Selection Maintains Photosynthesis in a Symbiotic Cyanobacterium Despite Redundancy With its Fern Host

Vertically inherited symbionts experience different physical, chemical, and population genetic environments than free-living organisms. As a result, they can experience long-term reductions in effective population size (Ne) and weaker purifying selection on genes that are less important in the host-associated environment. Over time, these forces result in gene loss. A comparative genomic approach using independently evolved symbiotic bacteria and free-living relatives can reveal which genes are important in the symbiotic state. We apply this approach to understand why some diazotrophic cyanobacteria evolving as vertically inherited symbionts of photosynthetic eukaryotic hosts have lost their ancestral capacity for photosynthesis while others have retained that capacity. We look specifically at Trichormus azollae, a diazotrophic cyanobacterium that remains photosynthetic after 50 to 90 Ma as a vertically inherited symbiont of Azolla ferns. We show that gene loss is ongoing, with different genes lost across the eight T. azollae strains examined. We apply molecular evolutionary models to genomes of T. azollae and free-living relatives, finding genome-wide signatures of drift in T. azollae consistent with long-term reductions in Ne. Ribosomal proteins and proteins from the energy-capturing photosynthetic light reactions are under stronger purifying selection than genes from other pathways, including nitrogen fixation and photosynthetic carbon fixation. Strong purifying selection is expected for the ribosome given its extraordinary levels of conservation, even in ancient vertically inherited symbionts. That genes in the light reactions are under strong purifying selection and never lost in any strain suggests that energy capture, likely required for energy-intensive nitrogen fixation, remains important to this symbiont.