Microbiome facing disturbance: common response of the rare biosphere from the three domains of life

Community assembly processes are complex and understanding them represent a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains life, in relation to an anthropogenic disturbance that had resulted in side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains) and a resilient community (attenuated stains). Unexpectedly, we found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of one non-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance, but are replaced by deterministic processes during recovery. This points to a major role of always-rare taxa in resilience, perhaps because they provide key functions required for ecosystem recovery.