Microbial
communities constitute the core component of biological
wastewater treatment processes. We conducted a meta-analysis based
on the 16S rRNA gene of temporal samples obtained from diverse full-scale
activated sludge and anaerobic digestion systems treating municipal
and industrial wastewater (collected in this study and published previously)
to investigate their community assembly mechanism and functional traits
over time, which are not currently well understood. The influent composition
was found to be the main driver of the microbial community’s
composition, and relatively large proportions of specialist (26.1%
and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in
both systems. Deterministic processes, especially homogeneous selection
events (accounting for >53.8% of assembly events), were consistently
identified as the dominant microbial community assembly mechanisms
in both systems over time. Significant and strong correlations (Pearson’s r = 0.51–0.92) were detected between the dynamics
of the temporal community and the functional compositions in both
systems, which suggests functional dependency. In contrast, the occurrence
of sludge bulking and foaming in the activated sludge system led to
an increase in stochastic assembly processes (i.e., limited dispersal
and undominated events), a shift toward functional redundancy and
less community diversity, a decreased community niche breadth index,
and a more compact co-association network. This study illustrates
that the mechanism of microbial community assembly and functional
traits over time can be used to diagnose system performance and provide
information on potential system malfunction.