A Dynamic Framework for Context-Dependent Microbial Assembly: Validation of the Domain-Specific Stochastic–Deterministic Integration Model

Microbial community assembly is governed by the interplay of stochastic and deterministic processes. However, most existing frameworks treat microbial communities as taxonomically homogeneous entities, overlooking the phylogenetic divergence and ecological distinctiveness of major microbial domains. Here, we present a new conceptual model—Domain-Specific Stochastic–Deterministic Integration (DSSDI)—that explicitly incorporates domain-level asymmetries, cross-domain interactions, and functional buffering into the community assembly process. Using 16S rRNA sequencing data from seasonal intertidal microbial communities, we tested four hypotheses derived from the DSSDI framework. Our results revealed that bacterial and archaeal communities differ in their stochastic–deterministic assembly patterns, spatial–temporal responses, network modularity, and functional robustness. Cross-domain cooperation emerged as a stabilizing factor, promoting metabolic complementarity and buffering against taxonomic turnover. This study introduces and validates the DSSDI framework as the first domain-explicit model of microbial community assembly, establishing a clear conceptual foundation and claiming priority for future theoretical and empirical developments in this field.