Here we investigate the importance of net CH₄ production and emissions in the carbon (C) budget of a small eutrophic lake by monitoring CH₄, CO₂ and O₂ during two consecutive years. During the study period, the lake was mostly a net emitter of both CH₄ and CO₂, while having a net autotrophic metabolism. The analyses suggest that during the whole study period 29 ± 23 % of C produced by net ecosystem production was ultimately converted to CH₄ and emitted to the atmosphere. When converted to global warming potential, CH₄ emission (in CO₂ equivalents) was about 3 to 9 times higher than CO₂ uptake from in-lake net ecosystem production over 100-years and 20-year timeframes, respectively. Our results suggest that the continuing eutrophication of inland waters will increase the amount of C released from lakes as CH₄ instead of CO_2> and may exacerbate the lake’s role in climate regulating processes.

Geographic coverage bounding coordinates	47.09 N, 8.08 E
Time frame - Begin date	2016, April 26th
Time frame - End date	2018, January 8th
General study design	The study was conducted in the small lake Soppensee situated in the Canton Lucerne, Switzerland (lake area: 23 ha, maximum depth: 26 m, mean depth: 12.2 m). Between April 2016 and January 2018, water column was sampled at several depth for dissolved gas concentration and water temperature on an approximately monthly basis. Moored instruments were installed to monitor water temperature at various depths and surface dissolved O2 and pCO₂. Inverted funnels were deployed to estimate CH₄ ebullition fluxes.
Methods description	Dissolved O₂, specific conductivity and water temperature profiles were measured using a multi-parameter sonde (Yellow Spring Instrument EXO2, after May 2017 a Seabird CTD profiler, SBE19) and 1-meter resolution is reported here. Dissolved CH₄ and CO₂ in the water column was measured using the headspace method (Vachon et al. 2019). Lake water was sampled at defined depth using a 5 L Niskin water sampler. Water from the Niskin bottle was gently poured into a 1-L glass bottle, letting overflow to replace 1-L bottle volume several times. A volume of 400 mL of water was carefully removed and replaced with ambient air without creating turbulence. The bottle was capped and shaken vigorously for at least 2 minutes. The headspace was transferred into a gas-tight atmospheric sampling bag (SupelTM Inert Multi-Layer Foil) for further gas analysis on a Cavity Ring-Down Spectrometer (Picarro G2201-i). In case of high CH₄ concentration (e.g. samples below 10 m in Soppensee), an additional dilution was applied before the analysis by subsampling the bag and diluting a known volume into a 50 ml glass gas-tight syringe (SGE Analytical Science, Australia) filled with synthetic air (Carbagas: 80% N2, 20% O2; ± 1%). In these cases, the gas was subsampled two or three times and the average was taken. The average coefficient of variation (C.V.) for all these diluted replicates was 5% (n = 67). Dissolved CO₂ and CH₄ in the lake water was back-calculated using the air-water volume ratio in the 1-L bottle, using atmospheric concentrations of pCH₄ and pCO₂ (2 and 400 matm, respectively), water temperature for the Henry’s constant and the local atmospheric pressure. For CO₂, we additionally applied a simple DIC mass balance in the bottle using alkalinity and carbonate system dissociation constants (Stumm and Morgan 1995) to account for carbonate system re-equilibration effect on the CO₂ balance in the bottle. Dissolved O₂ and CO₂ sensors were deployed at about 1.5 m depth on a mooring situated at the deepest point of the lake. The dissolved O₂ probe (miniDOT, Precision Measurements Engineering) logged temperature, dissolved O₂ concentration (mg O₂ L^-1) and saturation (%) every minute. CO₂ partial pressure (pCO₂; matm) was measured every hour by a GasPro probe (detection limit between 10-20 µatm) (Graziani et al. 2014) fitted with a copper mesh. Measurement of pCO₂ is based on equilibration of the surrounding water with a small-volume headspace containing a miniature nondispersive infrared (NDIR) detector (model IRC-A1; Alphasense) via diffusion through a gas permeable membrane (Teflon AF 2400; Biogeneral Inc.). Continuous pCO₂ measurements were not available during April 2016 to July 2016 and from September to November 2016. We measured gas ebullition fluxes using five bubble traps made of inverted funnels with collectors deployed over various sediment