects selected from 3-D numerical forecasts: during strong summer stratification (22 July and 23 August 2022) and during weak autumn stratification (19 and 26 October 2021). Lateral variability during strong thermal stratification in summer On 22 July and 23 August 2022, 3D numerical modeling combined with statistical analyses 28 , predicted the development of a dipole circulation consisting of an anticyclonic eddy (ACE) in the western part and a cyclonic eddy (CE) in the central region of the Grand Lac basin of Lake Geneva (Fig. 2 a, e). The flow pattern developed three days after a strong Bise (wind speeds > 2.5 m s - 1 ) ceased. We conducted field measurements along predefined transects that were selected based on the predictions from the numerical model and statistical analysis (Fig. 2 a, e). Velocity profiles obtained from ADCP measurements along these transects during both field campaigns confirmed the presence of the predicted dipole circulation (compare Fig. 2 a, e with 3a, e). July 2022 observations Vertical profiles of temperature, oxygen saturation (%), and dissolved oxygen (DO) from the July 2022 campaign (Fig. 2 b–d) reveal clear distinctions between the CE and ACE. In the CE, the thermocline is dome-shaped, indicating strong upward displacement of deeper waters; conversely, in the ACE, the thermocline exhibits a bowl-shaped configuration, with comparatively weaker downwelling (Fig. 2 b). This asymmetry is primarily driven by variations in the intensity of the horizontal circulation. Stronger cyclonic rotational velocities in the CE (Fig. 3 a) enhance upward motion, deform the density stratification and transport cooler, deeper waters into the thermocline and epilimnion. In contrast, the ACE, with lower rotational velocities, produces a less pronounced downwelling effect and, consequently, less thermocline deformation as was already observed in Lake Erie 35 . DO concentrations mirror the temperature pattern of the cyclonic and anticyclonic circulations (Fig. 2 c). In the CE, metalimnion DO levels were notably higher, coinciding with the upwelling of deeper, nutrient-rich water into this layer. A localized zone of oxygen supersaturation was observed near the center of the CE, corresponding to the maximum uplift of the thermocline (Fig. 3 d). This supersaturation probably results from enhanced primary production fueled by upwelled nutrient-rich deep water, which supports elevated phytoplankton growth 36 , 37 . In contrast, DO levels in the ACE were comparatively lower, consistent with weaker downwelling of nutrient-poor epilimnion waters. Furthermore, the deepening of isopycnals typically associated with anticyclones reduces nutrient availability in the well-illuminated surface layers, thereby limiting phytoplankton growth and DO production 8 . Comparing these data with data measured at the LéXPLORE platform (see Fig. 1 a for location), which is outside or at the edge of the dipole circulation, demonstrates the impact of these eddies on biochemical parameters. At the LéXPLORE platform, chlorophyll-a concentration peaked at approximately 30-m depth, with maximum DO and oxygen supersaturation above this depth (Fig. S1 a). Near the CE center, oxygen supersaturation was roughly 10% higher, driven by enhanced primary production associated with the upwelling of nutrient-rich deeper water. This upwelling not only brings nutrients into the photic zone but also raises the thermocline, thereby shifting the depths of maximum DO and chlorophyll-a concentrations closer to the surface than at LéXPLORE. These observations can be explained by “eddy pumping,” wherein mesoscale circulation enhances vertical nutrient transport and modulates the distribution of phytoplankton, oxygen, and other biogeochemical parameters 8 , 35 . In contrast to CE upwelling, the ACE deepens nutrient-poor surface layers. Thus, even measurements taken outside the core regions of the CE and ACE show altered thermal and biological structures compared to the LéXPLORE data, implying that eddy-driven processes extend over a horizontal range beyond the eddy centers. August 2022 observations During the August 2022 field observations, the dome- and bowl-shaped thermocline structures associated with CE and ACE, respectively, were again present but less pronounced than in July, primarily due to weaker circulation velocities (Fig. 2 f and 3 b). DO concentrations remained elevated near the thermocline, and oxygen supersaturation persisted within the CE, reinforcing the link between eddy-induced upwelling and enhanced oxygen production. The higher DO levels in CE compared to ACE observed during both field campaigns suggest that cyclonic circulation plays an important role in redistributing oxygen and supporting biochemical processes in the lake. Previous observations that ignored eddy circulation systems indicated that, due to the acceleration of physiological processes (nutrient uptake, growth, respiration) and development of the thermal stratification in spring 38 , the photic layer of oligo- to mesotrophic lakes such as Lake Geneva is often nutrient-limited in late summer and fall 39 , 40 . However, in cyclonic circulation systems, surface divergence leads to the upward transport of deeper, nutrient-rich water, effectively enriching the photic zone and stimulating phytoplankton growth 8 , 41 . This results in greater DO production in the epilimnion and metalimnion. Thus, the oxygen-enriched water at the CE core reflects the combined effects of physical upwelling and biological oxygen production, highlighting the role of CEs in sustaining primary productivity and modifying oxygen dynamics in large lakes. The observed coupled variations in temperature, DO, and conductivity highlight how eddy-driven vertical motions reshape stratification, enhance nutrient transport, and stimulate localized productivity in large lakes during summer, when the epilimnion and photic layers are often nutrient-depleted. By modulating thermocline depth and redistributing chemical constituents, mesoscale eddies play a crucial role in shaping spatial patterns of oxygen and nutrient availability, with profound implications for pelagic ecosystem dynamics and biochemical cycling. Lateral variability in weak thermal stratification during fall Numerical simulations forecast distinct eddy-controlled flow patterns during the fall on 19 and 26 October 2021, following Bise and Vent wind events. Observations on 19 October 2021 Numerical simulations predicted that a Bise event (Fig. 1 b) generated a dipole structure on 19 October in the western and central regions of the Grand Lac (Fig. 4 a; see also Fig. 1 c). This dipole closely resembled those observed in July and August 2022 under strong stratification as discussed above, but differed in its depth influence. The measured thermocline structure (Fig. 4 b) exhibits clear regional variations, with a bowl-shaped thermocline in the ACE, and a dome-shaped thermocline in the CE. Stretching in CE and compression in ACE are mainly driven by divergent and convergent flows associated with the mesoscale processes 42 . However, the CE field was not fully covered during the field campaign due to operational limitations. Furthermore, at approximately 14 km along the transect, a cold submesoscale filament emerged between CE and ACE due to frontogenesis (Fig. 3 c). This secondary circulation enhances density gradients and drives upwelling and downwelling cells, facilitating lateral exchanges and altering the vertical structure of the water column 34 . Measured velocity profiles along the predefined transect (Fig. 3 c) confirmed the presence of the ACE/CE dipole, highlighting the recurrence of such circulation patterns across different seasonal stratification regimes (Fig. S2) 34 . DO and conductivity profiles measured along the selected transect indicate upwelling and downwelling signatures, particularly in the thermocline layers of the CE and ACE (Fig. 4 c, d). Strong seasonal differences are revealed when comparing temperature, DO, and conductivity profiles between October and summer observations. Even though the characteristic dome- and bowl-shaped thermoclines persisted in the fall, oxygen supersaturation observed in the epilimnion and metalimnion during summer was absent. Instead, a DO maximum was recorded in the epilimnion, coinciding with the highest chlorophyll-a concentration at the LéXPLORE station (Fig. S1 c, d). However, chlorophyll-a levels in October were significantly lower than in July, consistent with seasonal declines in primary production. A key difference between the 19 October observations and those during summer stratification in 2021 is seen in the vertical distribution of DO. The summer data indicated DO supersaturation extending over a wide range of the stretched CE thermocline (Fig. 2 c, d), whereas the 19 October profiles revealed more pronounced oxygen depletion in specific CE depth layers compared to ACE (Fig. 4 c). The observed decline in metalimnetic DO is primarily attributed to microbial decomposition of organic matter (OM), a process intensified in upwelling regions where vertical transport introduces nutrient-rich waters to intermediate depths. As a result, a persistent metalimnetic oxygen minimum (MOM) was observed from late summer onward (Fig. S1 ), a phenomenon commonly associated with OM mineralization in hypolimnetic waters below 15 m 43 . The metalimnion serves as an ecological niche for certain phytoplankton species 44 and acts as a zone of OM accumulation due to settling processes, particularly in summer and in the fall 45 . The formation of biological niches within the metalimnion is governed by water column stability and the balance between light availability and nutrient supply 46 , 47 . As shown above, the observed circulation patterns influence all three factors. In CE, the seasonal dynamics of DO exhibit greater variability than in ACE, with increased DO levels during summer and enhanced DO consumption in the fall. The broader metalimnion in CE compared to ACE allows biological processes to occur across a wider depth range, thus contributing to more complex biochemical interactions. Observations on 26 October 2021 On 26 October, following a strong Vent event (Fig. 1 d), the hydrodynamic simulations forecast that in the center of the Grand Lac basin an ACE was generated instead of a CE (Fig. 4 e; see also Fig. 1 e). This change was accompanied by the formation of a strong submesoscale cyclonic eddy (SCE) between the two weak ACEs located in the western part and the center of the Grand Lac (Fig. 4 e). The SCE had a diameter of ~ 5 km, and its presence caused major changes in the mixed layer depth (MLD) across the basin. In particular, the MLD in the two ACEs remained at ~ 25 m, whereas it was significantly shallower at ~ 8 m in the core of the SCE due to pronounced pelagic upwelling (Fig. 4 f). The reversal of the rotational sense of the mesoscale eddy in the center of the Grand Lac (compared to 19 October 2021) effectively smoothed out the differences in the MLD and thermocline structure between the central and western parts of the lake that had been observed on 19 October (Fig. 4 f). Effects of mesoscale eddies on water-column structure and biochemical processes The substantial impact of mesoscale eddies on water-column structure and biochemical processes becomes apparent when the mean and standard deviations of water temperature, DO, and conductivity along the selected transects are determined at different depths. Strong stratification in the summer During summer, in regions influenced by the CE, temperature deviations of up to − 5°C at the thermocline clearly indicate the upward entrainment of colder, deeper water (Fig. 5 ). This process not only cools the upper layers but also transports nutrient-rich water into the euphotic zone, enhancing phytoplankton growth and driving observed increases in DO by 2.5 mg l − 1 . A conductivity reduction of up to 0.02 mS cm − 1 in CE indicates upward transport of deep, low-conductivity water, which generally contains fewer dissolved ions than surface waters 48 , 49 . Although biological processes such as phytoplankton nutrient uptake can influence conductivity at local scales, the consistent decrease observed in CE-affected regions suggests that physical mixing and transport play a more dominant role 50 . Conversely, in ACE regions, an increase in conductivity is observed, primarily due to the downwelling of high-conductivity surface and near-surface waters. This effect is driven by surface convergence within the ACE field, which compresses the thermocline and enhances the retention of ion-rich water in the upper layer 8 , 51 . Weak stratification in the fall During fall, in CE-influenced regions, the temperature deviation at the thermocline reached −2°C, indicating again entrainment of colder, deeper water into the upper layers. Simultaneously, DO deviations of up to −1 mg l − ¹ highlight the higher reduction of DO because of greater water column mineralization (WCM) in CE. Conductivity shows both increases and reductions of up to 0.005 mS cm − 1 in different depth layers of the thermocline. As is the case during summer, this can mainly be attributed to the combined effects of vertical transport of low-conductivity deep water and higher conductivity induced by OM decomposition. In the central areas of ACE, on the other hand, a constant increase of conductivity up to 0.005 mS cm − 1 can be found, which results from downward transport of warmer higher-conductivity surface water that is transported by surface convergence of ACE flow fields. Temperature, DO and conductivity deviations between CE and ACE in the thermocline can reach up to 4°C, 2 mg l - ¹ and 0.01 mS cm − 1 , respectively. In summary, the dipole circulation observed on 19 October produced lateral variability comparable to that in July. However, it extended over a greater depth range but with smaller gradients, emphasizing the intricate influence of seasonal changes in stratification, biochemical processes, and mesoscale dynamics. On 26 October 2021, the temperature deviation between the SCE and ACEs remained comparable to, or were slightly greater than the values recorded one week earlier. The DO deviation followed a pattern similar to previous observations, with reduced DO concentrations in upwelling regions and increased DO within the ACE. However, the magnitude of these DO variations remained relatively small (~ 0.2 mg l − ¹) compared to the more pronounced dipole structure observed the previous week. Conductivity measured within the SCE exhibited a more pronounced reduction than that observed in the 19 October CE event. This reduction is primarily due to the significant upward transport of deep, low-conductivity, cold water, which can reach the lake surface 53 . These findings highlight the complex interplay between mesoscale and submesoscale circulations in controlling water column stratification and mixing. Mesoscale CEs and ACEs can persist for days to weeks at nearly fixed locations, leading to sustained