Candidatus Atelocyanobacterium thalassa isolate SIO64986 Genome sequencing and assembly. Candidatus Atelocyanobacterium thalassa isolate SIO64986

Marine planktonic cyanobacteria capable of fixing molecular nitrogen (termed “diazotrophs”) are key in biogeochemical cycling, and the nitrogen fixed is one of the major external sources of nitrogen to the open ocean. Candidatus Atelocyanobacterium thalassa (UCYN-A) is a diazotrophic cyanobacterium known for its widespread geographic distribution in tropical and subtropical oligotrophic oceans, unusual streamlined genome, and symbiosis with a single-celled Prymnesiophyte alga. In 2012 a novel strain of this organism was also detected in coastal waters sampled from the Scripps Institute of Oceanography (SIO) pier. We analyzed the metagenome of this UCYN-A2 population, by concentrating cells by flow cytometry. Phylogenomic analysis provided strong bootstrap support for the monophyly of UCYN-A and UCYN-A2 within the marine Crocosphaera sp. and Cyanothece sp. clade. UCYN-A2 shares 1159 of the 1200 UCYN-A protein coding genes (96.6%) with high synteny, yet the average amino acid sequence identity between these orthologs is only 86%. UCYN-A2 lacks the same major pathways and proteins that are absent in UCYN-A1, suggesting that both strains can be grouped on the same functional and ecological level. Our results suggest that UCYN-A and UCYN-A2 had a common ancestor and diverged after genome reduction. These two variants may reflect adaptation of the host to different niches, which could be coastal and open ocean habitats.