Shifts in microbiome structure during summer stratification in temperate lakes

Temperate lakes often feature a seasonal stratification of the water column, resulting in a hypoxic or anoxic hypolimnion. This heavily impacts the microbiome, however, we only have started to understand how this perturbation effects the ecological connections between different microbes and their abilities for the biogeochemical cycling of elements. Here we present the spatiotemporal analysis of the microbiomes of two meso-/oligotrophic dimictic lakes experiencing summer stratification. By employing multivariate statistics and cooccurrence network analyses of 16S rRNA gene amplicon data, we observed the clustering of bacterial communities correlated to oxygen concentrations throughout stratification. Cooccurrence patterns among abundant and ubiquitous freshwater Actinobacteria and Proteobacteria suggested microbial niche partitioning potentially accompanied by differential specialization in carbon substrate metabolisms. The hypolimnion showed diverse communities with the potential for a wide variety of respiration processes. Hypoxic/anoxic
conditions distinctly defined a module of OTUs co-occurring in the hypolimnion during summer stratification, containing anaerobic Chloroflexi and Chlorobi, but also methanotrophs. We further detected a module including OTUs of the candidate division OP3, Planctomycetes and Nitrosomonadaceae, occurring at low temperatures in the hypolimnion, predominantly in the oxygen gradient before complete anoxic conditions developed.