Higher spatial than seasonal variation in floodplain soil eukaryotic microbial communities

Beta diversity, the compositional changes of community composition across space and time, is a key aspect of biodiversity with implications from species dynamics to ecosystem functioning. However, beta diversity and its drivers have received little attention, especially for microbial eukaryotes, including fungi and protists, which play key roles in soil functioning and in naturally dynamic ecosystems of high value for biodiversity conservation such as floodplains. We studied the spatiotemporal patterns of eukaryotic microbial diversity in a Swiss lowland floodplain. We sampled six well-contrasted habitats once per season over one year. Using high-throughput Illumina sequencing of the V9 region of the SSU rRNA gene, we determined the temporal vs. spatial patterns of alpha and beta diversity. We then identified the drivers of these patterns among soil conditions and functions and identified indicator amplicon sequence variants of habitats in each season. Each of the spatial and temporal components of beta diversity contributed more to total diversity than local alpha diversity. Furthermore, both alpha and beta diversity changed more strongly among habitats than among seasons and the drivers of these diversity components varied seasonally. These results contrast with a previous study at the same site showing a dominance of temporal over spatial variability in bacterial community composition. Our opposite results suggest that bacteria and micro-eukaryotes respond to different drivers. Microbial diversity patterns can thus differ quite substantially among seasons and taxa. As such, not considering the temporal component of microbial diversity might greatly underestimate the diversity and the complexity of assembly processes of soil microbial communities which may have important implications for land management.