A prerequisite to improve the predictability of microbial community dynamics is to understand their assembly mechanisms. To study factors that contribute to microbial community assembly, we examined temporal dynamics of genes in five aquatic metagenome time series, originating from marine off-shore or coastal sites and one lake, while focusing on a trait-based data evaluation. We expected to find gene-specific patterns for the temporal allele variability depending on the metacommunity size of carrier-taxa and variability of the milieu and the substrates that the resulting enzymes are exposed to. In more detail we hypothesized that a larger metacommunity would cause increased temporal variability of functional units, as shown previously for taxonomic units. Furthermore, we hypothesized that multi-copy genes feature higher temporal variability then single-copy genes, because gene multiplication is often the consequence of increased variability in (subtil) changes of substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins as they would be exposed to highly variable conditions. The first two hypotheses were confirmed in all, while an effect of the subcellular location of gene-products was only seen in three out of the five time series. The gene with highest allele variability throughout all datasets was an iron transporter, which also represents a target for phage infections. This finding points to the general importance of iron transporter mediated phage infections on the assembly and maintenance of diversity of aquatic prokaryotes.