| 14 Apr 2026
Variability of methane content in bottom waters of 46 African lakes
Abstract. Methane (CH4) accumulates in bottom waters of lakes, however, the extent and drivers of inter-lake variation in bottom-water CH4 concentrations are poorly understood and have been studied mainly in northern lakes. This limits predictions of how bottom-water CH4 concentrations respond to warming and eutrophication in lakes, and how these changes might influence surface-water CH4 concentrations and, consequently, CH4 emissions. We report 168 measurements of paired bottom- and surface-water CH4 concentrations from 46 African lakes spanning a wide range of surface area (SA; 0.02–67,075 km²) and maximum depth (2–180 m). Bottom-water CH4 concentrations ranged from 7 to 5,608,382 nmol L⁻¹, spanning six orders of magnitude, and increased with increasing stratification, quantified from vertical density profiles using potential energy anomaly (PEA) and mixed layer depth (MLD), and inferred from NH₄⁺ concentrations or vertical conductivity gradients. Surface-water CH4 concentrations ranged from 7 to 168,114 nmol L⁻¹ and increased with both bottom-water CH4 concentrations and vertical stratification (positively related to PEA and negatively to MLD). The most strongly stratified lakes exhibited high bottom-water CH4 concentrations, resulting in enhanced vertical transfer of CH4 to surface waters despite lower vertical diffusion coefficients. In addition, these lakes had shallower mixed layers and therefore thinner oxygenated surface layers, likely reducing CH4 removal via methane oxidation. The positive relationship between both bottom- and surface-water CH4 concentrations and chlorophyll-a (Chl-a) has previously been interpreted as reflecting enhanced methanogenesis driven by phytoplankton-derived organic matter delivered to sediments. However, such relationships may be indirect and should be interpreted cautiously, as Chl-a was negatively related to MLD in our dataset, and both bottom- and surface-water CH4 concentrations were also negatively related to MLD. The ratio of surface to bottom CH4 concentrations (surface:bottom CH4 ratio) may indicate the relative increase in surface CH4 in response to increases in bottom CH4 driven by warming and eutrophication. This ratio was negatively related to bottom depth, PEA, and MLD, and positively related to bottom-water O2, indicating that the relative increase in surface-water CH4 with increasing bottom-water CH4 is greater in shallower, less stratified systems than in deeper, more stratified systems. Diffusive CH4 emission rates were highest in shallower, less stratified systems, where the response of surface-water CH4 to increases in bottom-water CH4 is expected to be greatest, as indicated by high surface:bottom CH4 ratios. We further tested whether surface-water CH4 concentrations scale with simple metrics in a dataset including highly stratified, small, and deep crater lakes with elevated hypolimnetic CH4. A multiple linear regression using SA and Chl-a explained ~51 % of the variance and appears suitable for upscaling dissolved CH4 concentrations. This approach could enable large-scale extrapolation of diffusive CH4 emissions using spatial datasets for SA and remotely sensed Chl-a.
Competing interests: At least one of the (co-)authors is a member of the editorial board of Biogeosciences.
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