Metabolic characteristics and evolutionary history of the nitrogen-fixing cyanobacterial endosymbionts of pennate diatoms

Abstract Nitrogen-fixing cyanobacteria are important sources of bioavailable nitrogen on Earth. Some nitrogen-fixing cyanobacteria are endosymbionts of algae, and recently one of them, UCYN-A2, was shown to be an early-stage organelle (nitroplast) of haptophytes. These biological associations are important models for studying co-evolution and organellogenesis. Endosymbioses between Rhopalodiaceae diatoms and nitrogen-fixing cyanobacteria (spheroid bodies, SBs) are widespread in marine and freshwater ecosystems, but their adaptation and evolution remain unclear. We found that the genomes and metabolic characteristics of marine and freshwater SBs are remarkably similar. Purifying selection pressures dominated SB diversification both within marine and freshwater habitats and across habitat boundaries. The metabolic characteristics and genome reduction of SBs are substantially different from UCYN-A, suggesting different evolutionary journeys for the endosymbionts influenced by different hosts. We estimated that the marine SBs diversified ~185 Mya (95% highest posterior density (HPD): 340-88 Mya), which was within a prolonged oligotrophic period in the ocean, during which UCYN-A also diversified. The freshwater SBs diversified from the marine SBs ~137 Mya (95% HPD: 258-66 Mya) and further diversified ~80 Mya (95% HPD: 157-31 Mya), when sea level was increasing. Our study reveals the genetic and metabolic underpinnings characterizing the nitrogen-fixing cyanobacterial endosymbionts of Rhopalodiaceae diatoms.