spatial variability in both physical and biochemical processes. SCEs, on the other hand, are generally more transient and advective in nature (Fig. S3). They induce less pronounced long-term spatial variability when coexisting with larger, more persistent eddies 28 . Impact of mesoscale Eddies on Vertical Gradients of the Thermocline and DO One key finding from the four field observations is that cyclonic and anticyclonic circulations modify the shape and vertical structure of the thermocline. This influences thermal stratification, which can also be strongly modulated by seasonal variability. As shown above, the presence of these large-scale eddies and the interaction between circulations and stratification significantly alter the depth at which biological processes occur, particularly near or within the thermocline. To further examine the effects of these eddies, Brunt–Väisälä frequency ( N ²) and vertical DO gradients were analyzed along the four transects. Seasonal trends of vertical gradients of the thermocline and DO Above a certain N ² threshold, the trends in the vertical DO gradient and stratification strength N ² exhibit two distinct regimes above and below the thermocline that change with season (Fig. 7 ). During summer, the DO gradient in shallower regions, located primarily just above the thermocline, generally increases with depth when N ² reaches values between 10⁻⁴ and 10⁻³ s − 2 . As discussed in the previous section, this behavior may be attributed to enhanced localized oxygen production due to primary production in the upper thermocline layers in the upwelling zone near the CE center 36 , 37 . In contrast, in deeper regions, at the lower end of the thermocline, where primary production is absent and remineralization processes prevail, a negative vertical DO gradient is observed; this negative gradient becomes more pronounced as stratification strength N ² increases. These two patterns are clearly evident in both the July and August observations. During the fall, the same distinct relationships between the vertical DO gradient and N ² in the regions above and below the thermocline can still be observed on 19 October when an ACE/CE dipole is generated again. However, compared to the summer observations, the reduction of the DO gradient with increase of stratification in deeper layers is more pronounced than the increase of the DO gradient observed in shallower and near-surface layers. This is mainly due to a significant reduction of primary production in the fall due to dominant remineralization processes in hypolimnetic layers 43 , 53 . These observations highlight the role of stratification strength N ² on biological processes related to the production, respiration, and consumption of DO 46,47 . When the current regime changes from a dipole to two mesoscale ACEs separated by an SCE on 26 October, the DO vertical gradient becomes insignificant in the upper thermocline layer and is remarkably less impacted by stratification strength. However, a decreasing trend of the DO gradient with stratification strength can still be observed in the lower layers when N ² is greater than 10 − 4 s - 2 . When the depth distribution of N ² and the vertical gradient of DO along the different transects is determined (Fig. 8 ), it becomes evident that these differences in the vertical distribution (Fig. 7 ) are related to the horizontal spatial variability caused by the ACEs and the CEs. Spatial pattern in summer During summer, CE and ACE enhance maximum stratification strength with the strongest stratification observed near the centers of both CE and ACE. This coincides with regions where the maximum positive DO gradient is recorded (Fig. 5 ), in particular at the CE centers due to enhanced primary production. Increased solar radiation and weak wind-driven mixing establish a strong thermocline in temperate lakes 54 , 55 , and CE and ACE circulations further modify stratification. CE-induced upwelling transports cooler deep water upward, but the strong thermocline traps it below the surface mixed layer, locally sharpening the thermal gradient (Fig. 2 b, f). In contrast, ACE-induced downwelling plays a crucial role in strengthening stratification by compressing the thermocline and intensifying the vertical temperature gradient, thus suppressing vertical mixing. This process is well documented in oceanic studies, where mesoscale ACEs strengthen stratification by deepening the thermocline and inhibiting surface-deep water exchange 8 , 56 . This increases water column stability, requiring significant energy for mixing and delays stratification breakdown until fall cooling begins. In deep lakes such as Lake Geneva, persistent ACE activity can trap heat at depth, influencing nutrient cycling, oxygen dynamics, and the overall thermal structure 35 . Spatial pattern in fall Fall observations indicate intensified maximum stratification strength in ACE-influenced regions, whereas CE-influenced regions experience a reduction in maximum stratification strength. Notably, on October 26, when the mesoscale circulation pattern shifted from a dipole structure to a configuration dominated by two ACEs, the spatial and vertical variability of stratification strength remained largely unchanged, and the DO distribution became more uniform, with the greatest reductions occurring in regions where stratification is strengthened within the ACEs (Fig. 8 f, h). The thermocline weakens in fall due to surface cooling and wind-induced mixing, but CE and ACE affect this process differently. Cyclonic circulation disrupts stratification through upwelling-driven vertical mixing, bringing cooler deep water to the surface and reducing the temperature gradient between the epilimnion and hypolimnion 57 , 58 . This effect is amplified by cooling in the fall and increased wind stress, which enhance turbulent mixing and contribute to thermocline erosion 59 . As surface temperatures decrease, the density contrast between surface and deep layers diminishes, facilitating convective overturning and enhancing destratification 60 . On the other hand, anticyclonic circulation intensifies stratification through downwelling-driven thermocline compression 61 . Downwelling in ACE regions deepens the thermocline and insulates deeper layers from surface cooling 62 . As a result, stratification persists longer in these regions since vertical mixing and entrainment of cooler water from below are suppressed. Significance of mesoscale circulations These results highlight the critical role mesoscale circulations play in modulating both thermal and DO stratification, with their effects varying based on the sense of rotation and seasonal conditions. The mixed layer depth can vary laterally when a multi-eddy circulation pattern interplay is present. This is more evident under weak stratification (see also Fig. S2 as an example). Although many of these processes correspond to oceanic observations, notable differences arise, particularly those concerning the influence of CE during summer, when its impact on stratification is more pronounced compared to ocean settings. Thermal stratification strength is a fundamental driver of biological processes in lake ecosystems, regulating both primary production and remineralization 43 , 46 , 47 , 53 . As was shown above, strong stratification, mainly in ACE regions, compresses the thermocline, thus restricting vertical mixing and increasing the rate of oxygen depletion in deeper layers. In contrast, CE tend to widen the thermocline, increasing the depth range with moderate but persistent stratification, which enhances biological activity by facilitating nutrient exchange and oxygen production. Consequently, DO concentrations generally increase more in CE than in ACE during summer, reflecting enhanced primary production near the deep chlorophyll maximum (DCM) 63 . The thermocline also functions as both a habitat for phytoplankton species 44 and a zone for organic material accumulation and remineralization 45 . Strong stratification stabilizes the water column and promotes localized oxygen production, whereas weak stratification enhances aerobic remineralization by increasing oxygen penetration into deeper layers, accelerating organic matter decomposition 64 , 65 , 66 . Ultimately, the interplay between mesoscale circulation, stratification strength, and biological processes plays an important role in regulating lake ecosystem dynamics, with broad implications for oxygen availability, nutrient cycling, and heat distribution. Impact of Circulations at a Fixed Monitoring Station At present, lake ecosystem concepts and the assessment of long-term changes in lake system development are mainly based on measurements taken at fixed monitoring stations. However, our findings show that these measurements can be influenced by the presence of CEs or ACEs. The locations of these fixed stations are typically determined by factors such as the number and depth of lake basins, proximity to inflows and outflows, accessibility for sampling, and historical monitoring efforts. The temporal resolution of measurements is often weekly or monthly and is subject to variability due to weather conditions, logistical constraints, seasonal dynamics, and research priorities 67 . In Lake Geneva, the Commission Internationale pour la Protection des Eaux du Léman (CIPEL) has monitored the long-term trends of physical and biological processes at their SHL2 station since the 1960s (see Fig. 1 for location). This station is situated near the center of the lake, which is also the center of various mesoscale eddies; these can influence the measurements at this site (Fig. 2 , 6 ). Therefore, the physical and biological profiles, mainly in subsurface layers and the thermocline region, may be significantly affected by the eddy circulation dynamics, depending on the sense of rotation, intensity, and lifespan of the circulations. For example, on 19 October 2021, CIPEL conducted measurements at SHL2 nearly simultaneously with our field campaign. A comparison of the temperature and DO profiles obtained during our field campaign and those measured by CIPEL reveals a similar vertical structure (Fig. 10a, b). The effect of pelagic upwelling induced by the CE on temperature and DO profiles at SHL2 is evident when the profiles are compared to profiles at a reference station (i.e., LéXPLORE station) and in the ACE region. In the stretched thermocline caused by CE-induced upwelling, DO consumption at SHL2 increased significantly compared to the ACE region, likely due to enhanced remineralization of organic matter in the subsurface layer following the upward transport of nutrient- and particle-rich waters. However, in the epilimnion, DO concentrations increased, possibly due to enhanced gas exchange with the atmosphere and photosynthetic activity. The temperature and DO profiles measured at SHL2 on 19 and 26 October exhibit significant differences because the circulation in the center of the Grand Lac changed its sense of rotation (Fig. 3 , 4 ). On 26 October, the MLD was approximately 10 m deeper, and a notable DO reduction is seen in the thermocline at ~ 28 m depth (almost 10 m deeper than on 19 October; Fig. 10a, b). At that time of the year, atmospheric cooling alone is unlikely to cause such rapid and pronounced changes in thermal stratification and oxygen distribution within just one week. Instead, the observed variations are attributed to changes in the mesoscale circulation pattern, which modulate vertical mixing, stratification, and biochemical processes. The deepening of the MLD is consistent with a transition from cyclonic to anticyclonic circulation in the center of the lake, which typically enhances downward mixing, redistributing heat and DO deeper into the water column leading to an overall depletion of oxygen in the thermocline. It is clear that the monitoring data collected at SHL2 are significantly modulated by cyclonic and anticyclonic circulation patterns. Analysis of temporal variations in nutrient concentrations and thermal stratification at SHL2 in 2021 reveals episodic uplifts of nutrients along with thermocline displacement (Fig. 10c, d, and S5). These periodic upwelling events suggest that mesoscale circulations play a crucial role in modulating vertical transport of both heat and biochemical properties. Comparisons of temperature profiles at SHL2 and LéXPLORE (located near the edge of the CE) further confirm that pelagic upwelling occurs at SHL2 during certain periods (Fig. S4). However, it is important to note that LéXPLORE may, at times, be located within a cold filament zone associated with fronts or lateral mixing processes 34 or can be impacted by nearshore upwelling 68 ; these can also contribute to temperature variations. Longterm Significance We document here, for the first time in a lake, the significant lateral variability induced by the interplay between mesoscale near-surface circulations and submesoscale eddies, emphasizing the complexity of the 3D physical-biochemical interactions. These data were obtained during four different field campaigns after strong Bise and Vent wind events in Lake Geneva. The frequent occurrence of strong Bise and Vent wind events that take place throughout the year in Lake Geneva is well documented 33 . Therefore, the systematic lateral variability observed in this study is not an isolated phenomenon, but instead a recurring dynamic feature. It is probably also present in other large, deep lakes where wind-driven circulation interacts with topographic constraints to generate mesoscale circulations and submesoscale eddies. We reveal that this mesoscale-driven lateral variability can lead to heterogeneous environmental conditions, influencing nutrient transport, oxygen distribution, and plankton dynamics, and thus must be considered when designing long-term water quality management strategies. The structure of the wind field over the lake suggests that the interplay between pelagic upwelling and downwelling in mesoscale circulations can occur throughout the stratification period. Further research is required to quantify these effects across different temporal and spatial scales. In this study, we focused on quantifying the extreme values of lateral variability between the centers of mesoscale circulations and submesoscale eddies, where pelagic upwelling and downwelling drive pronounced gradients. Our detailed transect measurements across these circulation features (Fig. 2 – 4 ) reveal that physical and biochemical properties do not change abruptly between these extreme values, but instead transition progressively. The observed dome-shaped and bowl-shaped thermoclines in CEs and ACEs, respectively, create strong horizontal gradients between eddy cores and their outer edges, reinforcing the notion that mesoscale and submesoscale variability is a complex 3D phenomenon that extends over large areas of the lake. Our findings challenge classical single-point, one-dimensional monitoring and modeling approaches, which inherently oversimplify lake