Freshwater ecosystems are the largest natural source of the greenhouse gas methane (CH₄), with shallow lakes a particular hot spot. Eutrophication and warming generally increase lake CH₄ emissions but their impacts on the sole biological methane sink - methane oxidation - and methane-oxidizer community dynamics are poorly understood. We used the world’s longest-running freshwater climate-change mesocosm experiment to determine how methane-oxidizing bacterial (MOB) abundance and composition, and methane oxidation potential in the sediment respond to eutrophication, short-term nitrogen addition and warming. After nitrogen addition, MOB abundance and methane oxidation potential increased, while warming increased MOB abundance without altering methane oxidation potential. MOB community composition was driven by both temperature and nutrient availability. Eutrophication increased relative abundance of type I MOB Methyloparacoccus. Warming favoured type II MOB Methylocystis over type I MOB Methylomonadaceae, shifting the MOB community from type I dominance to type I and II co-dominance, thereby altering MOB community traits involved in growth and stress-responses. This shift to slower-growing MOB may explain why higher MOB abundance in warmed mesocosms did not coincide with higher methane oxidation potential. Overall, we show that eutrophication and warming differentially change the MOB community, resulting in an altered ability to mitigate CH₄ emissions from shallow lakes.

The top 4 cm of the sediment was sampled and analyzed in the lab using potential methane oxidation incubations, DNA extractions, qPCR of the pmoA gene and 16S amplicon sequencing.

Contains data on methane oxidation potential, MOB abundance, apparent cell-specific activity, NMDS plotting and relative abundance of the different MOB genera and families, including the raw data used to calculate those values.