depths (Vachon et al. 2019). In May 2016, two funnels (opening of 0.79 m2) were deployed 4 m below the water surface over 10 m and 21 m deep sediments. Another bubble trap (also 0.79 m2) was installed in June 2017 over 15 m deep sediments, also moored at 4 m below surface. Two smaller funnels (0.25 m2) (Delwiche et al. 2015) were installed in April 2017 at shallower depths (about 10 cm above sediments at 3 and 6 m) to allow better spatial coverage. All bubble traps were moored with an inverted-V configuration to avoid disturbing the sediments below them. For sampling gas accumulation, the traps were gently brought to the surface (except for the 2 shallow funnels that could be sampled from a tube at the surface) and the gas volume was sampled using a 60-ml plastic syringe. Total gas flux (mmol m^-2 d^-1) received by each funnel was calculated using the Law of Ideal gases using in situ water temperature and atmospheric pressure, and by accounting for funnel area and deployment duration. Total gas flux was multiplied by the fraction of CH₄ found in the bubbles (0.596 at 3m, 0.675 at 6m, 0.61 at 10m, 0.561 at 15m and 0.555 at 21m). These proportion were estimated by first measuring the CH₄ fraction in the sediment bubbles at various depths (Langenegger et al. 2019) and by correcting for gas exchange with water during the ascend using a discrete bubble model (SiBu-GUI: Single Bubble – Dissolution Model / Version 1.2.6a) (McGinnis et al. 2006). The simulations were performed using an initial bubble diameter of 5 mm (McGinnis et al. 2006; Delsontro et al. 2015).
Laboratory, field, or other analytical methods	DIC concentrations were derived from dissolved CO₂ and total alkalinity (Alk) using water temperature and the carbonate system dissociation constants (Stumm and Morgan 1995). Measured Alk in 2016 varied between around 3 meq L^-1 in surface waters and 4 meq L^-1 in bottom waters (Canton of Lucerne, pers. comm.). A significant linear relationship was found between specific conductivity at 20°C (cond) and Alk (meq L^-1) measurements performed twice a year between 2008 and 2016 by the Canton of Lucerne monitoring program (Alk = 0.012 × cond - 0.52, r² = 0.98, n=96). From this relationship, we estimated Alk for each profile of the whole study using specific conductivity measured by the multi-parameter sonde.
Quality control	For water column dissolved gases a second sample was occasionally taken for a given depth to test for replicability of the method (n = 8). The average coefficient of variation (C.V.) for all the replicates was 9.7% and 10.6% for CH₄ and CO₂, respectively. Both O₂ and pCO₂ probes were frequently deployed in bubbled lake water (in a bucket with aquarium pumps) for several hours and check for gas atmospheric equilibrium values. Continuous pCO₂ and O₂ measurements were in excellent agreement with manual sampling.
References	Delsontro, T., D. F. McGinnis, B. Wehrli, and I. Ostrovsky. 2015. Size does matter: Importance of large bubbles and small-scale hot spots for methane transport. Environ. Sci. Technol. 49: 1268–1276. doi:10.1021/es5054286 Delwiche, K., S. Senft-Grupp, and H. Hemond. 2015. A novel optical sensor designed to measure methane bubble sizes in situ. Limnol. Oceanogr. 13: 712–721. doi:10.1002/lom3.10060 Graziani, S., S. E. Beaubien, S. Bigi, and S. Lombardi. 2014. Spatial and temporal pCO2 marine monitoring near Panarea Island (Italy) using multiple low-cost gaspro sensors. Environ. Sci. Technol. 48: 12126–12133. doi:10.1021/es500666u Langenegger, T., D. Vachon, D. Donis, and D. F. McGinnis. 2019. What the bubble knows: Lake methane dynamics revealed by sediment gas bubble composition. Limnol. Oceanogr. 64: 1526–1544. doi:10.1002/lno.11133 McGinnis, D. F., J. Greinert, Y. Artemov, S. E. Beaubien, and a. Wüest. 2006. Fate of rising methane bubbles in stratified waters: How much methane reaches the atmosphere? J. Geophys. Res. 111: C09007. doi:10.1029/2005JC003183 Stumm, W., and J. J. Morgan. 1995. Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters, 3rd Editio. Wiley-Interscience. Vachon, D., T. Langenegger, D. Donis, and D. F. McGinnis. 2019. Influence of water column stratification and mixing patterns on the fate of methane produced in deep sediments of a small eutrophic lake. Limnol. Oceanogr. 1–15. doi:10.1002/lno.11172

Water column profiles and high-frequency measurements of dissolved O2, CO2 and CH4 in a small eutrophic lake (Soppensee, Switzerland)