dynamics by assuming uniform conditions over large spatial scales. Instead, adaptive monitoring strategies 69 that evolve with an improved understanding of lake system dynamics should be implemented. Adaptive monitoring integrates high-frequency multi-point observations, remote sensing, and numerical modeling. This significantly enhances the accuracy of long-term water quality assessments, thus providing robust information to support sustainable lake management and climate change adaptation strategies. Summary and Conclusions This study revealed that mesoscale circulations, in particular, cyclonic (CE) and anticyclonic eddies (ACE), play a fundamental role in regulating the spatial distribution of thermal stratification, dissolved oxygen, and conductivity in large lakes. Targeted field campaigns, guided by 3D hydrodynamic simulations, were conducted during periods of strong (summer) and weak (fall) thermal stratification to capture as yet unknown dynamics of the spatial distribution in large lakes and to quantify extreme values of the lateral variability that occur between the centers of CEs and ACEs. Based on our field observations, the following insights into mixed layer dynamics were obtained: The dome- and bowl-shaped thermocline structures associated with CEs and ACEs confirm that mesoscale circulations generate significant lateral and vertical variability in physical and biochemical properties, leading to localized regions of oxygen enrichment and depletion depending on the season. In summer, oxygen supersaturation was detected across a greater depth range near the centers of CEs compared to the centers of ACEs and to a reference station located outside these circulations. In the fall, a metalimnetic oxygen minimum (MOM), a feature commonly associated with organic matter remineralization, occurs over a wider depth range in CE-dominated regions compared to ACEs. These findings suggest that mesoscale circulations influence organic matter remineralization and nutrient cycling, with implications for both primary production and oxygen consumption rates across different depths. CEs and ACEs significantly alter the depth at which biological processes occur, particularly near or within the thermocline. These circulations modify the shape and vertical displacement of the thermocline, thereby influencing thermal stratification and DO gradients. The vertical gradient of DO in the pelagic zone of the lake begins to intensify when stratification strength reaches O (10⁻⁴–10⁻³ s - 2 ), with significant depth-dependent variations above this threshold. During summer, in shallower regions, particularly near the thermocline, the DO gradient generally increases with depth as stratification strength intensifies. Both CE and ACE centers exhibit localized increases in stratification strength, which correspond to the maximum positive vertical DO gradient. In contrast, in deeper layers, where primary production is absent and remineralization dominates, a negative vertical DO gradient develops during late summer and the fall and becomes more pronounced as stratification strength increases above a certain threshold. These patterns, which are consistently observed in summer and fall, highlight the crucial role of mesoscale circulations in modulating vertical DO distribution and stratification dynamics in large lakes. These dynamics have direct implications for nutrient cycling, primary production, and overall water quality in large, stratified lakes. Traditional monitoring at fixed locations cannot capture the full extent of lateral and vertical transport processes, potentially leading to misinterpretations of long-term water quality trends, since measurements at these stations may be influenced by cyclonic or anticyclonic circulations. As a result, measurements may capture the dynamics of mesoscale processes reported in this study, but may not represent longterm development conditions. Instead, adaptive monitoring strategies that evolve as our understanding of lake system dynamics advances should be applied. The observed coupled spatial variations in temperature, DO, and conductivity highlight how eddy-driven vertical motions reshape stratification, enhance nutrient transport, and stimulate localized productivity in large lakes. Mesoscale eddies play a crucial role in shaping spatial patterns of oxygen and nutrient availability, with profound implications for pelagic ecosystem dynamics and biochemical cycling. The discussed mechanisms and driving forces, and their interactions in controlling mesoscale eddy interplay are not lake specific. Therefore, these processes can be expected to play a key role in the spatial variability of other large lakes under similar conditions. They should be considered when developing long-term lake management concepts. Future research should aim to quantify the long-term impact of circulation-driven transport on nutrient cycling and oxygen availability, incorporating these dynamics into predictive models; this will improve lake response assessments under changing climate conditions. Methods Study site Lake Geneva ( Lac Léman ), situated between Switzerland and France, is the largest freshwater lake in Western Europe, with a surface area of 582 km² and a total volume of approximately 89 km³. The lake has a mean depth of 172 m and a maximum depth of ~ 309 m. It is an oligomictic lake, with strong seasonal thermal stratification typically developing from spring to fall. During winter, weak stratification and occasional full or partial overturning occur. The width of Lake Geneva corresponds to approximately 2.4 Rossby radii during mean summer stratification. The Rossby deformation radius is defined as L = NH/f , with buoyancy frequency N , depth scale H , and the Coriolis parameter f . The Coriolis force affects the lake’s hydrodynamics 30,55,70,71 . The main inflow, the Rhône River, enters the lake at the eastern end, and leaves at the western end. In summer, the river plume flows as an interflow in the thermocline layer. The lake’s theoretical (water) residence time (also called flushing time in the literature) is 11.3 years (CIPEL, 2022), indicating that river-induced flow is negligible at the study site. Hydrodynamic simulations We employed the Massachusetts Institute of Technology General Circulation Model (MITgcm) 72 , a state-of-the-art 3D hydrodynamic model that solves the 3D incompressible Navier-Stokes equations under the Boussinesq approximation, incorporating the Coriolis force and an implicit free surface formulation that allows for the realistic simulation of both barotropic and baroclinic motions. The model has been extensively validated against field measurements and remote sensing data for simulating mesoscale processes in Lake Geneva 19,28,30,70,73 . In Lake Geneva, MITgcm has been successfully applied to study internal seiches 74 , near-shore currents 30,70 , river plume dispersion 75 , coastal upwelling 68 , frontal dynamics 71,73 , and mesoscale circulation patterns 19,28 , MITgcm simulations for Lake Geneva were conducted for 2021 and 2022 to investigate the evolution of its mesoscale and submesoscale hydrodynamics. The model was forced using high-resolution meteorological forecasting data from the COnsortium for Small-scale Modeling atmospheric model (COSMO, Swiss Federal Office of Meteorology and Climatology, MeteoSwiss) 76 . The forcing parameters included the wind field, air temperature, relative humidity, and solar radiation, all of which were interpolated where necessary to match the spatial and temporal discretization of the hydrodynamic model. Two numerical grids were employed to achieve a balance between computational efficiency and the resolution required to capture fine-scale processes. The first configuration was a Low-Resolution (LR) grid, with a horizontal resolution of 173–260 m and 35 vertical layers, initialized on 26 December 2020 using a horizontally uniform temperature profile from CIPEL (Commission Internationale pour la Protection des Eaux du Léman) station SHL2 (see Fig. 1 for location). The model was run from rest, using an integration time step of 20 s, with a spin-up period of approximately six months to allow for dynamical equilibration. The output from the LR simulation was then used to initialize a High-Resolution (HR) model, with a horizontal resolution of 113 m and 50 vertical layers. The HR grid had a fine vertical discretization with a surface layer thickness of 0.35 m; layer thickness gradually increased to 5 m at depth, allowing for enhanced resolution of thermocline dynamics, internal wave motions, and near-surface processes. The HR model was initialized on 7 July 2021 and ran continuously for nearly twelve months. The initial time step was 6 s, which was gradually increased to 30 s for numerical stability. Field observations Recent studies demonstrated that eddy patterns in Lake Geneva can be reliably predicted using MITgcm simulation forecasts driven by forecasted meteorological data from the COSMO model 28 . These model forecasts are instrumental in guiding the selection of field measurement transects prior to field campaigns, thus ensuring efficient data collection. In the present study, the transects extended from the predicted eddy in the western part of the Grand Lac basin to the eddy in its central region (Fig. 1c, e), covering key areas of interest for understanding mesoscale hydrodynamics. Each field campaign lasted approximately 6 to 8 hours, allowing for high-resolution spatial data collection. At predefined locations (spaced ~ 250 m to 1 km) along the transects, vertical profiles of temperature, DO and conductivity were taken using a Sea and Sun Marine Tech Conductivity-Temperature-Depth (CTD) multiparameter probe (CTD90M). Measurements were made over the upper ~ 50 m of the water column to ensure that the base of the thermocline was reached. The instrument was equipped with a RINKO III fast-response optical DO sensor and a high-precision temperature sensor (JFE Advantech). At a descent rate of ~ 10 cm s - ¹, data was logged at a frequency of 7 Hz, yielding a vertical resolution of approximately 1.5 cm. To characterize the hydrodynamic conditions associated with the CE/ACE structures, an Acoustic Doppler Current Profiler (ADCP, Teledyne Marine Workhorse Sentinel) equipped with a bottom-tracking module was employed. To ensure statistical robustness, vertical profiles of current velocity were recorded at each station for a minimum duration of 10 minutes. The ADCP was configured with 100 bins of 1-m vertical resolution, and a blanking distance of 2 m to minimize interference from near-surface reflections. The transducer was positioned at a depth of 0.5 m, and the high-resolution processing mode was activated to enhance measurement accuracy. Tilt and heading angles were continuously monitored using built-in sensors, and post-processing was performed following the manufacturer’s guidelines to correct for potential measurement artefacts. Declarations Acknowledgments We thank the Swiss National Science Foundation (SNSF Grant 178866) for supporting this research. The spatiotemporal meteorological data were provided by the Federal Office of Meteorology and Climatology in Switzerland (MeteoSwiss). We also extend our appreciation to the Commission Internationale pour la Protection des Eaux du Léman (CIPEL) for in situ temperature, dissolved oxygen and nutrients measurements. The profiles at CIPEL SHL2 station for 2021 were provided by the Eco-Informatics ORE INRA Team at the French National Institute for Agricultural Research (SOERE OLA-IS, INRA Thonon-les-Bains, France). Author contributions SH-Z conducted the field campaigns and implemented the numerical simulation. SH-Z conducted the data analyses, created the figures, and led the writing of the manuscript. UL and DB led the revision and critically reviewed the manuscript. All authors provided feedback on the manuscript. All authors contributed to the article and approved the submitted version. Funding declaration The project was financially supported by Swiss National Science Foundation (SNSF) Grant No. 178866. Competing interests The authors declare no competing interests. Data availability The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request. References Troitskaya, E. et al. Cyclonic circulation and upwelling in Lake Baikal. Aquat. Sci. 77 , 171–182. https://doi.org/10.1007/s00027-014-0372-4 (2015). Li, Y. et al. Modeling a large coastal upwelling event in Lake Superior. J. Geophys. Res. Oceans 126, e2020JC016512 (2021). https://doi.org/10.1029/2020JC016512 Ueno, H. et al. Review of oceanic mesoscale processes in the North Pacific: physical and biogeochemical impacts. Prog Oceanogr. 212 , 102955. https://doi.org/10.1016/j.pocean.2022.102955 (2023). Romanovsky, V. V. & Shabunin, G. D. Currents and vertical water exchange in Lake Issyk Kul. 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Lett. 49, e2022GL100262 (2022). https://doi.org/10.1029/2022GL100262 Reiss, R. S., Lemmin, U., Monin, C. & Barry, D. A. Strong bottom currents in large, deep Lake Geneva generated by higher vertical-mode Poincaré waves. Commun. Earth Environ. 5 , 480. https://doi.org/10.1038/s43247-024-01146-2 (2024). Soulignac, F. et al. Rapid changes in river plume dynamics caused by advected wind-driven coastal upwelling as observed in Lake Geneva. Limnol. Oceanogr. 66 , 3116–3133. https://doi.org/10.1002/lno.11858 (2021). Voudouri, A., Avgoustoglou, E. & Kaufmann, P. Impacts of observational data assimilation on operational forecasts. In Perspectives on Atmospheric Sciences 143–149 (Springer, Cham, https://doi.org/10.1007/978-3-319-35095-0_20 (2017). Additional Declarations No competing interests reported. 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1","display":"","copyAsset":false,"role":"figure","size":143714,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003e(a)\u003c/strong\u003e Lake Geneva’s bathymetry and the surrounding mountainous topography. The lake is composed of two basins: a large deep eastern basin called the \u003cem\u003eGrand Lac\u003c/em\u003e, and a shallow, narrow western basin, the \u003cem\u003ePetit Lac\u003c/em\u003e. \u003cem\u003eBise \u003c/em\u003eand \u003cem\u003eVent \u003c/em\u003eare the two strong, dominant large-scale winds blowing over most of Lake Geneva. Yellow circle: CIPEL long-term monitoring station SHL2, where physical and biological parameters are measured (usually monthly); red circle: LéXPLORE platform. \u003cstrong\u003e(b)\u003c/strong\u003e Average wind speed and direction during the \u003cem\u003eBise \u003c/em\u003eevent that lasted from 7 to 14 October 2021. \u003cstrong\u003e(c)\u003c/strong\u003eDirections and magnitude of (simulated) near-surface current velocity patterns that formed one day after the \u003cem\u003eBise \u003c/em\u003eceased. \u003cstrong\u003e(d)\u003c/strong\u003e Average wind speed and direction during the \u003cem\u003eVent\u003c/em\u003e event that lasted from 19 to 22 October 2021. \u003cstrong\u003e(e)\u003c/strong\u003eNear-surface (simulated) flow patterns that formed one day after the \u003cem\u003eVent\u003c/em\u003e ceased. Flow patterns are dominated by three large-scale eddies. ACE: mesoscale Anti-Cyclonic Eddy (clockwise rotating), CE: mesoscale Cyclonic Eddy (counterclockwise rotating); black circular arrows give sense of rotation. Note the change in gyre pattern produced by the different winds. V and D in (a) are the deltas of the Venoge and the Dranse rivers, respectively. These markers will be used in the figures below as reference points. Colorbars indicate the range of the parameters.