Background: Submerged plants composed of charophytes (green algae) and angiosperms develop dense vegetation in small, shallow lakes and in littoral zones of large lakes. Many small, oligotrophic plant species have declined due to drainage and fertilization of lakes, while some tall, eutrophic species have increased. Although plant distribution has been thoroughly studied, the physiochemical dynamics and biological challenges in plant-dominated lakes have been grossly understudied, even though they may offer the key to species persistence.Scope: Small plant-dominated lakes function as natural field laboratories with eco-physiological processes in dense vegetation dictating extreme environmental variability, intensive photosynthesis and carbon cycling. Those processes can be quantified on a whole lake basis at high temporal resolution by continuously operating sensors for light, temperature, oxygen, etc. We explore this hitherto hidden world.Conclusions: Dense plant canopies attenuate light and wind-driven turbulence and generate separation between warm surface water and colder bottom waters. Daytime vertical stratification becomes particularly strong in dense charophyte vegetation, but stratification is a common feature in small, shallow lakes also without plants. Surface cooling at night induces mixing of the water column. Daytime stratification in plant stands may induce hypoxia or anoxia in dark bottom waters by respiration, while surface waters develop oxygen supersaturation by photosynthesis. Intensive photosynthesis and calcification in shallow charophyte lakes depletes dissolved inorganic carbon (DIC) in surface waters, whereas DIC is replenished by respiration and carbonate dissolution in bottom waters and returned to surface waters before sunrise. Extreme diel changes in temperature, DIC and oxygen in dense vegetation can induce extensive rhythmicity of photosynthesis and respiration and become a severe challenge to the survival of organisms. Large phosphorus pools are bound in plant tissue and carbonate precipitates. Future studies should test the importance of this phosphorus sink for ecosystem processes and competition between phytoplankton and plants.

Ponds, wetlands, and shallow lakes (collectively “shallow waterbodies”) are among the most biogeochemically active freshwater ecosystems. Measurements of gross primary production (GPP), respiration (R), and net ecosystem production (NEP) are rare in shallow waterbodies compared to larger and deeper lakes, which can bias our understanding of lentic ecosystem processes. In this study, we calculated GPP, R, and NEP in 26 small, shallow waterbodies across temperate North America and Europe. We observed high rates of GPP (mean 8.4 g O ₂ m ⁻³ d ⁻¹ ) and R (mean −9.1 g O ₂ m ⁻³ d ⁻¹ ), while NEP varied from net heterotrophic to autotrophic. Metabolism rates were affected by depth and aquatic vegetation cover, and the shallowest waterbodies had the highest GPP, R, and the most variable NEP. The shallow waterbodies from this study had considerably higher metabolism rates compared to deeper lakes, stressing the importance of these systems as highly productive biogeochemical hotspots.

Freshwaters emit significant amounts of CO₂ on a global scale. However, emissions remain poorly constrained from the diverse range of aquatic systems. The drivers and regulators of CO₂ gas flux from standing waters require further investigation to improve knowledge on both global-scale estimates and system-scale carbon balances. Often, lake–atmosphere gas fluxes are estimated from empirical models of gas transfer velocity and air–water concentration gradient. Direct quantification of the gas flux circumvents the uncertainty associated with the use of empirical models from contrasting systems. Existing methods to measure CO₂ gas flux are often expensive (e.g. eddy covariance) or require a high workload in order to overcome the limitations of single point measurements using floating chambers. We added a small air pump, a timer and an exterior tube to ventilate the floating chamber headspace and passively regulate excess air pressure. By automating evacuation of the chamber headspace, continuous measurements of lake CO₂ gas flux can be obtained with minimal effort. We present the chamber modifications and an example of operation from a small forest lake. The modified floating chamber performed well in the field and enabled continuous measurements of CO₂ gas flux with 40 min intervals. Combining the direct measurements of gas flux with measurements of air and waterside CO₂ partial pressure also enabled calculation of gas exchange velocity. Building and using the floating chamber is straightforward. However, because an air pump is used to restart measurements by thinning the chamber headspace with atmospheric air, the duration of the air pump pause–pulse cycle is critical and should be adjusted depending on system characteristics. This may result in shorter deployment duration, but this restriction can be circumvented by providing a stronger power source. The simple design makes modifications of the chamber dimensions and technical additions for particular applications and systems easy. This should make this approach to measuring gas flux flexible and appropriate in a wide range of different systems.

Ponds are regarded as greenhouse gas (GHG) emission hot spots, but how hot are they? We examined this question by measuring methane (CH₄) and carbon dioxide (CO₂) fluxes in six forest and open land ponds on grasslands in Denmark during summer and winter. We used floating chambers with do-it-yourself sensors and automated headspace venting, allowing for 7404 hourly measurements. We found highly variable gas fluxes within ponds and between seasons and pond types. Ebullitive CH₄ fluxes were more variable than diffusive CH₄ fluxes. Ebullition was absent when total CH₄ fluxes were lowest (15 µmol m⁻² h⁻¹), dominant (> 90%) at the highest fluxes (> 400 µmol m⁻² h⁻¹), and increased with water temperature. In summer, a minor daily increase in diffusive fluxes was found on days with high wind speed, while CH₄ ebullition remained constant. CO₂ fluxes paralleled the day-night balance of photosynthesis and respiration. Mean CH₄ ebullition in open and forest ponds exceeded CH₄ diffusive fluxes 4.1 and 7.1-fold in summer (avg. 22.5 °C) and 2.3 and 2.5-fold in winter (9.6 °C), respectively. CO₂ emissions were higher on a molar basis than CH₄ emissions, both in summer and winter, while their annual global warming potentials were similar. Mean annual gas emissions from open and forest ponds (1092 and 2527 g CO₂e m⁻² y⁻¹) are naturally high due to extensive external input of dissolved CO₂ and organic carbon relative to pond area and volume.