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The contribution of oxic methane production to greenhouse gas emissions from lakes is globally relevant, yet uncertainties remain about the levels up to which methanogenesis can counterbalance methanotrophy by leading to CH4 oversaturation in productive surface waters. Here, we explored the biogeochemical and microbial community variation patterns in a meromictic soda lake, in the East African Rift Valley (Kenya), showing an extraordinarily high concentration of methane in oxic waters (up to 156 µmol L−1). Vertical profiles of dissolved gases and their isotopic signature indicated a biogenic origin of CH4. A bloom of Oxyphotobacteria co-occurred with abundant hydrogenotrophic and acetoclastic methanogens, mostly found within suspended aggregates promoting the interactions between Bacteria, Cyanobacteria, and Archaea. Moreover, aggregate sedimentation appeared critical in connecting the lake compartments through biomass and organic matter transfer. Our findings provide insights into understanding how hydrogeochemical features of a meromictic soda lake, the origin of carbon sources, and the microbial community profiles, could promote methane oversaturation and production up to exceptionally high rates., Fazi et al. report on an extraordinarily high biogenic methane concentration detected in the surface water of Lake Sonachi, Kenya. Using gas chromatography and microbiome profiling, they determine that these high concentrations are associated with cyanobacterial blooms and help provide insight to methanogenesis in meromictic soda lakes.

Saline-alkaline lakes of the East African Rift are known to have an extremely high primary production supporting a potent carbon cycle. To date, a full description of carbon pools in these lakes is still missing. More specifically, there is not detailed information on the quality of dissolved organic matter (DOM), the main carbon energy source for heterotrophs prokaryotes. We report the first exhaustive description of DOM molecular properties in the water column of a meromictic saline-alkaline lake of the East African Rift. DOM availability, fate and origin were studied either quantitatively, in terms of dissolved organic carbon (DOC) and nitrogen (DON) or qualitatively, in terms of optical properties (absorbance) and molecular characterization of solid-phase extracted DOM (SPE-DOM) through negative electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). DOM availability was high (DOC ∼ 8.1 mM in surface waters) and meromixis imprinted a severe quantitative and qualitative change on DOM pool. At the surface, DOM was rich in aliphatic and moderately in aromatic molecules and thus mirroring autochthonous microbial production together with photodegradation. At the bottom changes were extreme: DOC increased up to 5 times (up to 50 mM) and, molecular signature drifted to saturated, reduced and non-aromatic DOM suggesting intense microbial activity within organic sediments. At the chemocline, DOC was retained indicating that this interface is a highly reactive layer in terms of DOM processing. These findings underline that saline-alkaline lakes of the East African Rift are carbon processing hot spots and their investigation may broaden our understanding of carbon cycling in inland waters at large.