\u003c/p\u003e","description":"","filename":"1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/302bc6fae0fe3851e7c480b7.jpg"},{"id":97368829,"identity":"afb5a53a-273e-4cb7-a59e-1cc092a1a26d","added_by":"auto","created_at":"2025-12-03 16:23:00","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":100451,"visible":true,"origin":"","legend":"\u003cp\u003e\u0026nbsp;(a) Simulated near-surface velocity (black arrows) and temperature (color) for 22 July 2022. The flow pattern was generated by \u003cem\u003eBise\u003c/em\u003e winds (wind speeds \u0026gt; 2.5 m s\u003csup\u003e-1\u003c/sup\u003e) that ceased three days earlier. The black line marks the preselected transect along which the field measurements were conducted. Contour plots based on profile measurements of: (b) temperature, (c) dissolved oxygen (DO) and (d) oxygen saturation measured from west-to-east along the predefined transect shown in (a). (e) Simulated near-surface velocity and temperature for 23 August 2022. The black line marks the preselected transect along which the field measurements were taken. Contour plots based on profile measurements of: (f) temperature, (g) DO and (h) oxygen saturation measured from west-to-east along the predefined transect shown in (e). Legends indicate the range of the parameters.\u003c/p\u003e","description":"","filename":"2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/24d8e4578c28aaa6141fc175.jpg"},{"id":97278016,"identity":"cb9e3210-0d02-45f5-9d51-4f3923fe7aa1","added_by":"auto","created_at":"2025-12-02 16:20:23","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":92598,"visible":true,"origin":"","legend":"\u003cp\u003eHorizontal velocity field obtained from Acoustic Doppler Current Profiler (ADCP) measurements taken along the predefined transects on: \u003cstrong\u003e(a)\u003c/strong\u003e22 July 2022 (transect in Fig. 2a), \u003cstrong\u003e(b)\u003c/strong\u003e23 August 2022 (transect in Fig. 2e), \u003cstrong\u003e(c)\u003c/strong\u003e19 October 2021 and \u003cstrong\u003e(d)\u003c/strong\u003e 26 October 2021 (transects in Fig. 4a and b). Above each panel, the locations of the mesoscale eddies, a submesoscale eddy and a filament are marked. ACE: Anticyclonic Eddy (clockwise rotating); CE: Cyclonic Eddy (counterclockwise rotating); SCE: Submesoscale Cyclonic Eddy (counterclockwise rotating). Colorbars give the range of horizontal velocity. Circular/curved arrows: sense of circulation. Slanted red and blue arrows: direction of the currents around the circulations; positive values: currents towards the north; negative values: towards the south.\u003c/p\u003e","description":"","filename":"3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/3f6f957a0461fcfcf88d7417.jpg"},{"id":97368227,"identity":"8aeedb5f-6fd7-45a4-9d5b-9ad913f7c7fc","added_by":"auto","created_at":"2025-12-03 16:21:51","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":94058,"visible":true,"origin":"","legend":"\u003cp\u003e(a) Simulation of near-surface velocity (black arrows) and temperature (color) for 19 October 2021. The flow pattern was generated by \u003cem\u003eBise\u003c/em\u003e winds (Fig. 1b). The green line marks the preselected transect along which the field measurements were carried out. Contour plots based on profiles of: (b) temperature, (c) Dissolved Oxygen (DO) and (d) conductivity (Con) measured from west-to-east along the predefined transect shown in (a). (e) Simulation of near-surface velocity and temperature for 26 October 2021 generated by a \u003cem\u003eVent\u003c/em\u003ewind (Fig. 1d). The green line marks the preselected transect along which the field measurements were taken. Contour plots based on profiles of: (f) temperature, (g) DO and (h) conductivity measured from west-to-east along the predefined transect shown in (e). Legends give the range of the parameters.\u003c/p\u003e","description":"","filename":"4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/77f0880e9d40a8aa01d04bcf.jpg"},{"id":97368377,"identity":"a08a9405-e251-493c-a0ad-4ce02a7c5bd7","added_by":"auto","created_at":"2025-12-03 16:22:06","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":83962,"visible":true,"origin":"","legend":"\u003cp\u003eContour plots of standard deviations from the mean profiles based on profile measurements along the transects. Left column: July 2022. Right column: August 2022. (a) and (b) temperature. (c) and (d) Dissolved Oxygen (DO) \u0026nbsp;(e) and (f) conductivity (Con). Legends indicate the parameter ranges.\u003cstrong\u003e \u003c/strong\u003eMean vertical profiles of (g) temperature, (h) DO, and (i) conductivity for both the July and August 2022 field campaigns (see legend).\u003c/p\u003e","description":"","filename":"5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/efc983463c51e2847fc7c900.jpg"},{"id":97278023,"identity":"e6ad955f-6050-4930-be7f-96b166a37ca2","added_by":"auto","created_at":"2025-12-02 16:20:23","extension":"jpg","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":84611,"visible":true,"origin":"","legend":"\u003cp\u003eContour plots of standard deviations from the mean profiles based on profile measurements along the transects. Deviations (left column) from mean profiles (right column). Top: for 19 October 2021 of(a) and (b) temperature, (c) and (d) dissolved oxygen (DO), and (e) and (f) conductivity (Con). Bottom: for 26 October 2021 of (g) and (h) temperature , (i) and (j) issolved oxygen (DO) from the mean DO profile shown in (j), and (k) deviations in conductivity. Legends indicate the range of the parameters.\u003c/p\u003e","description":"","filename":"6.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/4e5d211371c92a548e3f209e.jpg"},{"id":97278021,"identity":"47d382f1-912f-4265-a2c6-cd7d159f9d60","added_by":"auto","created_at":"2025-12-02 16:20:23","extension":"jpg","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":82551,"visible":true,"origin":"","legend":"\u003cp\u003eThe relationship between Brunt–Väisälä frequency (\u003cem\u003eN\u003c/em\u003e²), vertical gradient (∂DO/∂z) of dissolved oxygen (DO), and depth on (a) 22 July 2022, (b) 23 August 2022, (c) 19 October 2021, and (d) 26 October 2021. Legends give the depth range.\u003c/p\u003e","description":"","filename":"7.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/5a67f820a06ea0652e4ae073.jpg"},{"id":97278027,"identity":"f93bf014-3766-4581-afee-ba1d586ae17b","added_by":"auto","created_at":"2025-12-02 16:20:23","extension":"jpg","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":111007,"visible":true,"origin":"","legend":"\u003cp\u003eSpatial variability of Brunt–Väisälä frequency (\u003cem\u003eN\u003c/em\u003e²) from west to east along the predefined transect shown in Fig.2a and f for \u0026nbsp;2022: (a) 22 July and (b) 23 August, along with the associated vertical gradient of dissolved oxygen (∂DO/∂z) for (c) 22 July and (d) 23 August. Similarly, the spatial variability of \u003cem\u003eN\u003c/em\u003e² from west to east along the predefined transect shown in Fig. 6a and f is presented for 2021: (e) 19 October and (f) 26 October, with the corresponding ∂DO/∂\u003cem\u003ez\u003c/em\u003efor (g) 19 October and (h) 26 October.\u003c/p\u003e","description":"","filename":"8.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/ce7026b78f621bbc2d2f040a.jpg"},{"id":97278029,"identity":"0728788c-5e5e-4f50-966b-f34c148a86e7","added_by":"auto","created_at":"2025-12-02 16:20:23","extension":"jpg","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":80593,"visible":true,"origin":"","legend":"\u003cp\u003eComparison of \u003cstrong\u003e(a)\u003c/strong\u003e temperature and \u003cstrong\u003e(b)\u003c/strong\u003e dissolved oxygen (DO) profiles measured at the centers of ACE and CE on 19 October 2021with those measured by CIPEL at station SHL2 on the same day; our profiles taken at SHL2 on 26 October 2021 are also shown. See legend in (a) for station identification; locations of the profile stations indicated in the legend are shown in Fig. 4a. “Edge of ACE” is a reference point which is unaffected by eddy motion. Note that SHL2 is located inside the CE field (see Fig. 1). \u003cstrong\u003e(c)\u003c/strong\u003eMeasured profiles of temperature and \u003cstrong\u003e(d)\u003c/strong\u003etotal nitrogen for 2021 at station SHL2 provided by CIPEL. The red vertical lines in \u003cstrong\u003e(c)\u003c/strong\u003e and \u003cstrong\u003e(d)\u003c/strong\u003e indicate the date when SHL2 and our profiles were measured almost simultaneously on 19 October 2021; these profiles are given in panels \u003cstrong\u003e(a)\u003c/strong\u003e and \u003cstrong\u003e(b)\u003c/strong\u003e.\u003c/p\u003e","description":"","filename":"9.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/39620f2a85cd81876fc9c308.jpg"},{"id":97664699,"identity":"88930881-c654-4484-981b-676c2b156dee","added_by":"auto","created_at":"2025-12-08 09:13:12","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2051696,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/f460da1f-44c4-477d-9d47-d802fb562d44.pdf"},{"id":97278044,"identity":"e61d2e38-2313-418c-bf26-4cd8ec77acf2","added_by":"auto","created_at":"2025-12-02 16:20:23","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":5707292,"visible":true,"origin":"","legend":"","description":"","filename":"SupportingInformation.docx","url":"https://assets-eu.researchsquare.com/files/rs-8156830/v1/20f426f3eacc40279b64c720.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Mesoscale eddies drive complex, large-scale three-dimensional biochemical variability in the mixed layer of a large lake (Lake Geneva)","fulltext":[{"header":"Introduction","content":"\u003cp\u003eIn oceans, Coriolis force-generated cyclonic (counterclockwise rotating in the Northern Hemisphere) and anticyclonic (clockwise rotating) circulations, such as gyres and eddies, are recognized as principal mesoscale processes that transport mass, momentum, heat and biogeochemical parameters\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e,\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e,\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u003c/sup\u003e; thus they can affect physical and biochemical dynamics horizontally and vertically\u003csup\u003e\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e,\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e\u003c/sup\u003e. Pelagic upwelling/downwelling associated with cyclonic/anticyclonic circulation can increase/decrease nutrient supply to the euphotic zone by raising/lowering the nutricline, which in turn enhances/weakens primary production\u003csup\u003e\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e,\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e,\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e,\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e,\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e\u003c/sup\u003e and thereby changes, for example, Dissolved Oxygen (DO) levels\u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e,\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e,\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e. At present, comparable information relating to large lakes is scarce.\u003c/p\u003e\u003cp\u003eLateral variability of hydrodynamic processes and water quality parameters in marine ecosystems or large lakes, which is caused by the presence of large scale eddies, is often assessed by remote sensing\u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e,\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e,\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e,\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e,\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e,\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e,\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e and Autonomous Underwater Vehicle (AUV) surveys\u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e,\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e,\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e,\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e\u003c/sup\u003e. Remote sensing offers exceptional lateral resolution, but is restricted to the near-surface layers and can be biased by cloud cover\u003csup\u003e\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e,\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e; the use of AUVs in lakes is limited\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eTo effectively manage lake water quality, it is essential to understand how lateral variability due to mesoscale eddy interplay affects the interaction of physical and biochemical processes. In this study, mesoscale eddies are defined as coherent structures whose dimensions are determined by the size of the lake basin; in Lake Geneva, they are limited by the width of the basin and have a typical diameter of ~\u0026thinsp;10 km. They have fixed locations\u003csup\u003e\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u003c/sup\u003e. Submesoscale eddies are smaller in diameter (~\u0026thinsp;3 to 5 km) and move between mesoscale eddies\u003csup\u003e\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e. Their impact on water quality parameters is poorly understood, primarily due to the scarcity of spatially distributed, high-resolution biochemical observations in the water-column. In many lakes, assessment of biological, chemical, and physical processes is traditionally conducted using single station monitoring data\u003csup\u003e\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e\u003c/sup\u003e. Following such an approach in large lakes, however, fails to take into consideration circulation-induced lateral variability caused by Coriolis force.\u003c/p\u003e\u003cp\u003eSurveys employing Conductivity-Temperature-Depth (CTD) and Acoustic Doppler Current Profiler (ADCP) instruments can collect data at high spatial and vertical resolution. In the past, the challenge was to predict when and where to sample effectively to capture the spatial variability caused by mesoscale eddies. However, recent advances in high-resolution hydrodynamic models\u003csup\u003e\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e,\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e,\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e\u003c/sup\u003e, when coupled with enhanced statistical analysis techniques, remote sensing and numerical weather forecasting models, now allow the spatial distribution of mesoscale processes in large lakes to be accurately predicted\u003csup\u003e\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e,\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u003c/sup\u003e. As a result, field campaigns can be efficiently planned in advance to obtain biological-chemical-physical data with high spatial and vertical resolution and thus quantify the 3D effect of mesoscale circulations.