Macroorganism gut serves as microbial refuge for aquatic microorganisms to facilitate metacommunities recovery under environmental stress.

Environmental stress typically leads to a reduction in microbial diversity in a single habitat, yet the dispersal and adaptation of microorganisms across distinct habitats under such conditions are often overlooked. Here, we investigated the role of the macroorganism (mangrove crab) gut as a "refuge" for aquatic bacteria under arsenic (As) stress. Results from a gradient As stress experiment showed that 20.2-49.4% of bacterial taxa were eliminated from the water, and of these eliminated taxa, 25.8-53.1% migrated into the host gut. The community assembly of migrated taxa were increasingly governed by deterministic processes, which played a dominant regulatory role. Experimental validation using isolated aquatic bacteria confirmed they can migrate into gut under arsenic stress, and subsequently be released back into aquatic environment when transferred to stress-free system. Comparative genomics analysis exhibited the migrated/shared species have abundant enrichment in functional pathways related to chemotaxis, flagellum synthesis and oxidative phosphorylation compared to the eliminated species, indicating greater migratory capacity and adaptation to the low-oxygen, acidic habitat of the gut. Our findings revealed a novel microbial adaptation strategy wherein macroorganism gut serve as microbial “refuge” under environmental stress, which is an important modifier of ecological resilience in a metacommunity setting.