The failure and revival of closed microbial ecosystems: evidence from the shifts in microbial and chemical diversities

Abstract Closed microbial ecosystems (CES) are vital models for studying ecosystem stability and resilience, especially in carbon cycling. This study explored algae-bacteria CES using real-time pressure dynamics, 16S rRNA sequencing, and ultrahigh-resolution mass spectrometry. The system exhibited biphasic stability: an initial high-activity phase (Days 1–8) with robust carbon cycling and diverse communities dominated by Pseudomonas. Subsequent re-stabilization (Days 31–45) involved a functional shift toward Brevundimonas and photoheterotrophic Porphyrobacter, coupled with dissolved organic matter (DOM) chemodiversity loss and accumulation of recalcitrant lignin/Carboxyl-rich alicyclic molecules–like compounds. Declining carbon cycling intensity correlated with microbial diversity erosion and DOM simplification, revealing a self-reinforcing feedback loop threatening ecosystem persistence. This work advances frameworks for anticipating tipping points in natural ecosystems under anthropogenic stressors, offering actionable insights for conservation and bioremediation strategies.