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.

群落组装过程极为复杂，解析其内在机制是微生物生态学领域的一大挑战。
本研究以拉斯科洞窟作为稳定且封闭的实验环境，针对人为干扰后同时存在的三类微生物群落——抗性群落（附着于未被染色的石灰岩基质）、受干扰群落（见于黑色污渍区域）与恢复性群落（见于衰减污渍区域），量化分析生命三域内微生物群落动态过程中随机过程与确定性过程的相对重要性。
令人意外的是，我们发现了四种可解释生命三域菌群在稳定环境下对干扰响应的模型。
具体而言，我们提出了一种尚未见诸报道的模型，该模型聚焦于长期稀有微生物类群：即便在受到干扰后，随机过程仍占据主导地位，但在群落恢复阶段，随机过程会被确定性过程所取代。
这一发现表明，长期稀有类群在群落恢复力中发挥着关键作用，其原因可能在于这些类群可为生态系统恢复提供必需的核心功能。