Stability of the cnidarian–dinoflagellate symbiosis is primarily determined by symbiont cell-cycle arrest

The cnidarian-dinoflagellate symbiosis relies on the regulation of resident symbiont populations to maintain biomass stability; however, the relative importance of host regulatory mechanisms [cell-cycle arrest (CC), apoptosis (AP), autophagy (AU), and expulsion (EX)] during symbiosis onset and maintenance is largely unknown. Here, we inoculated a symbiont-free (aposymbiotic) model cnidarian (<i>Exaiptasia diaphana</i>: "Aiptasia") with either its native symbiont <i>Breviolum minutum</i> or one of three non-native symbionts: <i>Symbiodinium microadriaticum</i>, <i>Cladocopium goreaui,</i> and <i>Durusdinium trenchii</i>. We then measured and compared host AP, host AU, symbiont EX, and symbiont cell-cycle phase for up to a year with these different symbionts and used these discrete measurements to inform comparative models of symbiont population regulation. Our models showed a general pattern, where regulation through AP and AU is reduced after onset, followed by an overshoot of the symbiont population that requires a strong regulatory response, dealt with by strong CC and increased EX. As colonization progresses into symbiosis maintenance, CC remains crucial for achieving steady-state symbiont populations, with our models estimating that CC regulates 10-fold more cells (60 to 90%) relative to the other mechanisms. Notably though, our models also revealed that <i>D. trenchii</i> is less tightly regulated than <i>B. minutum</i>, consistent with <i>D. trenchii's</i> reputation as a suboptimal partner for this cnidarian. Overall, our models suggest that single regulatory mechanisms do not accurately replicate observed symbiont colonization patterns, reflecting the importance of all mechanisms working concomitantly. This ultimately sheds light on the cell biology underpinning the stability of this ecologically significant symbiosis.