Biosynthesis gene cluster‐containing species drive microbial community stability under thermal stress through enhanced ecological cohesion

Abstract Understanding the mechanisms that govern the ecological stability of microbial communities is critical to elucidating how microbes adapt to changes in their environment. Here, we investigated microbial assembly and changes during spontaneous fermentation, in which the temperature naturally increased from 20°C to 65°C, to determine how thermal stress shapes community dynamics and resilience. Longitudinal metagenomic sampling revealed that heterogeneous selection favored thermotolerant taxa, while ecological drift exerted a stronger influence on fungal communities, indicating that both deterministic and stochastic processes jointly contributed to the community assembly. Specifically, bacterial turnover was primarily driven by heterogeneous selection and dispersal limitation, while fungal assembly was driven by homogeneous selection and drift. Furthermore, the infer Community Assembly Mechanisms by Phylogenetic‐bin‐based null model analysis identified 27 bacterial and 140 fungal groups that exhibited significant compositional shifts along the thermal gradient. Among these, 11 biosynthesis gene cluster (BGC)‐containing species could enhance the microbial community stability by strengthening positive cohesion among species (all species: 0.303–0.464; without BGC‐containing species: 0.289–0.461). By removal simulations, we further identified six BGC‐containing species (two bacteria and four fungi) that were critical for maintaining robustness to the changes under thermal stress. Co‐culture experiments confirmed that their presence increased community biomass by at least 50.08% compared with the control without these six species. Taken together, our results suggest that BGC‐containing species can maintain the microbial community stability by reinforcing ecological cohesion and increasing biomass production under high‐temperature stress.