Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake

In warm monomictic lakes, the hypolimnion is important for accumulating and decomposing organic matter derived from surface production, and the regenerated nutrients will be supplied to the epilimnion through winter vertical mixing. So far, we know little about microbial community composition and function in the hypolimnion when the significant thermal stratification disappears. In this study, we investigated microbial community compositions and functional gene contents by means of metagenomics along a depth profile in the warm monomictic alpine Lake Fuxian during holomictic period. Overall, bacteria were the dominant microbial group at different water depths, while phages had their high relative abundance in the epilimnion. We observed slight thermal but strong chemical stratification even during this typical winter overturn. The anaerobic respiration with nitrate and sulfate as the terminal electron acceptors was accumulated at bottom of hypolimnionin as indicated through metabolic pathway reconstruction. We were able to get 440 metagenome-assembled genomes (MAGs) and unraveled a high genomic diversity of freshwater pelagic microbiomes along this depth profile. We furthermore defined a new class of Plancto_FXH1 of Planctomycetes from these MAGs, of which a distinct nitrate reduction operon was identified. Representatives of this phylum mainly thrive in the hypolimnion as previously suspected, but few lineages were detected in the epilimnion. In summary, metagenomics enabled us to find a new group of Planctomycetes, probably involved in denitrification in the hypolimnion in Lake Fuxian, which expand our knowledge on denitrifying bacterial diversity and their denitrification potential in deep freshwater lakes.