Organizational down-scaling reveals distinct microbial dynamics in a lake littoral sediment

Lake littoral sediments are dynamic environments supporting diverse ecological functions, yet the temporal dynamics of their microbial communities remain understudied. This study investigated the temporal changes in microbial communities within the surficial sediments of Lake Bourget, with a high temporal resolution (2.3 ± 2 days over five months). We hypothesized that analyzing microbial dynamics at multiple organizational scales would reveal finer insights into temporal changes and the ecological processes shaping them (deterministic vs. stochastic). Temporal patterns were examined at community and sub-community scales using ß-diversity metrics and module detection in a co-occurrence network. At the community scale, temporal dynamics of microbial communities were limited, with a null model indicating that stochastic processes, such as ecological drift and homogenizing, predominantly governed microbial changes, while deterministic processes by environmental filtering played a minimal role. This result was supported by a variance partitioning indicating environmental parameters explained only 17.4 % of temporal variation. Community downscaling enabled to identify six different microbial modules exhibiting unique temporal dynamics. The two largest modules showed contrasting associations with environmental variables, highlighting distinct ecological niches succeeding over time. Compared to community scale, environmental parameters explained more variation of module pattern (up to 51% for Module M3), suggesting that deterministic processes, such as selection by environmental filters, play a more dominant role in the microbial dynamics at the module scale than at the community scale. These findings highlight the importance of considering multiple organizational scales to gain a deeper understanding of the ecological processes governing microbial dynamics in ecosystems.