Microbial community composition seasonality and drift over years in small freshwater ecosystems

Small freshwater ecosystems are highly diverse, widely distributed, may be identified as major actors in greenhouse gas fluxes and are potential stocks of freshwater for human usages. In principle, they are more sensitive to environmental disturbance than large aquatic ecosystems because their small volumes provide low buffering capacity. However, little is yet known about their microbial biodiversity and function and how it is structured over time. Yet, understanding the structuring of microbial primary producers, predators, parasites and degraders in these ecosystems is essential to appreciate and model their functioning in the next decades. We investigated the spatial distribution and temporal dynamics of microorganisms of the three domains of life (bacteria, archaea, microbial eukaryotes) at the intra- (seasonal) and inter-annual (pluri-annual) scale in five small freshwater ecosystems. We focused on four ponds and a brook located in northwestern France under temperate climate that we studied for eight years (2011-2019) at seasonal frequency. Microbial diversity was assessed through Illumina MiSeq sequencing of 16S and 18S rDNA amplicons. Several abiotic parameters (physical and chemical) were measured in situ and in the laboratory to characterise the environmental conditions. Multivariate statistical analyses were conducted to identify temporal patterns and link them to environment changes. Microbial communities differed among the ecosystems despite their spatial proximity, likely due to differences in local environmental conditions. Microbial eukaryotic and prokaryotic communities exhibited seasonal temporal patterns and a shift in composition over the years. Microbial communities experienced a strong turnover at the seasonal scale leading to a low fraction (< 2%) of recurrent taxa. In each ecosystem, the measured physico-chemical parameters slightly influenced the microbial community variance over time. These results suggest that biotic interactions but also dormancy, immigration and genetic evolution superimpose to environmental selection through time. Understanding their interplay will be essential to explain microbial community composition change in these ecosystems.