微生物群落組裝的經典理論，多建立在一項隱含前提之上：不同分類單元可在共享的生態維度中被比較，從而以棲位差異或隨機等價性加以描述。然而，當此一前提被延伸至跨域尺度時，其有效性便值得重新檢視。不同微生物域在演化歷史、生理限制與生態策略上的根本差異，可能使其無法被視為完全可比較的生態單位。在此情境下，關鍵問題不再只是不同微生物群是否遵循相同的組裝機制，而是：這些群體是否能在單一理論框架中被一致地描述與比較。若生態單位在本質上不可完全通約，則現有無論基於棲位、 中性，或兩者整合的理論，都可能僅捕捉到群落結構的部分面向。為回應此一理論缺口，我們提出「領域特異的隨機–決定性整合」（Domain-Specific Stochastic–Deterministic Integration, DSSDI）框架。DSSDI 將群落組裝重新概念化為一個具領域解析度的過程，其中隨機與決定性力量在不同微生物域之間呈現不對稱作用，而跨域交互作用則進一步形塑更高層次的結構組織。在此框架下，生態功能的穩定性不再僅源自域內的功能冗餘，而是來自於領域特異組裝動力與跨域互補作用的整合。

Classical theories of microbial community assembly are largely built upon an implicit assumption: that ecological units are comparable within shared dimensions, allowing taxa to be evaluated in terms of niche differentiation or stochastic equivalence. However, the validity of this assumption becomes uncertain when extended across microbial domains. Fundamental differences in evolutionary history, physiological constraints, and ecological strategies may render these domains only partially comparable as ecological units. Under such conditions, the central question is not simply whether different microbial groups follow distinct assembly mechanisms, but whether they can be coherently described within a unified theoretical framework. If ecological units are not fully commensurable across domains, then existing models—whether niche-based, neutral, or integrative—may capture only a subset of the processes shaping community structure. To address this limitation, we propose the Domain-Specific Stochastic–Deterministic Integration (DSSDI) framework. DSSDI reconceptualizes community assembly as a domain-resolved process, in which stochastic and deterministic forces act asymmetrically across microbial domains, while cross-domain interactions generate higher-order structural organization. Within this framework, ecological functional stability does not arise solely from within-domain functional redundancy, but from the integration of domain-specific assembly dynamics and cross-domain complementarity.