Unexpected microbial rhodopsin dynamics in sync with phytoplankton blooms

The surface ocean is the largest sunlit environment on Earth where marine microalgae are known as the main drivers of global productivity. However, rhodopsin phototrophs are actually the most abundant metabolic group, suggesting a major role in the biogeochemical cycles. While previous studies have shown that rhodopsin-containing bacterioplankton thrive in the most severely nutrient-depleted environments, growing evidence suggest that this type of phototrophy may also be relevant in nutrient-rich environments. To examine its role in productive waters, we investigated the monthly rhodopsin dynamics in the upwelling system of the Southern California Bight by measuring retinal–the photoreactive chromophore essential for rhodopsin function–in seawater. Unlike oligotrophic regions, rhodopsin levels peaked during the highly productive spring phytoplankton bloom, coinciding with the highest chlorophyll concentrations. Heterotrophic bacterial abundances, particularly within the order Flavobacteriales, correlated strongly with rhodopsin concentrations, allowing us to build linear models to predict rhodopsin distributions in a productive environment. Metagenomic data further showed that Flavobacteriales also dominated the rhodopsin gene pool when the highest rhodopsin levels were recorded, underscoring their key contribution to light-driven energy capture. Overall, our findings reveal that rhodopsin phototrophy plays a substantial role in productive marine systems, broadening its recognized importance far beyond oligotrophic oceans.