Codon usage bias maps ocean microbiome adaptation to temperature-nutrients regimes

Abstract

Microbial communities underpin ocean productivity and biogeochemistry, but their functional adaptation to environmental gradients remains poorly understood. Codon usage bias (CUB), a marker of translational efficiency, constrains growth rate potential, yet its role in functional adaptation across natural communities is underexplored. By analysing 589 metagenome-derived microbial communities from the global ocean, we demonstrate that CUB in 320 metabolism-related gene groups capture genomic adaptation to distinct temperature and nutrient concentrations. We identified four adaptation signatures shaped by distinct temperature-nutrient regimes, revealing how microbes optimize protein synthesis in their ecological niche. This genome-centric approach deepens our understanding of functional adaptation in uncultured marine microbes and provides a framework to inform ocean biogeochemical models and predict microbial responses to climate-driven changes.