\u003c/p\u003e\u003cp\u003eThis field study in Lake Geneva examines for the first time the intricate interplay between mesoscale circulations and the resultant lateral variability of water quality parameters in a lake environment. Based on predictions generated by high-resolution, 3D hydrodynamic simulations, field measurement campaigns were designed to capture data sets to address the following questions:\u003c/p\u003e\u003cp\u003e\u003cul\u003e\u003cli\u003e\u003cp\u003eDoes the interplay of mesoscale eddies influence the thermal structure, conductivity, and Dissolved Oxygen (DO) levels within the epilimnion and metalimnion?\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eDoes this pattern vary with seasonal stratification conditions?\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eAre routine monitoring programs affected by the presence/absence of mesoscale eddies?\u003c/p\u003e\u003c/li\u003e\u003c/ul\u003e\u003c/p\u003e\u003cp\u003eOur findings reveal the critical role that mesoscale eddies play in thermal dynamics, and in governing biochemical distributions in a stratified lake. This knowledge, presently lacking, improves the predictive capabilities for quantifying ecological responses to physical processes in large lake systems.\u003c/p\u003e\u003cp\u003eThe Supporting Information (SI) section provides additional clarifications/details on certain topics mentioned in the text.\u003c/p\u003e"},{"header":"Results and Discussion","content":"\u003cp\u003eThe two dominant winds over Lake Geneva—the northeast \u003cem\u003eBise\u003c/em\u003e and the southwest \u003cem\u003eVent\u003c/em\u003e—drive basin-scale circulations and govern stratification and vertical mixing (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eb,c)\u003csup\u003e33\u003c/sup\u003e. Their interaction with the lake’s complex bathymetry organizes the flow into mesoscale eddies, filaments, and frontal structures\u003csup\u003e\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e,\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ed,e). To quantify how these mesoscale features modulate physical and biogeochemical fields, we conducted four model-informed field campaigns with transects selected from 3-D numerical forecasts: during strong summer stratification (22 July and 23 August 2022) and during weak autumn stratification (19 and 26 October 2021).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003eLateral variability during strong thermal stratification in summer\u003c/h2\u003e\u003cp\u003eOn 22 July and 23 August 2022, 3D numerical modeling combined with statistical analyses\u003csup\u003e\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u003c/sup\u003e, predicted the development of a dipole circulation consisting of an anticyclonic eddy (ACE) in the western part and a cyclonic eddy (CE) in the central region of the \u003cem\u003eGrand Lac\u003c/em\u003e basin of Lake Geneva (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea, e). The flow pattern developed three days after a strong \u003cem\u003eBise\u003c/em\u003e (wind speeds \u0026gt; 2.5 m s\u003csup\u003e-\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e) ceased. We conducted field measurements along predefined transects that were selected based on the predictions from the numerical model and statistical analysis (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea, e). Velocity profiles obtained from ADCP measurements along these transects during both field campaigns confirmed the presence of the predicted dipole circulation (compare Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ea, e with 3a, e).\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eJuly 2022 observations\u003c/h3\u003e\n\u003cp\u003eVertical profiles of temperature, oxygen saturation (%), and dissolved oxygen (DO) from the July 2022 campaign (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eb–d) reveal clear distinctions between the CE and ACE. In the CE, the thermocline is dome-shaped, indicating strong upward displacement of deeper waters; conversely, in the ACE, the thermocline exhibits a bowl-shaped configuration, with comparatively weaker downwelling (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eb). This asymmetry is primarily driven by variations in the intensity of the horizontal circulation. Stronger cyclonic rotational velocities in the CE (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ea) enhance upward motion, deform the density stratification and transport cooler, deeper waters into the thermocline and epilimnion. In contrast, the ACE, with lower rotational velocities, produces a less pronounced downwelling effect and, consequently, less thermocline deformation as was already observed in Lake Erie\u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eDO concentrations mirror the temperature pattern of the cyclonic and anticyclonic circulations (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ec). In the CE, metalimnion DO levels were notably higher, coinciding with the upwelling of deeper, nutrient-rich water into this layer. A localized zone of oxygen supersaturation was observed near the center of the CE, corresponding to the maximum uplift of the thermocline (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ed). This supersaturation probably results from enhanced primary production fueled by upwelled nutrient-rich deep water, which supports elevated phytoplankton growth\u003csup\u003e\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e,\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u003c/sup\u003e. In contrast, DO levels in the ACE were comparatively lower, consistent with weaker downwelling of nutrient-poor epilimnion waters. Furthermore, the deepening of isopycnals typically associated with anticyclones reduces nutrient availability in the well-illuminated surface layers, thereby limiting phytoplankton growth and DO production\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003eComparing these data with data measured at the LéXPLORE platform (see Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ea for location), which is outside or at the edge of the dipole circulation, demonstrates the impact of these eddies on biochemical parameters. At the LéXPLORE platform, chlorophyll-a concentration peaked at approximately 30-m depth, with maximum DO and oxygen supersaturation above this depth (Fig. \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003ea). Near the CE center, oxygen supersaturation was roughly 10% higher, driven by enhanced primary production associated with the upwelling of nutrient-rich deeper water. This upwelling not only brings nutrients into the photic zone but also raises the thermocline, thereby shifting the depths of maximum DO and chlorophyll-a concentrations closer to the surface than at LéXPLORE. These observations can be explained by “eddy pumping,” wherein mesoscale circulation enhances vertical nutrient transport and modulates the distribution of phytoplankton, oxygen, and other biogeochemical parameters\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e,\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e. In contrast to CE upwelling, the ACE deepens nutrient-poor surface layers. Thus, even measurements taken outside the core regions of the CE and ACE show altered thermal and biological structures compared to the LéXPLORE data, implying that eddy-driven processes extend over a horizontal range beyond the eddy centers.\u003c/p\u003e\n\u003ch3\u003eAugust 2022 observations\u003c/h3\u003e\n\u003cp\u003eDuring the August 2022 field observations, the dome- and bowl-shaped thermocline structures associated with CE and ACE, respectively, were again present but less pronounced than in July, primarily due to weaker circulation velocities (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ef and \u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eb). DO concentrations remained elevated near the thermocline, and oxygen supersaturation persisted within the CE, reinforcing the link between eddy-induced upwelling and enhanced oxygen production. The higher DO levels in CE compared to ACE observed during both field campaigns suggest that cyclonic circulation plays an important role in redistributing oxygen and supporting biochemical processes in the lake.\u003c/p\u003e\u003cp\u003ePrevious observations that ignored eddy circulation systems indicated that, due to the acceleration of physiological processes (nutrient uptake, growth, respiration) and development of the thermal stratification in spring\u003csup\u003e\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e\u003c/sup\u003e, the photic layer of oligo- to mesotrophic lakes such as Lake Geneva is often nutrient-limited in late summer and fall\u003csup\u003e\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e,\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u003c/sup\u003e. However, in cyclonic circulation systems, surface divergence leads to the upward transport of deeper, nutrient-rich water, effectively enriching the photic zone and stimulating phytoplankton growth\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e,\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e\u003c/sup\u003e. This results in greater DO production in the epilimnion and metalimnion. Thus, the oxygen-enriched water at the CE core reflects the combined effects of physical upwelling and biological oxygen production, highlighting the role of CEs in sustaining primary productivity and modifying oxygen dynamics in large lakes.\u003c/p\u003e\u003cp\u003eThe observed coupled variations in temperature, DO, and conductivity highlight how eddy-driven vertical motions reshape stratification, enhance nutrient transport, and stimulate localized productivity in large lakes during summer, when the epilimnion and photic layers are often nutrient-depleted. By modulating thermocline depth and redistributing chemical constituents, mesoscale eddies play a crucial role in shaping spatial patterns of oxygen and nutrient availability, with profound implications for pelagic ecosystem dynamics and biochemical cycling.\u003c/p\u003e\n\u003ch3\u003eLateral variability in weak thermal stratification during fall\u003c/h3\u003e\n\u003cp\u003eNumerical simulations forecast distinct eddy-controlled flow patterns during the fall on 19 and 26 October 2021, following \u003cem\u003eBise\u003c/em\u003e and \u003cem\u003eVent\u003c/em\u003e wind events.\u003c/p\u003e\n\u003ch3\u003eObservations on 19 October 2021\u003c/h3\u003e\n\u003cp\u003eNumerical simulations predicted that a \u003cem\u003eBise\u003c/em\u003e event (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eb) generated a dipole structure on 19 October in the western and central regions of the \u003cem\u003eGrand Lac\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ea; see also Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ec). This dipole closely resembled those observed in July and August 2022 under strong stratification as discussed above, but differed in its depth influence. The measured thermocline structure (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eb) exhibits clear regional variations, with a bowl-shaped thermocline in the ACE, and a dome-shaped thermocline in the CE. Stretching in CE and compression in ACE are mainly driven by divergent and convergent flows associated with the mesoscale processes\u003csup\u003e\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e\u003c/sup\u003e. However, the CE field was not fully covered during the field campaign due to operational limitations. Furthermore, at approximately 14 km along the transect, a cold submesoscale filament emerged between CE and ACE due to frontogenesis (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ec). This secondary circulation enhances density gradients and drives upwelling and downwelling cells, facilitating lateral exchanges and altering the vertical structure of the water column\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. Measured velocity profiles along the predefined transect (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003ec) confirmed the presence of the ACE/CE dipole, highlighting the recurrence of such circulation patterns across different seasonal stratification regimes (Fig. S2)\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eDO and conductivity profiles measured along the selected transect indicate upwelling and downwelling signatures, particularly in the thermocline layers of the CE and ACE (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ec, d). Strong seasonal differences are revealed when comparing temperature, DO, and conductivity profiles between October and summer observations. Even though the characteristic dome- and bowl-shaped thermoclines persisted in the fall, oxygen supersaturation observed in the epilimnion and metalimnion during summer was absent. Instead, a DO maximum was recorded in the epilimnion, coinciding with the highest chlorophyll-a concentration at the LéXPLORE station (Fig. \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003ec, d). However, chlorophyll-a levels in October were significantly lower than in July, consistent with seasonal declines in primary production.\u003c/p\u003e\u003cp\u003eA key difference between the 19 October observations and those during summer stratification in 2021 is seen in the vertical distribution of DO. The summer data indicated DO supersaturation extending over a wide range of the stretched CE thermocline (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003ec, d), whereas the 19 October profiles revealed more pronounced oxygen depletion in specific CE depth layers compared to ACE (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ec). The observed decline in metalimnetic DO is primarily attributed to microbial decomposition of organic matter (OM), a process intensified in upwelling regions where vertical transport introduces nutrient-rich waters to intermediate depths. As a result, a persistent metalimnetic oxygen minimum (MOM) was observed from late summer onward (Fig. \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e), a phenomenon commonly associated with OM mineralization in hypolimnetic waters below 15 m\u003csup\u003e43\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eThe metalimnion serves as an ecological niche for certain phytoplankton species\u003csup\u003e\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e\u003c/sup\u003e and acts as a zone of OM accumulation due to settling processes, particularly in summer and in the fall\u003csup\u003e\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e\u003c/sup\u003e. The formation of biological niches within the metalimnion is governed by water column stability and the balance between light availability and nutrient supply\u003csup\u003e\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e,\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e\u003c/sup\u003e. As shown above, the observed circulation patterns influence all three factors. In CE, the seasonal dynamics of DO exhibit greater variability than in ACE, with increased DO levels during summer and enhanced DO consumption in the fall. The broader metalimnion in CE compared to ACE allows biological processes to occur across a wider depth range, thus contributing to more complex biochemical interactions.