The illusion of functional stability: functional redundancy does not equal functional insurance in a natural-engineered aquatic continuum.

Functional redundancy-the capacity of multiple species to perform similar ecological functions-is widely regarded as a buffer that stabilizes ecosystem processes. However, whether functional redundancy truly translates into functional insurance remains unverified in microbial communities. Here, by integrating metagenomics and metatranscriptomics from 52 samples across a natural-engineered aquatic continuum in the Yanjin River watershed, China, results show that functional redundancy and functional insurance are fundamentally decoupled. We constructed a dual-layer analytical framework linking genomic functional overlap (effect trait) with transcriptional response heterogeneity (response trait) and developed a functional insurance index (FII) that quantifies whether redundant species respond differently to environmental variation. Our results reveal a striking paradox: engineered systems harbor the highest genomic functional redundancy yet the lowest functional insurance, because their functionally redundant species respond synchronously to perturbations-creating an illusion of stability. In contrast, natural communities exhibit lower absolute redundancy but significantly higher insurance, driven by diversified transcriptional responses among functionally similar species. Critically, only FII-not redundancy, response diversity, or asynchrony alone-significantly predicted CO2 and CH4 concentrations and DOM compositional stability, closing the evidence chain from genotype through phenotype to ecosystem function. These findings challenge the prevailing assumption that functional redundancy ensures functional insurance and reveal that conventional redundancy-based assessments may systematically overestimate or underestimate the functional stability of aquatic ecosystems.