Hidden Strategies Beneath a Single Nucleotide: Contrasting Physiology in Lichen Photobiont Strains

ABSTRACT

Lichen photobionts exhibit significant physiological variability with important ecological implications. While this variability is relatively well studied at the interspecific level, it has rarely been examined at the intraspecific level. Here, we investigated the physiological responses to temperature and irradiance of two Trebouxia lynniae strains differing by a single nucleotide polymorphism in the ITS2 region. Both strains were isolated and characterized through biomass accumulation, chlorophyll fluorescence, pigment quantification, transmission electron microscopy, metabolomic profiling and whole‐genome sequencing. Despite sharing 99.4% and 99.9% of their nuclear and plastid genomes, respectively, the two strains displayed distinct photosynthesis performance analogous to that of the sun and shade leaves. In addition, one strain accumulated higher levels of amino acids and soluble sugars, whereas the other showed greater citrate content and cytoplasmic lipid bodies accumulation, suggesting contrasting strategies for energy storage and stress response. Genomic analysis identified over 1,600 genes carrying non‐synonymous mutations; interestingly, most variants were associated with genes involved in transcriptional regulation, protein turnover and signal transduction rather than core metabolic functions. These findings highlight how closely related strains can diverge functionally and point to a potential role of regulatory processes in shaping photobiont diversity and adaptation to environmental conditions.