\u003c/p\u003e\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e\u003ch2\u003eObservations on 26 October 2021\u003c/h2\u003e\u003cp\u003eOn 26 October, following a strong \u003cem\u003eVent\u003c/em\u003e event (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ed), the hydrodynamic simulations forecast that in the center of the \u003cem\u003eGrand Lac\u003c/em\u003e basin an ACE was generated instead of a CE (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ee; see also Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003ee). This change was accompanied by the formation of a strong submesoscale cyclonic eddy (SCE) between the two weak ACEs located in the western part and the center of the \u003cem\u003eGrand Lac\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ee). The SCE had a diameter of ~ 5 km, and its presence caused major changes in the mixed layer depth (MLD) across the basin. In particular, the MLD in the two ACEs remained at ~ 25 m, whereas it was significantly shallower at ~ 8 m in the core of the SCE due to pronounced pelagic upwelling (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ef). The reversal of the rotational sense of the mesoscale eddy in the center of the \u003cem\u003eGrand Lac\u003c/em\u003e (compared to 19 October 2021) effectively smoothed out the differences in the MLD and thermocline structure between the central and western parts of the lake that had been observed on 19 October (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003ef).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eEffects of mesoscale eddies on water-column structure and biochemical processes\u003c/h3\u003e\n\u003cp\u003eThe substantial impact of mesoscale eddies on water-column structure and biochemical processes becomes apparent when the mean and standard deviations of water temperature, DO, and conductivity along the selected transects are determined at different depths.\u003c/p\u003e\n\u003ch3\u003eStrong stratification in the summer\u003c/h3\u003e\n\u003cp\u003eDuring summer, in regions influenced by the CE, temperature deviations of up to − 5°C at the thermocline clearly indicate the upward entrainment of colder, deeper water (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e). This process not only cools the upper layers but also transports nutrient-rich water into the euphotic zone, enhancing phytoplankton growth and driving observed increases in DO by 2.5 mg l\u003csup\u003e− 1\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eA conductivity reduction of up to 0.02 mS cm\u003csup\u003e− 1\u003c/sup\u003e in CE indicates upward transport of deep, low-conductivity water, which generally contains fewer dissolved ions than surface waters\u003csup\u003e\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e,\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e\u003c/sup\u003e. Although biological processes such as phytoplankton nutrient uptake can influence conductivity at local scales, the consistent decrease observed in CE-affected regions suggests that physical mixing and transport play a more dominant role\u003csup\u003e\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e\u003c/sup\u003e. Conversely, in ACE regions, an increase in conductivity is observed, primarily due to the downwelling of high-conductivity surface and near-surface waters. This effect is driven by surface convergence within the ACE field, which compresses the thermocline and enhances the retention of ion-rich water in the upper layer\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e,\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\u003ch2\u003eWeak stratification in the fall\u003c/h2\u003e\u003cp\u003eDuring fall, in CE-influenced regions, the temperature deviation at the thermocline reached −2°C, indicating again entrainment of colder, deeper water into the upper layers. Simultaneously, DO deviations of up to −1 mg l\u003csup\u003e−\u003c/sup\u003e¹ highlight the higher reduction of DO because of greater water column mineralization (WCM) in CE. Conductivity shows both increases and reductions of up to 0.005 mS cm\u003csup\u003e− 1\u003c/sup\u003e in different depth layers of the thermocline. As is the case during summer, this can mainly be attributed to the combined effects of vertical transport of low-conductivity deep water and higher conductivity induced by OM decomposition. In the central areas of ACE, on the other hand, a constant increase of conductivity up to 0.005 mS cm\u003csup\u003e− 1\u003c/sup\u003e can be found, which results from downward transport of warmer higher-conductivity surface water that is transported by surface convergence of ACE flow fields. Temperature, DO and conductivity deviations between CE and ACE in the thermocline can reach up to 4°C, 2 mg l\u003csup\u003e-\u003c/sup\u003e¹ and 0.01 mS cm\u003csup\u003e− 1\u003c/sup\u003e, respectively. In summary, the dipole circulation observed on 19 October produced lateral variability comparable to that in July. However, it extended over a greater depth range but with smaller gradients, emphasizing the intricate influence of seasonal changes in stratification, biochemical processes, and mesoscale dynamics.\u003c/p\u003e\u003cp\u003eOn 26 October 2021, the temperature deviation between the SCE and ACEs remained comparable to, or were slightly greater than the values recorded one week earlier. The DO deviation followed a pattern similar to previous observations, with reduced DO concentrations in upwelling regions and increased DO within the ACE. However, the magnitude of these DO variations remained relatively small (~ 0.2 mg l\u003csup\u003e−\u003c/sup\u003e¹) compared to the more pronounced dipole structure observed the previous week. Conductivity measured within the SCE exhibited a more pronounced reduction than that observed in the 19 October CE event. This reduction is primarily due to the significant upward transport of deep, low-conductivity, cold water, which can reach the lake surface\u003csup\u003e\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eThese findings highlight the complex interplay between mesoscale and submesoscale circulations in controlling water column stratification and mixing. Mesoscale CEs and ACEs can persist for days to weeks at nearly fixed locations, leading to sustained spatial variability in both physical and biochemical processes. SCEs, on the other hand, are generally more transient and advective in nature (Fig. S3). They induce less pronounced long-term spatial variability when coexisting with larger, more persistent eddies\u003csup\u003e\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\u003ch2\u003eImpact of mesoscale Eddies on Vertical Gradients of the Thermocline and DO\u003c/h2\u003e\u003cp\u003eOne key finding from the four field observations is that cyclonic and anticyclonic circulations modify the shape and vertical structure of the thermocline. This influences thermal stratification, which can also be strongly modulated by seasonal variability. As shown above, the presence of these large-scale eddies and the interaction between circulations and stratification significantly alter the depth at which biological processes occur, particularly near or within the thermocline. To further examine the effects of these eddies, Brunt–Väisälä frequency (\u003cem\u003eN\u003c/em\u003e²) and vertical DO gradients were analyzed along the four transects.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e\u003ch2\u003eSeasonal trends of vertical gradients of the thermocline and DO\u003c/h2\u003e\u003cp\u003eAbove a certain \u003cem\u003eN\u003c/em\u003e² threshold, the trends in the vertical DO gradient and stratification strength \u003cem\u003eN\u003c/em\u003e² exhibit two distinct regimes above and below the thermocline that change with season (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). During summer, the DO gradient in shallower regions, located primarily just above the thermocline, generally increases with depth when \u003cem\u003eN\u003c/em\u003e² reaches values between 10⁻⁴ and 10⁻³ s\u003csup\u003e− 2\u003c/sup\u003e. As discussed in the previous section, this behavior may be attributed to enhanced localized oxygen production due to primary production in the upper thermocline layers in the upwelling zone near the CE center\u003csup\u003e\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e,\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u003c/sup\u003e. In contrast, in deeper regions, at the lower end of the thermocline, where primary production is absent and remineralization processes prevail, a negative vertical DO gradient is observed; this negative gradient becomes more pronounced as stratification strength \u003cem\u003eN\u003c/em\u003e² increases. These two patterns are clearly evident in both the July and August observations.\u003c/p\u003e\u003cp\u003eDuring the fall, the same distinct relationships between the vertical DO gradient and \u003cem\u003eN\u003c/em\u003e² in the regions above and below the thermocline can still be observed on 19 October when an ACE/CE dipole is generated again. However, compared to the summer observations, the reduction of the DO gradient with increase of stratification in deeper layers is more pronounced than the increase of the DO gradient observed in shallower and near-surface layers. This is mainly due to a significant reduction of primary production in the fall due to dominant remineralization processes in hypolimnetic layers\u003csup\u003e\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e,\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e\u003c/sup\u003e. These observations highlight the role of stratification strength \u003cem\u003eN\u003c/em\u003e² on biological processes related to the production, respiration, and consumption of DO\u003csup\u003e46,47\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eWhen the current regime changes from a dipole to two mesoscale ACEs separated by an SCE on 26 October, the DO vertical gradient becomes insignificant in the upper thermocline layer and is remarkably less impacted by stratification strength. However, a decreasing trend of the DO gradient with stratification strength can still be observed in the lower layers when \u003cem\u003eN\u003c/em\u003e² is greater than 10\u003csup\u003e− 4\u003c/sup\u003e s\u003csup\u003e-\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e. When the depth distribution of \u003cem\u003eN\u003c/em\u003e² and the vertical gradient of DO along the different transects is determined (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003e), it becomes evident that these differences in the vertical distribution (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e) are related to the horizontal spatial variability caused by the ACEs and the CEs.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec14\" class=\"Section2\"\u003e\u003ch2\u003eSpatial pattern in summer\u003c/h2\u003e\u003cp\u003eDuring summer, CE and ACE enhance maximum stratification strength with the strongest stratification observed near the centers of both CE and ACE. This coincides with regions where the maximum positive DO gradient is recorded (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e), in particular at the CE centers due to enhanced primary production. Increased solar radiation and weak wind-driven mixing establish a strong thermocline in temperate lakes\u003csup\u003e\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e,\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e\u003c/sup\u003e, and CE and ACE circulations further modify stratification. CE-induced upwelling transports cooler deep water upward, but the strong thermocline traps it below the surface mixed layer, locally sharpening the thermal gradient (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eb, f).\u003c/p\u003e\u003cp\u003eIn contrast, ACE-induced downwelling plays a crucial role in strengthening stratification by compressing the thermocline and intensifying the vertical temperature gradient, thus suppressing vertical mixing. This process is well documented in oceanic studies, where mesoscale ACEs strengthen stratification by deepening the thermocline and inhibiting surface-deep water exchange\u003csup\u003e\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e,\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e\u003c/sup\u003e. This increases water column stability, requiring significant energy for mixing and delays stratification breakdown until fall cooling begins. In deep lakes such as Lake Geneva, persistent ACE activity can trap heat at depth, influencing nutrient cycling, oxygen dynamics, and the overall thermal structure\u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec15\" class=\"Section2\"\u003e\u003ch2\u003eSpatial pattern in fall\u003c/h2\u003e\u003cp\u003eFall observations indicate intensified maximum stratification strength in ACE-influenced regions, whereas CE-influenced regions experience a reduction in maximum stratification strength. Notably, on October 26, when the mesoscale circulation pattern shifted from a dipole structure to a configuration dominated by two ACEs, the spatial and vertical variability of stratification strength remained largely unchanged, and the DO distribution became more uniform, with the greatest reductions occurring in regions where stratification is strengthened within the ACEs (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003ef, h).\u003c/p\u003e\u003cp\u003eThe thermocline weakens in fall due to surface cooling and wind-induced mixing, but CE and ACE affect this process differently. Cyclonic circulation disrupts stratification through upwelling-driven vertical mixing, bringing cooler deep water to the surface and reducing the temperature gradient between the epilimnion and hypolimnion\u003csup\u003e\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e,\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e\u003c/sup\u003e. This effect is amplified by cooling in the fall and increased wind stress, which enhance turbulent mixing and contribute to thermocline erosion\u003csup\u003e\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eAs surface temperatures decrease, the density contrast between surface and deep layers diminishes, facilitating convective overturning and enhancing destratification\u003csup\u003e\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e\u003c/sup\u003e. On the other hand, anticyclonic circulation intensifies stratification through downwelling-driven thermocline compression\u003csup\u003e\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e\u003c/sup\u003e. Downwelling in ACE regions deepens the thermocline and insulates deeper layers from surface cooling\u003csup\u003e\u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e\u003c/sup\u003e. As a result, stratification persists longer in these regions since vertical mixing and entrainment of cooler water from below are suppressed.