Abstract
Mutualistic endosymbiosis is a cornerstone of evolutionary innovation, enabling organisms to exploit diverse niches unavailable to individual species. However, our knowledge about the early evolutionary stage of this relationship remains limited. The association between the ciliate Tetrahymena utriculariae and its algal endosymbiont Micractinium tetrahymenae indicates an incipient stage of photoendosymbiosis. Although T. utriculariae cells rely on endosymbiotic algae to grow in low-oxygen conditions, they gradually lose the endosymbionts in oxic conditions. In this study, comparative phylogenomics revealed accelerated evolution in mitochondrial DNA and nucleus-encoded mitochondrial genes in T. utriculariae. Symbiotic cells displayed elongated mitochondria that interacted intimately with endosymbionts. Inhibition of mitochondrial fatty acid oxidation reduced host fitness but increased the endosymbiont population. Time-series transcriptomics revealed physiological fine-tuning of the host across day-night cycles, highlighting symbiosis-associated regulatory adjustments. Endosymbiotic algae downregulated photosynthesis-related genes compared with free-living cells, which correlated with reduced chlorophyll content, suggesting a shift toward host resource exploitation to compensate for diminished photosynthetic capacity. Under oxic conditions, symbiotic T. utriculariae cells exhibited lower fitness than aposymbiotic cells. Our results demonstrate that incipient endosymbioses employ mitochondrial remodeling and endosymbiont metabolic reprogramming to actively regulate transitions between mutualistic and parasitic states, revealing how symbiotic partnerships navigate environmental pressures during their incipient stage of evolutionary establishment.