Single-cell genomics reveals the genome content of the uncultured cyanobacterial diazotroph UCYN-A3

Abstract

The unicellular cyanobacteria Candidatus Atelocyanobacterium thalassa (hereafter, UCYN-A) are important nitrogen fixers that live in symbiosis with the haptophyte algae Braarudosphaera bigelowii and its close relative species. Although the UCYN-A phylogenetic group includes at least six sublineages, only the genomes of UCYN-A1 and UCYN-A2 had been sequenced to date. Therefore, despite its biogeochemical relevance, comparative genomics on the UCYN-A phylogenetic group has been limited by the poor representation of genomic data. Here, using a high-throughput DNA sequencing approach on a single sorted cell from the South Atlantic Ocean, we reconstructed about 65% of the genome of the UCYN-A3 sublineage. We show that although the genomic content of UCYN-A3 is very similar to the previously sequenced UCYN-A1 and UCYN-A2 sublineages, there are some differential genomic features such as the presence of genes for cell shape and cell wall biogenesis, as well as genes implicated in pyrimidine metabolism that are only present in UCYN-A2 and UCYN-A3. Also, comparative genomics suggests that the three sublineages form a monophyletic group that diverged from a common ancestor with a reduced genome, with UCYN-A2 being the closest to UCYN-A3 and UCYN-A1 its relative. Finally, phylogenomic and molecular clock analyses were also performed to estimate the age of divergence of the UCYN-A1, UCYN-A2 and UCYN-A3 sublineages both within the UCYN-A group and in a broader phylogenetic context, thus providing a paleo-oceanographic context for when these UCYN-A sublineages originated