Ecological restoration reduces greenhouse gas emissions by altering planktonic and sedimentary microbial communities in a shallow eutrophic lake.

Ecological restoration is a promising approach to alleviate eutrophication. However, its impacts on greenhouse gas (GHG) emissions and the underlying microbial mechanisms in different habitats of lakes remain unclear. To address this knowledge gap, we measured carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes at both water-air and sediment-water interfaces of eutrophic (Caohai) and restored area (Dapokou) of Dianchi Lake, a typical eutrophic lake in China. Meanwhile, we investigated the responses of planktonic and sedimentary bacterial and fungal communities by high-throughput sequencing. Our results indicated that 6 years of ecological restoration significantly reduced CO2 and N2O fluxes by 1.0-3.6 and 2.2-2.8 folds respectively, with more pronounced variations at the water-air interface than the sediment-water interface. Ecological restoration also shifted the structures of planktonic bacterial and fungal communities remarkably, leading to a significant reduction in the relative abundances of Actinobacteriota (by 70.94%), Bacteroidota (by 61.65%), Planctomycetota (by 74.18%) and Chytridiomycota (by 95.44%). Correlation analyses further suggested that GHG fluxes at the water-air interface were significantly correlated with planktonic microbial community composition (P < 0.05), and the significant reduction of CO2 and N2O fluxes under ecological restoration could be attributed to the decreased abundances of organic matter decomposers (such as hgcI_clade, Sporichthyaceae and Acidibacter) and increased abundances of autotrophs (such as Hydrogenophaga and Cyanobium_PCC-6307) in water. Collectively, our findings verify the importance of ecological restoration in reducing GHG emissions in inland lake ecosystems, providing new insights for addressing global climate change and advancing carbon neutrality.