This dataset consists of vertical profiles of dissolved CH₄, CO₂ and O₂ concentrations measured approximately every month (less often in winter) and surface water daily measurement of O₂ and CO₂ concentrations, which is used to complete a whole lake mass balance in a small eutrophic lake in Switzerland. The dataset is from April 2016 to January 2018. All the samples were taken in the center of the lake at the deepest point (26 m). Additional data are water temperature (profiles and surface high-frequency) and CH₄ ebullition rates from a set of 5 inverted funnels. Weather data of the nearest meteorological station Egolzwil is available through the MeteoSwiss online download platform IDAweb at https://gate.meteoswiss.ch/idaweb/login.do.

Dataset filename: Water_column_temperature_oxygen_profiles.txt

Dataset description: This table reports 20 profiles of water temperature and dissolved oxygen concentration for each meter depth (down to 25 meters) in the center of Soppensee between April 2016 and January 2018. Volume of each 1-meter lake stratum is also displayed. Tab delimited.

Column name	Description	Units	Code explanation	Data format	Missing data code
Date	Date of the measured profile			yyyy-mm-dd	blank cell
Depth	Depth of measurement	meter below surface, m			blank cell
Vol	Volume of the lake stratum at the corresponding depth	Cubic meter, m3			blank cell
Temp	Water temperature at corresponding depth	Celcius, °C			blank cell
O2conc	Concentration of dissolved oxygen	mmol/m3			blank cell

Dataset filename: Water_column_gas_concentration_profiles.txt

Dataset description: This table reports 20 profiles of dissolved methane concentration, dissolved carbon dioxide and dissolved inorganic carbon at sampling depth (down to 25 meters) in the center of Soppensee between April 2016 and January 2018. Tab delimited.

Column name	Description	Units	Code explanation	Data format	Missing data code
Date	Date of the measured profile			yyyy-mm-dd	blank cell
Depth	Depth of measurement	meter below surface, m			blank cell
CH4conc	Concentration of dissolved methane	mmol/m3			blank cell
CO2conc	Concentration of dissolved carbon dioxide	mmol/m3			blank cell
DICconc	Concentration of dissolved inorganic carbon	mmol/m3			blank cell

Dataset filename: daily_surface_temperature_amd_gas_concentration.txt

Dataset description: Daily averaged surface water temperature, dissolved oxygen, dissolved methane and carbon dioxide partial pressure in Soppensee between April 2016 and January 2018. Ice cover and whole lake daily CH₄ ebullition is also given. Tab delimited.

*Column name*	*Description*	*Units*	*Code explanation*	*Data format*	*Missing data code*
date	Date of corresponding measurement			yyyy-mm-dd	blank cell
ice	Ice cover on the lake		0 = ice free, 1 = ice covered		blank cell
waterT	Water temperature measured every minute at surface of lake (~1m) and daily averaged.	Celcius, °C			blank cell
DO	Dissolved oxygen measured at surface of lake (~1.5m). Measured every minute and daily averaged.	mg O₂ / L			blank cell
CH4	Point measurement of dissolved methane measured at surface of lake (0.5 m). Measured once during the day between 9AM and 4PM.	mmol/m3			blank cell
pCO2	Carbon dioxide partial pressure measured at surface of lake (~1.5m). Measured every hour and daily averaged.	matm			blank cell
ebu	Daily whole lake average CH₄ ebullition estimated from 5 inverted funnels	mmol CH₄/m²/d			blank cell

Dataset filename: methane_ebullition_Soppensee.txt

Dataset description: Methane ebullition reaching the atmosphere averaged over the time between two visits of the lake at five different depths in Soppensee between April 2016 and January 2018. Tab delimited.

Column name	Description	Units	Code explanation	Data format	Missing data code
date_start	Date of the start of the funnel deployment			yyyy-mm-dd	blank cell
date_stop	Date of the funnel measurement			yyyy-mm-dd	blank cell
days	Number of days of the deployment	days			blank cell
depth	Water column depth at the funnel location, i.e. distance between sediments and air-water interface.	Meters, m			blank cell
ebu_total	Volume of gas measured in the gas collector of the funnel during the deployment per m² per day	ml / m² / d			blank cell
CH4_rate	Daily averaged methane ebullition rate during the deployment.	mmol / m² / d			blank cell

Data from: Methane emission offsets carbon dioxide uptake in a small productive lake

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Works referencing this dataset