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec16\" class=\"Section2\"\u003e\u003ch2\u003e\u003cem\u003eSignificance of mesoscale circulations\u003c/em\u003e\u003c/h2\u003e\u003cp\u003eThese results highlight the critical role mesoscale circulations play in modulating both thermal and DO stratification, with their effects varying based on the sense of rotation and seasonal conditions. The mixed layer depth can vary laterally when a multi-eddy circulation pattern interplay is present. This is more evident under weak stratification (see also Fig. S2 as an example).\u003c/p\u003e\u003cp\u003eAlthough many of these processes correspond to oceanic observations, notable differences arise, particularly those concerning the influence of CE during summer, when its impact on stratification is more pronounced compared to ocean settings. Thermal stratification strength is a fundamental driver of biological processes in lake ecosystems, regulating both primary production and remineralization\u003csup\u003e\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e,\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e,\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e,\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e\u003c/sup\u003e. As was shown above, strong stratification, mainly in ACE regions, compresses the thermocline, thus restricting vertical mixing and increasing the rate of oxygen depletion in deeper layers. In contrast, CE tend to widen the thermocline, increasing the depth range with moderate but persistent stratification, which enhances biological activity by facilitating nutrient exchange and oxygen production.\u003c/p\u003e\u003cp\u003eConsequently, DO concentrations generally increase more in CE than in ACE during summer, reflecting enhanced primary production near the deep chlorophyll maximum (DCM)\u003csup\u003e\u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e63\u003c/span\u003e\u003c/sup\u003e. The thermocline also functions as both a habitat for phytoplankton species\u003csup\u003e\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e\u003c/sup\u003e and a zone for organic material accumulation and remineralization\u003csup\u003e\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e\u003c/sup\u003e. Strong stratification stabilizes the water column and promotes localized oxygen production, whereas weak stratification enhances aerobic remineralization by increasing oxygen penetration into deeper layers, accelerating organic matter decomposition\u003csup\u003e\u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e,\u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e65\u003c/span\u003e,\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e\u003c/sup\u003e. Ultimately, the interplay between mesoscale circulation, stratification strength, and biological processes plays an important role in regulating lake ecosystem dynamics, with broad implications for oxygen availability, nutrient cycling, and heat distribution.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec17\" class=\"Section2\"\u003e\u003ch2\u003eImpact of Circulations at a Fixed Monitoring Station\u003c/h2\u003e\u003cp\u003eAt present, lake ecosystem concepts and the assessment of long-term changes in lake system development are mainly based on measurements taken at fixed monitoring stations. However, our findings show that these measurements can be influenced by the presence of CEs or ACEs. The locations of these fixed stations are typically determined by factors such as the number and depth of lake basins, proximity to inflows and outflows, accessibility for sampling, and historical monitoring efforts. The temporal resolution of measurements is often weekly or monthly and is subject to variability due to weather conditions, logistical constraints, seasonal dynamics, and research priorities\u003csup\u003e\u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e67\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e\u003cp\u003eIn Lake Geneva, the Commission Internationale pour la Protection des Eaux du Léman (CIPEL) has monitored the long-term trends of physical and biological processes at their SHL2 station since the 1960s (see Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e for location). This station is situated near the center of the lake, which is also the center of various mesoscale eddies; these can influence the measurements at this site (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e, \u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). Therefore, the physical and biological profiles, mainly in subsurface layers and the thermocline region, may be significantly affected by the eddy circulation dynamics, depending on the sense of rotation, intensity, and lifespan of the circulations.\u003c/p\u003e\u003cp\u003eFor example, on 19 October 2021, CIPEL conducted measurements at SHL2 nearly simultaneously with our field campaign. A comparison of the temperature and DO profiles obtained during our field campaign and those measured by CIPEL reveals a similar vertical structure (Fig.\u0026nbsp;10a, b). The effect of pelagic upwelling induced by the CE on temperature and DO profiles at SHL2 is evident when the profiles are compared to profiles at a reference station (i.e., LéXPLORE station) and in the ACE region. In the stretched thermocline caused by CE-induced upwelling, DO consumption at SHL2 increased significantly compared to the ACE region, likely due to enhanced remineralization of organic matter in the subsurface layer following the upward transport of nutrient- and particle-rich waters. However, in the epilimnion, DO concentrations increased, possibly due to enhanced gas exchange with the atmosphere and photosynthetic activity.\u003c/p\u003e\u003cp\u003eThe temperature and DO profiles measured at SHL2 on 19 and 26 October exhibit significant differences because the circulation in the center of the \u003cem\u003eGrand Lac\u003c/em\u003e changed its sense of rotation (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e, \u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). On 26 October, the MLD was approximately 10 m deeper, and a notable DO reduction is seen in the thermocline at ~ 28 m depth (almost 10 m deeper than on 19 October; Fig.\u0026nbsp;10a, b). At that time of the year, atmospheric cooling alone is unlikely to cause such rapid and pronounced changes in thermal stratification and oxygen distribution within just one week. Instead, the observed variations are attributed to changes in the mesoscale circulation pattern, which modulate vertical mixing, stratification, and biochemical processes. The deepening of the MLD is consistent with a transition from cyclonic to anticyclonic circulation in the center of the lake, which typically enhances downward mixing, redistributing heat and DO deeper into the water column leading to an overall depletion of oxygen in the thermocline.\u003c/p\u003e\u003cp\u003eIt is clear that the monitoring data collected at SHL2 are significantly modulated by cyclonic and anticyclonic circulation patterns. Analysis of temporal variations in nutrient concentrations and thermal stratification at SHL2 in 2021 reveals episodic uplifts of nutrients along with thermocline displacement (Fig.\u0026nbsp;10c, d, and S5). These periodic upwelling events suggest that mesoscale circulations play a crucial role in modulating vertical transport of both heat and biochemical properties. Comparisons of temperature profiles at SHL2 and LéXPLORE (located near the edge of the CE) further confirm that pelagic upwelling occurs at SHL2 during certain periods (Fig. S4). However, it is important to note that LéXPLORE may, at times, be located within a cold filament zone associated with fronts or lateral mixing processes\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e or can be impacted by nearshore upwelling\u003csup\u003e\u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e68\u003c/span\u003e\u003c/sup\u003e; these can also contribute to temperature variations.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec18\" class=\"Section2\"\u003e\u003ch2\u003eLongterm Significance\u003c/h2\u003e\u003cp\u003eWe document here, for the first time in a lake, the significant lateral variability induced by the interplay between mesoscale near-surface circulations and submesoscale eddies, emphasizing the complexity of the 3D physical-biochemical interactions. These data were obtained during four different field campaigns after strong \u003cem\u003eBise\u003c/em\u003e and \u003cem\u003eVent\u003c/em\u003e wind events in Lake Geneva.\u003c/p\u003e\u003cp\u003eThe frequent occurrence of strong \u003cem\u003eBise\u003c/em\u003e and \u003cem\u003eVent\u003c/em\u003e wind events that take place throughout the year in Lake Geneva is well documented\u003csup\u003e\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e. Therefore, the systematic lateral variability observed in this study is not an isolated phenomenon, but instead a recurring dynamic feature. It is probably also present in other large, deep lakes where wind-driven circulation interacts with topographic constraints to generate mesoscale circulations and submesoscale eddies. We reveal that this mesoscale-driven lateral variability can lead to heterogeneous environmental conditions, influencing nutrient transport, oxygen distribution, and plankton dynamics, and thus must be considered when designing long-term water quality management strategies. The structure of the wind field over the lake suggests that the interplay between pelagic upwelling and downwelling in mesoscale circulations can occur throughout the stratification period. Further research is required to quantify these effects across different temporal and spatial scales.\u003c/p\u003e\u003cp\u003eIn this study, we focused on quantifying the extreme values of lateral variability between the centers of mesoscale circulations and submesoscale eddies, where pelagic upwelling and downwelling drive pronounced gradients. Our detailed transect measurements across these circulation features (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e–\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e) reveal that physical and biochemical properties do not change abruptly between these extreme values, but instead transition progressively. The observed dome-shaped and bowl-shaped thermoclines in CEs and ACEs, respectively, create strong horizontal gradients between eddy cores and their outer edges, reinforcing the notion that mesoscale and submesoscale variability is a complex 3D phenomenon that extends over large areas of the lake.\u003c/p\u003e\u003cp\u003eOur findings challenge classical single-point, one-dimensional monitoring and modeling approaches, which inherently oversimplify lake dynamics by assuming uniform conditions over large spatial scales. Instead, adaptive monitoring strategies\u003csup\u003e\u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e69\u003c/span\u003e\u003c/sup\u003e that evolve with an improved understanding of lake system dynamics should be implemented. Adaptive monitoring integrates high-frequency multi-point observations, remote sensing, and numerical modeling. This significantly enhances the accuracy of long-term water quality assessments, thus providing robust information to support sustainable lake management and climate change adaptation strategies.\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec20\" class=\"Section2\"\u003e\u003cdiv id=\"Sec21\" class=\"Section3\"\u003e\u003c/div\u003e\u003c/div\u003e\u003cdiv id=\"Sec22\" class=\"Section2\"\u003e\u003cdiv id=\"Sec23\" class=\"Section3\"\u003e\u003c/div\u003e\u003c/div\u003e"},{"header":"Summary and Conclusions","content":"\u003cp\u003eThis study revealed that mesoscale circulations, in particular, cyclonic (CE) and anticyclonic eddies (ACE), play a fundamental role in regulating the spatial distribution of thermal stratification, dissolved oxygen, and conductivity in large lakes. Targeted field campaigns, guided by 3D hydrodynamic simulations, were conducted during periods of strong (summer) and weak (fall) thermal stratification to capture as yet unknown dynamics of the spatial distribution in large lakes and to quantify extreme values of the lateral variability that occur between the centers of CEs and ACEs. Based on our field observations, the following insights into mixed layer dynamics were obtained:\u003c/p\u003e\u003cul\u003e\u003cli\u003e\u003cp\u003eThe dome- and bowl-shaped thermocline structures associated with CEs and ACEs confirm that mesoscale circulations generate significant lateral and vertical variability in physical and biochemical properties, leading to localized regions of oxygen enrichment and depletion depending on the season.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eIn summer, oxygen supersaturation was detected across a greater depth range near the centers of CEs compared to the centers of ACEs and to a reference station located outside these circulations.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eIn the fall, a metalimnetic oxygen minimum (MOM), a feature commonly associated with organic matter remineralization, occurs over a wider depth range in CE-dominated regions compared to ACEs. These findings suggest that mesoscale circulations influence organic matter remineralization and nutrient cycling, with implications for both primary production and oxygen consumption rates across different depths.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eCEs and ACEs significantly alter the depth at which biological processes occur, particularly near or within the thermocline. These circulations modify the shape and vertical displacement of the thermocline, thereby influencing thermal stratification and DO gradients.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eThe vertical gradient of DO in the pelagic zone of the lake begins to intensify when stratification strength reaches \u003cem\u003eO\u003c/em\u003e(10⁻⁴–10⁻³ s\u003csup\u003e-\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e), with significant depth-dependent variations above this threshold. During summer, in shallower regions, particularly near the thermocline, the DO gradient generally increases with depth as stratification strength intensifies. Both CE and ACE centers exhibit localized increases in stratification strength, which correspond to the maximum positive vertical DO gradient.