The Failure and Revival of Closed Microbial Ecosystems: Evidence from the Shifts in Microbial and Chemical Diversities

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(CRAM)-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.