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eIn contrast, in deeper layers, where primary production is absent and remineralization dominates, a negative vertical DO gradient develops during late summer and the fall and becomes more pronounced as stratification strength increases above a certain threshold.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eThese patterns, which are consistently observed in summer and fall, highlight the crucial role of mesoscale circulations in modulating vertical DO distribution and stratification dynamics in large lakes. These dynamics have direct implications for nutrient cycling, primary production, and overall water quality in large, stratified lakes.\u003c/p\u003e\u003c/li\u003e\u003cli\u003e\u003cp\u003eTraditional monitoring at fixed locations cannot capture the full extent of lateral and vertical transport processes, potentially leading to misinterpretations of long-term water quality trends, since measurements at these stations may be influenced by cyclonic or anticyclonic circulations. As a result, measurements may capture the dynamics of mesoscale processes reported in this study, but may not represent longterm development conditions. Instead, adaptive monitoring strategies that evolve as our understanding of lake system dynamics advances should be applied.\u003c/p\u003e\u003c/li\u003e\u003c/ul\u003e\u003cp\u003eThe observed coupled spatial variations in temperature, DO, and conductivity highlight how eddy-driven vertical motions reshape stratification, enhance nutrient transport, and stimulate localized productivity in large lakes. Mesoscale eddies play a crucial role in shaping spatial patterns of oxygen and nutrient availability, with profound implications for pelagic ecosystem dynamics and biochemical cycling. The discussed mechanisms and driving forces, and their interactions in controlling mesoscale eddy interplay are not lake specific. Therefore, these processes can be expected to play a key role in the spatial variability of other large lakes under similar conditions. They should be considered when developing long-term lake management concepts.\u003c/p\u003e\u003cp\u003eFuture research should aim to quantify the long-term impact of circulation-driven transport on nutrient cycling and oxygen availability, incorporating these dynamics into predictive models; this will improve lake response assessments under changing climate conditions.\u003c/p\u003e"},{"header":"Methods","content":"\u003ch2\u003eStudy site\u003c/h2\u003e\n\u003cp\u003eLake Geneva (\u003cem\u003eLac Léman\u003c/em\u003e), situated between Switzerland and France, is the largest freshwater lake in Western Europe, with a surface area of 582 km² and a total volume of approximately 89 km³. The lake has a mean depth of 172 m and a maximum depth of ~ 309 m. It is an oligomictic lake, with strong seasonal thermal stratification typically developing from spring to fall. During winter, weak stratification and occasional full or partial overturning occur.\u003c/p\u003e\n\u003cp\u003eThe width of Lake Geneva corresponds to approximately 2.4 Rossby radii during mean summer stratification. The Rossby deformation radius is defined as \u003cem\u003eL = NH/f\u003c/em\u003e, with buoyancy frequency \u003cem\u003eN\u003c/em\u003e, depth scale \u003cem\u003eH\u003c/em\u003e, and the Coriolis parameter \u003cem\u003ef\u003c/em\u003e. The Coriolis force affects the lake’s hydrodynamics\u003csup\u003e30,55,70,71\u003c/sup\u003e. The main inflow, the Rhône River, enters the lake at the eastern end, and leaves at the western end. In summer, the river plume flows as an interflow in the thermocline layer. The lake’s theoretical (water) residence time (also called flushing time in the literature) is 11.3 years (CIPEL, 2022), indicating that river-induced flow is negligible at the study site.\u003c/p\u003e\n\u003ch2\u003eHydrodynamic simulations\u003c/h2\u003e\n\u003cp\u003eWe employed the Massachusetts Institute of Technology General Circulation Model (MITgcm)\u003csup\u003e72\u003c/sup\u003e, a state-of-the-art 3D hydrodynamic model that solves the 3D incompressible Navier-Stokes equations under the Boussinesq approximation, incorporating the Coriolis force and an implicit free surface formulation that allows for the realistic simulation of both barotropic and baroclinic motions.\u003c/p\u003e\n\u003cp\u003eThe model has been extensively validated against field measurements and remote sensing data for simulating mesoscale processes in Lake Geneva\u003csup\u003e19,28,30,70,73\u003c/sup\u003e. In Lake Geneva, MITgcm has been successfully applied to study internal seiches\u003csup\u003e74\u003c/sup\u003e, near-shore currents\u003csup\u003e30,70\u003c/sup\u003e, river plume dispersion\u003csup\u003e75\u003c/sup\u003e, coastal upwelling\u003csup\u003e68\u003c/sup\u003e, frontal dynamics\u003csup\u003e71,73\u003c/sup\u003e, and mesoscale circulation patterns\u003csup\u003e19,28\u003c/sup\u003e,\u003c/p\u003e\n\u003cp\u003eMITgcm simulations for Lake Geneva were conducted for 2021 and 2022 to investigate the evolution of its mesoscale and submesoscale hydrodynamics. The model was forced using high-resolution meteorological forecasting data from the COnsortium for Small-scale Modeling atmospheric model (COSMO, Swiss Federal Office of Meteorology and Climatology, MeteoSwiss)\u003csup\u003e76\u003c/sup\u003e. The forcing parameters included the wind field, air temperature, relative humidity, and solar radiation, all of which were interpolated where necessary to match the spatial and temporal discretization of the hydrodynamic model.\u003c/p\u003e\n\u003cp\u003eTwo numerical grids were employed to achieve a balance between computational efficiency and the resolution required to capture fine-scale processes. The first configuration was a Low-Resolution (LR) grid, with a horizontal resolution of 173–260 m and 35 vertical layers, initialized on 26 December 2020 using a horizontally uniform temperature profile from CIPEL (Commission Internationale pour la Protection des Eaux du Léman) station SHL2 (see Fig.\u0026nbsp;1 for location). The model was run from rest, using an integration time step of 20 s, with a spin-up period of approximately six months to allow for dynamical equilibration. The output from the LR simulation was then used to initialize a High-Resolution (HR) model, with a horizontal resolution of 113 m and 50 vertical layers. The HR grid had a fine vertical discretization with a surface layer thickness of 0.35 m; layer thickness gradually increased to 5 m at depth, allowing for enhanced resolution of thermocline dynamics, internal wave motions, and near-surface processes. The HR model was initialized on 7 July 2021 and ran continuously for nearly twelve months. The initial time step was 6 s, which was gradually increased to 30 s for numerical stability.\u003c/p\u003e\n\u003ch2\u003eField observations\u003c/h2\u003e\n\u003cp\u003eRecent studies demonstrated that eddy patterns in Lake Geneva can be reliably predicted using MITgcm simulation forecasts driven by forecasted meteorological data from the COSMO model\u003csup\u003e28\u003c/sup\u003e. These model forecasts are instrumental in guiding the selection of field measurement transects prior to field campaigns, thus ensuring efficient data collection. In the present study, the transects extended from the predicted eddy in the western part of the \u003cem\u003eGrand Lac\u003c/em\u003e basin to the eddy in its central region (Fig.\u0026nbsp;1c, e), covering key areas of interest for understanding mesoscale hydrodynamics. Each field campaign lasted approximately 6 to 8 hours, allowing for high-resolution spatial data collection.\u003c/p\u003e\n\u003cp\u003eAt predefined locations (spaced ~ 250 m to 1 km) along the transects, vertical profiles of temperature, DO and conductivity were taken using a Sea and Sun Marine Tech Conductivity-Temperature-Depth (CTD) multiparameter probe (CTD90M). Measurements were made over the upper ~ 50 m of the water column to ensure that the base of the thermocline was reached. The instrument was equipped with a RINKO III fast-response optical DO sensor and a high-precision temperature sensor (JFE Advantech). At a descent rate of ~ 10 cm s\u003csup\u003e-\u003c/sup\u003e¹, data was logged at a frequency of 7 Hz, yielding a vertical resolution of approximately 1.5 cm.\u003c/p\u003e\n\u003cp\u003eTo characterize the hydrodynamic conditions associated with the CE/ACE structures, an Acoustic Doppler Current Profiler (ADCP, Teledyne Marine Workhorse Sentinel) equipped with a bottom-tracking module was employed. To ensure statistical robustness, vertical profiles of current velocity were recorded at each station for a minimum duration of 10 minutes. The ADCP was configured with 100 bins of 1-m vertical resolution, and a blanking distance of 2 m to minimize interference from near-surface reflections. The transducer was positioned at a depth of 0.5 m, and the high-resolution processing mode was activated to enhance measurement accuracy. Tilt and heading angles were continuously monitored using built-in sensors, and post-processing was performed following the manufacturer’s guidelines to correct for potential measurement artefacts.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe thank the Swiss National Science Foundation (SNSF Grant 178866) for supporting this research. The spatiotemporal meteorological data were provided by the Federal Office of Meteorology and Climatology in Switzerland (MeteoSwiss). We also extend our appreciation to the Commission Internationale pour la Protection des Eaux du L\u0026eacute;man (CIPEL) for in situ temperature, dissolved oxygen and nutrients measurements. The profiles at CIPEL SHL2 station for 2021 were provided by the Eco-Informatics ORE INRA Team at the French National Institute for Agricultural Research (SOERE OLA-IS, INRA Thonon-les-Bains, France).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSH-Z conducted the field campaigns and implemented the numerical simulation. SH-Z conducted the data analyses, created the figures, and led the writing of the manuscript. UL and DB led the revision and critically reviewed the manuscript. All authors provided feedback on the manuscript. All authors contributed to the article and approved the submitted version.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding declaration\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe project was financially supported by Swiss National Science Foundation (SNSF) Grant No. 178866.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors\u0026nbsp;declare no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eTroitskaya, E. et al. Cyclonic circulation and upwelling in Lake Baikal. \u003cem\u003eAquat. 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In Perspectives on Atmospheric Sciences 143\u0026ndash;149 (Springer, Cham, \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1007/978-3-319-35095-0_20\u003c/span\u003e\u003cspan address=\"10.1007/978-3-319-35095-0_20\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e (2017).\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Mesoscale eddies, Cyclonic and anticyclonic circulations, Mixed layer dynamics, Thermal stratification, Dissolved oxygen gradients, Biogeochemical cycling, Large lakes","lastPublishedDoi":"10.21203/rs.3.rs-8156830/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8156830/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe influence of three-dimensional (3D) hydrodynamic processes, in particular that of mesoscale cyclonic (CEs) and anticyclonic eddies (ACEs), on water quality in lakes is largely unexplored. In this study, high-resolution field measurements based on 3D forecasting simulations allowed examination of how mesoscale eddies modulate the spatial distribution of key water quality parameters such as dissolved oxygen (DO), conductivity, and thermal stratification in Lake Geneva. The analysis focuses on periods of strong (summer) and weak (fall) thermal stratification. Results reveal that the interplay between simultaneously occurring CEs and ACEs (diameters\u0026thinsp;~\u0026thinsp;10 km) causes lateral variability in water quality by regulating the strength, the extent, and the shape of the metalimnion, a critical stratification interface. Compared to profiles taken at a station outside these eddies, CEs are characterized by higher DO concentrations, a shallower mixed layer, and a thicker metalimnion, whereas ACEs exhibit opposite trends. Within the mixed layer and metalimnion, DO production in summer and consumption in the fall occur across a wider depth range in the thicker metalimnion induced by CEs, whereas ACEs compress the metalimnion and limit vertical exchange. It is demonstrated that, depending on the season, extreme values of vertical DO gradients are primarily controlled by CEs or ACEs, which influence the depth distribution and intensity of biological processes, with potential implications for lake ecosystem dynamics.\u003c/p\u003e","manuscriptTitle":"Mesoscale eddies drive complex, large-scale three-dimensional biochemical variability in the mixed layer of a large lake (Lake Geneva)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-02 16:20:18","doi":"10.21203/rs.3.rs-8156830/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-12-23T10:27:49+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-19T08:20:39+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-15T02:37:18+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"155028518767587655737128012418821500585","date":"2025-12-03T06:06:45+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"226506787605779455574899875640944668398","date":"2025-12-02T16:28:59+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"229988705292685112604416183662957887604","date":"2025-12-02T10:28:24+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-12-01T04:13:12+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-11-28T19:39:33+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-11-26T13:01:15+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-11-24T13:15:19+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-11-24T13:10:50+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"07f28097-61bd-408f-8797-1c7da2930321","owner":[],"postedDate":"December 2nd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[{"id":58875511,"name":"Earth and environmental sciences/Climate sciences"},{"id":58875512,"name":"Earth and environmental sciences/Environmental sciences"},{"id":58875513,"name":"Earth and environmental sciences/Hydrology"},{"id":58875514,"name":"Earth and environmental sciences/Ocean sciences"}],"tags":[],"updatedAt":"2025-12-23T10:38:41+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-02 16:20:18","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8156830","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8156830","identity":"rs-8156830","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}